489 def set_calc_resolving_power(self):
-490 return 0
+ 490 def set_calc_resolving_power(self):
+491 return 0
![\"CoreMS](\"https://github.com/EMSL-Computing/CoreMS/blob/v2.0.0/docs/CoreMS.COLOR_small.png?raw=true\")
\n\n\n\n
\n
\n
![\"CoreMS](\"https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg\")
\n
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Table of Contents
\n\n\n- Introduction\n
\n- Installation\n
\n- Execution
\n \n- Sibling Projects
\n \n
\n\n
\n\nCoreMS
\n\nCoreMS is a comprehensive mass spectrometry framework for software development and data analysis of small molecules analysis.
\n\nData handling and software development for modern mass spectrometry (MS) is an interdisciplinary endeavor requiring skills in computational science and a deep understanding of MS. To enable scientific software development to keep pace with fast improvements in MS technology, we have developed a Python software framework named CoreMS. The goal of the framework is to provide a fundamental, high-level basis for working with all mass spectrometry data types, allowing custom workflows for data signal processing, annotation, and curation. The data structures were designed with an intuitive, mass spectrometric hierarchical structure, thus allowing organized and easy access to the data and calculations. Moreover, CoreMS supports direct access for almost all vendors\u2019 data formats, allowing for the centralization and automation of all data processing workflows from the raw signal to data annotation and curation.
\n\nCoreMS aims to provide
\n\n\n- logical mass spectrometric data structure
\n- self-containing data and metadata storage
\n- modern molecular formulae assignment algorithms
\n- dynamic molecular search space database search and generator
\n
\n\n
\n\nCurrent Version
\n\n2.0
\n\n
\n\nMain Developers/Contact
\n\n\n\n
\n\nContributing
\n\nAs an open source project, CoreMS welcomes contributions of all forms. Before contributing, please see our Dev Guide
\n\n
\n\n\n\n\n\n\n- Bruker Solarix (CompassXtract)
\n- Bruker Solarix transients, ser and fid (FT magnitude mode only)
\n- ThermoFisher (.raw)
\n- Spectroswiss signal booster data-acquisition station (.hdf5)
\n- MagLab ICR data-acquisition station (FT and magnitude mode) (.dat)
\n- ANDI NetCDF for GC-MS (.cdf)
\n- Generic mass list in profile and centroid mde (include all delimiters types and Excel formats)
\n- CoreMS exported processed mass list files(excel, .csv, .txt, pandas dataframe as .pkl)
\n- CoreMS self-containing Hierarchical Data Format (.hdf5)
\n- Pandas Dataframe
\n- Support for cloud Storage using s3path.S3path(see examples of usage here: S3 Support)
\n
\n\n\n\n\n- Pandas data frame (can be saved using pickle, h5, etc)
\n- Text Files (.csv, tab separated .txt, etc)
\n- Microsoft Excel (xlsx)
\n- Automatic JSON for metadata storage and reuse
\n- Self-containing Hierarchical Data Format (.hdf5) including raw data and ime-series data-point for processed data-sets with all associated metadata stored as json attributes
\n
\n\nData structure types
\n\n\n- LC-MS
\n- GC-MS
\n- Transient
\n- Mass Spectra
\n- Mass Spectrum
\n- Mass Spectral Peak
\n- Molecular Formula
\n
\n\nIn progress data structures
\n\n\n- IMS-MS
\n- LC-IMS-MS
\n- Collections
\n- Molecular Structure
\n
\n\n
\n\nAvailable features
\n\n\n\n\n- Apodization, Zerofilling, and Magnitude mode FT
\n- Manual and automatic noise threshold calculation
\n- Peak picking using apex quadratic fitting
\n- Experimental resolving power calculation
\n- Frequency and m/z domain calibration functions:
\n- LedFord equation
\n- Linear equation
\n- Quadratic equation
\n- Automatic search most abundant Ox homologue series
\n- Automatic local (SQLite) or external (PostgreSQL) database check, generation, and search
\n- Automatic molecular formulae assignments algorithm for ESI(-) MS for natural organic matter analysis
\n- Automatic fine isotopic structure calculation and search for all isotopes
\n- Flexible Kendrick normalization base
\n- Kendrick filter using density-based clustering
\n- Kendrick classification
\n- Heteroatoms classification and visualization
\n
\n\nGC-MS Signal Processing, Calibration, and Compound Identification
\n\n\n- Baseline detection, subtraction, smoothing
\n- m/z based Chromatogram Peak Deconvolution,
\n- Manual and automatic noise threshold calculation
\n- First and second derivatives peak picking methods
\n- Peak Area Calculation
\n- Retention Index Calibration
\n- Automatic local (SQLite) or external (MongoDB or PostgreSQL) database check, generation, and search
\n- Automatic molecular match algorithm with all spectral similarity methods
\n
\n\nHigh Resolution Mass Spectrum Simulations
\n\n\n- Peak shape (Lorentz, Gaussian, Voigt, and pseudo-Voigt)
\n- Peak fitting for peak shape definition
\n- Peak position in function of data points, signal to noise and resolving power (Lorentz and Gaussian)
\n- Prediction of mass error distribution
\n- Calculated ICR Resolving Power based on magnetic field (B), and transient time(T)
\n
\n\n
\n\nInstallation
\n\n\n\nBy default the molecular formula database will be generated using SQLite
\n\nTo use Postgresql the easiest way is to build a docker container:
\n\n\n
docker-compose up -d\n
\n
\n- Change the url_database on MSParameters.molecular_search.url_database to: \"postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp\"
\n- Set the url_database env variable COREMS_DATABASE_URL to: \"postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp\"
\n
\n\nThermo Raw File Access:
\n\nTo be able to open thermo file a installation of pythonnet is needed:
\n\n\n- Windows: \n
\n
pip install pythonnet\n
\n
\n
\n\n\n- Mac and Linux:\n
\n
brew install mono\npip install pythonnet \n
\n
\n
\n\n
\n\nDocker stack
\n\nAnother option to use CoreMS is to run the docker stack that will start the CoreMS containers
\n\nMolecular Database and Jupyter Notebook Docker Containers
\n\nA docker container containing:
\n\n\n- A custom python distribution will all dependencies installed
\n- A Jupyter notebook server with workflow examples
\n- A PostgreSQL database for the molecular formulae assignment
\n
\n\nIf you don't have docker installed, the easiest way is to install docker for desktop
\n\n\nStart the containers using docker-compose (easiest way):
\n\nOn docker-compose-jupyter.yml there is a volume mapping for the tests_data directory with the data provided for testing, to change to your data location:
\n\n\nlocate the volumes on docker-compose-jupyter.yml:
\n\n\n
volumes:\n - ./tests/tests_data:/home/CoreMS/data\n
\n
change \"./tests/tests_data\" to your data directory location
\n\n\n
volumes:\n - path_to_your_data_directory:/home/corems/data\n
\n
save the file and then call:
\n\n\n
docker-compose -f docker-compose-jupyter.yml up\n
\n
Another option is to manually build the containers:
\n\n\nBuild the corems image:
\n\n\n
docker build -t corems:local .\n
\n
Start the database container:
\n\n\n
docker-compose up -d \n
\n
Start the Jupyter Notebook:
\n\n\n
docker run --rm -v ./data:/home/CoreMS/data corems:local\n
\n
Open your browser, copy and past the URL address provided in the terminal: http://localhost:8888/?token=<token>.
Open the CoreMS-Tutorial.ipynb
\n\n
\n\nSimple Script Example
\n\nMore examples can be found under the directory examples/scripts, examples/notebooks
\n\n\n- Basic functionality example
\n
\n\n\n
from corems.transient.input.brukerSolarix import ReadBrukerSolarix\nfrom corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas\nfrom corems.mass_spectrum.output.export import HighResMassSpecExport\nfrom matplotlib import pyplot\n\nfile_path= 'tests/tests_data/ftms/ESI_NEG_SRFA.d'\n\n# Instatiate the Bruker Solarix reader with the filepath\nbruker_reader = ReadBrukerSolarix(file_path)\n\n# Use the reader to instatiate a transient object\nbruker_transient_obj = bruker_reader.get_transient()\n\n# Calculate the transient duration time\nT = bruker_transient_obj.transient_time\n\n# Use the transient object to instatitate a mass spectrum object\nmass_spectrum_obj = bruker_transient_obj.get_mass_spectrum(plot_result=False, auto_process=True)\n\n# The following SearchMolecularFormulas function does the following\n# - searches monoisotopic molecular formulas for all mass spectral peaks\n# - calculates fine isotopic structure based on monoisotopic molecular formulas found and current dynamic range\n# - searches molecular formulas of correspondent calculated isotopologues\n# - settings are stored at SearchConfig.json and can be changed directly on the file or inside the framework class\n\nSearchMolecularFormulas(mass_spectrum_obj, first_hit=False).run_worker_mass_spectrum()\n\n# Iterate over mass spectral peaks objs within the mass_spectrum_obj\nfor mspeak in mass_spectrum_obj.sort_by_abundance():\n\n # If there is at least one molecular formula associated, mspeak returns True\n if mspeak:\n\n # Get the molecular formula with the highest mass accuracy\n molecular_formula = mspeak.molecular_formula_lowest_error\n\n # Plot mz and peak height\n pyplot.plot(mspeak.mz_exp, mspeak.abundance, 'o', c='g')\n\n # Iterate over all molecular formulas associated with the ms peaks obj\n for molecular_formula in mspeak:\n\n # Check if the molecular formula is a isotopologue\n if molecular_formula.is_isotopologue:\n\n # Access the molecular formula text representation and print\n print (molecular_formula.string)\n\n # Get 13C atoms count\n print (molecular_formula['13C'])\n else:\n # Get mz and peak height\n print(mspeak.mz_exp,mspeak.abundance)\n\n# Save data\n## to a csv file\nmass_spectrum_obj.to_csv("filename")\nmass_spectrum_obj.to_hdf("filename")\n# to pandas Datarame pickle\nmass_spectrum_obj.to_pandas("filename")\n\n# Extract data as a pandas Dataframe\ndf = mass_spectrum_obj.to_dataframe()\n
\n
\n\nUML Diagrams
\n\nUML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS classes can be found here.
\n\n
\n\nCiting CoreMS
\n\nIf you use CoreMS in your work, please use the following citation:\nVersion 2.0.0 Release on GitHub, archived on Zenodo:
\n\n
\n\nYuri E. Corilo, William R. Kew, Lee Ann McCue (2021, March 27). EMSL-Computing/CoreMS: CoreMS 2.0.0 (Version v2.0.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641552\n
\n\n
\n\nThis material was prepared as an account of work sponsored by an agency of the\nUnited States Government. Neither the United States Government nor the United\nStates Department of Energy, nor Battelle, nor any of their employees, nor any\njurisdiction or organization that has cooperated in the development of these\nmaterials, makes any warranty, express or implied, or assumes any legal\nliability or responsibility for the accuracy, completeness, or usefulness or\nany information, apparatus, product, software, or process disclosed, or\nrepresents that its use would not infringe privately owned rights.
\n\nReference herein to any specific commercial product, process, or service by\ntrade name, trademark, manufacturer, or otherwise does not necessarily\nconstitute or imply its endorsement, recommendation, or favoring by the United\nStates Government or any agency thereof, or Battelle Memorial Institute. The\nviews and opinions of authors expressed herein do not necessarily state or\nreflect those of the United States Government or any agency thereof.
\n\n PACIFIC NORTHWEST NATIONAL LABORATORY\n operated by\n BATTELLE\n for the\n UNITED STATES DEPARTMENT OF ENERGY\n under Contract DE-AC05-76RL01830\n
\n"}, {"fullname": "corems.timeit", "modulename": "corems", "qualname": "timeit", "kind": "function", "doc": "\n", "signature": "(method):", "funcdef": "def"}, {"fullname": "corems.SuppressPrints", "modulename": "corems", "qualname": "SuppressPrints", "kind": "class", "doc": "\n"}, {"fullname": "corems.get_filenames", "modulename": "corems", "qualname": "get_filenames", "kind": "function", "doc": "\n", "signature": "(app=None):", "funcdef": "def"}, {"fullname": "corems.get_filename", "modulename": "corems", "qualname": "get_filename", "kind": "function", "doc": "\n", "signature": "(app=None):", "funcdef": "def"}, {"fullname": "corems.get_dirname", "modulename": "corems", "qualname": "get_dirname", "kind": "function", "doc": "\n", "signature": "(app=None):", "funcdef": "def"}, {"fullname": "corems.get_dirnames", "modulename": "corems", "qualname": "get_dirnames", "kind": "function", "doc": "\n", "signature": "(app=None):", "funcdef": "def"}, {"fullname": "corems.chunks", "modulename": "corems", "qualname": "chunks", "kind": "function", "doc": "Yield successive n-sized chunks from lst.
\n", "signature": "(lst, n):", "funcdef": "def"}, {"fullname": "corems.corems_md5", "modulename": "corems", "qualname": "corems_md5", "kind": "function", "doc": "\n", "signature": "(fname):", "funcdef": "def"}, {"fullname": "corems.chroma_peak", "modulename": "corems.chroma_peak", "kind": "module", "doc": "\n"}, {"fullname": "corems.chroma_peak.calc", "modulename": "corems.chroma_peak.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.chroma_peak.calc.ChromaPeakCalc", "modulename": "corems.chroma_peak.calc.ChromaPeakCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.chroma_peak.calc.ChromaPeakCalc.GCPeakCalculation", "modulename": "corems.chroma_peak.calc.ChromaPeakCalc", "qualname": "GCPeakCalculation", "kind": "class", "doc": "Class for performing peak calculations in GC chromatography.
\n\nMethods
\n\n\ncalc_area(self, tic: List[float], dx: float) -> None: Calculate the area under the curve of the chromatogram.linear_ri(self, right_ri: float, left_ri: float, left_rt: float, right_rt: float) -> float: Calculate the retention index using linear interpolation.calc_ri(self, rt_ri_pairs: List[Tuple[float, float]]) -> int: Calculate the retention index based on the given retention time - retention index pairs.
\n"}, {"fullname": "corems.chroma_peak.calc.ChromaPeakCalc.GCPeakCalculation.calc_area", "modulename": "corems.chroma_peak.calc.ChromaPeakCalc", "qualname": "GCPeakCalculation.calc_area", "kind": "function", "doc": "Calculate the area under the curve of the chromatogram.
\n\nParameters
\n\n\n- tic (List[float]):\nThe total ion current (TIC) values.
\n- dx (float):\nThe spacing between data points.
\n
\n", "signature": "(self, tic: list[float], dx: float) -> None:", "funcdef": "def"}, {"fullname": "corems.chroma_peak.calc.ChromaPeakCalc.GCPeakCalculation.linear_ri", "modulename": "corems.chroma_peak.calc.ChromaPeakCalc", "qualname": "GCPeakCalculation.linear_ri", "kind": "function", "doc": "Calculate the retention index using linear interpolation.
\n\nParameters
\n\n\n- right_ri (float):\nThe retention index at the right reference point.
\n- left_ri (float):\nThe retention index at the left reference point.
\n- left_rt (float):\nThe retention time at the left reference point.
\n- right_rt (float):\nThe retention time at the right reference point.
\n
\n\nReturns
\n\n\n- float: The calculated retention index.
\n
\n", "signature": "(\tself,\tright_ri: float,\tleft_ri: float,\tleft_rt: float,\tright_rt: float) -> float:", "funcdef": "def"}, {"fullname": "corems.chroma_peak.calc.ChromaPeakCalc.GCPeakCalculation.calc_ri", "modulename": "corems.chroma_peak.calc.ChromaPeakCalc", "qualname": "GCPeakCalculation.calc_ri", "kind": "function", "doc": "Calculate the retention index based on the given retention time - retention index pairs.
\n\nParameters
\n\n\n- rt_ri_pairs (List[Tuple[float, float]]):\nThe list of retention time - retention index pairs.
\n
\n", "signature": "(self, rt_ri_pairs: list[tuple[float, float]]) -> None:", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory", "modulename": "corems.chroma_peak.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "kind": "module", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase", "kind": "class", "doc": "Base class for chromatographic peak (ChromaPeak) objects.
\n\nParameters
\n\n\n- chromatogram_parent (Chromatogram):\nThe parent chromatogram object.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- start_index (int):\nThe start index of the peak.
\n- index (int):\nThe index of the peak.
\n- final_index (int):\nThe final index of the peak.
\n
\n\nAttributes
\n\n\n- start_scan (int):\nThe start scan of the peak.
\n- final_scan (int):\nThe final scan of the peak.
\n- apex_scan (int):\nThe apex scan of the peak.
\n- chromatogram_parent (Chromatogram):\nThe parent chromatogram object.
\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- _area (float):\nThe area of the peak.
\n
\n\nProperties
\n\n\n- retention_time : float. \nThe retention time of the peak.
\n- tic : float. \nThe total ion current of the peak.
\n- area : float. \nThe area of the peak.
\n- rt_list : list. \nThe list of retention times within the peak.
\n- tic_list : list.\nThe list of total ion currents within the peak.
\n
\n\nMethods
\n\n\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.__init__", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.__init__", "kind": "function", "doc": "\n", "signature": "(\tchromatogram_parent,\tmass_spectrum_obj,\tstart_index,\tindex,\tfinal_index)"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.start_scan", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.start_scan", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.final_scan", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.final_scan", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.apex_scan", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.apex_scan", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.chromatogram_parent", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.chromatogram_parent", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.mass_spectrum", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.retention_time", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.retention_time", "kind": "variable", "doc": "Retention Time
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.tic", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.tic", "kind": "variable", "doc": "Total Ion Current
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.area", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.area", "kind": "variable", "doc": "Peak Area
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.rt_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.rt_list", "kind": "variable", "doc": "Retention Time List
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.tic_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.tic_list", "kind": "variable", "doc": "Total Ion Current List
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak", "kind": "class", "doc": "Data dependent peak (DataDependentPeak) object.
\n\nParameters
\n\n\n- chromatogram_parent (Chromatogram):\nThe parent chromatogram object.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- peak_indexes (tuple):\nThe start, apex and final indexes of the peak.
\n- eic_data (EIC_Data):\nThe EIC data object.
\n- Attributes
\n- --------
\n- _eic_data (EIC_Data):\nThe EIC data object.
\n- _possible_molecular_formulae (list):\nThe list of possible molecular formulas.
\n
\n\nProperties
\n\n\n- eic_rt_list : list. \nEIC retention time list.
\n- eic_list : list.\nEIC list.
\n- targeted_molecular_formulas : list.\nThe list of possible molecular formulas.
\n
\n\nMethods
\n\n\n- add_dependent_mass_spectrum(mass_spectrum).
\nAdd a dependent mass spectrum to the peak. \n- add_molecular_formula(molfform).
\nAdd a molecular formula to the peak. \n
\n", "bases": "ChromaPeakBase"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.__init__", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.__init__", "kind": "function", "doc": "\n", "signature": "(\tchromatogram_parent,\tmass_spectrum_obj,\tpeak_indexes,\teic_data: corems.mass_spectra.factory.LC_Temp.EIC_Data,\tpossible_molform=None)"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.add_dependent_mass_spectrum", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.add_dependent_mass_spectrum", "kind": "function", "doc": "Add a dependent mass spectrum to the peak.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.add_molecular_formula", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.add_molecular_formula", "kind": "function", "doc": "Add a molecular formula to the peak.
\n\nParameters
\n\n\n- molfform (str):\nThe molecular formula.
\n
\n", "signature": "(self, molfform):", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.eic_rt_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.eic_rt_list", "kind": "variable", "doc": "EIC Retention Time List
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.eic_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.eic_list", "kind": "variable", "doc": "EIC List
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.targeted_molecular_formulas", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.targeted_molecular_formulas", "kind": "variable", "doc": "Targeted Molecular Formulas
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak", "kind": "class", "doc": "Class representing a peak in a gas chromatography (GC) chromatogram.
\n\nParameters
\n\n\n- chromatogram_parent (Chromatogram):\nThe parent chromatogram object.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object associated with the peak.
\n- indexes (tuple):\nThe indexes of the peak in the chromatogram.
\n
\n\nAttributes
\n\n\n- _compounds (list):\nList of compounds associated with the peak.
\n- _ri (float or None):\nRetention index of the peak.
\n
\n\nMethods
\n\n\n- __len__(). Returns the number of compounds associated with the peak.
\n- __getitem__(position). Returns the compound at the specified position.
\n- remove_compound(compounds_obj). Removes the specified compound from the peak.
\n- clear_compounds(). Removes all compounds from the peak.
\n- add_compound(compounds_dict, spectral_similarity_scores, ri_score=None, similarity_score=None). Adds a compound to the peak with the specified attributes.
\n- ri(). Returns the retention index of the peak.
\n- highest_ss_compound(). Returns the compound with the highest spectral similarity score.
\n- highest_score_compound(). Returns the compound with the highest similarity score.
\n- compound_names(). Returns a list of names of compounds associated with the peak.
\n
\n", "bases": "ChromaPeakBase, corems.chroma_peak.calc.ChromaPeakCalc.GCPeakCalculation"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.__init__", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.__init__", "kind": "function", "doc": "\n", "signature": "(chromatogram_parent, mass_spectrum_obj, indexes)"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.remove_compound", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.remove_compound", "kind": "function", "doc": "\n", "signature": "(self, compounds_obj):", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.clear_compounds", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.clear_compounds", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.add_compound", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.add_compound", "kind": "function", "doc": "Adds a compound to the peak with the specified attributes.
\n\nParameters
\n\n\n- compounds_dict (dict):\nDictionary containing the compound information.
\n- spectral_similarity_scores (dict):\nDictionary containing the spectral similarity scores.
\n- ri_score (float or None, optional):\nThe retention index score of the compound. Default is None.
\n- similarity_score (float or None, optional):\nThe similarity score of the compound. Default is None.
\n
\n", "signature": "(\tself,\tcompounds_dict,\tspectral_similarity_scores,\tri_score=None,\tsimilarity_score=None):", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.ri", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.ri", "kind": "variable", "doc": "Returns the retention index of the peak.
\n\nReturns
\n\n\n- float or None: The retention index of the peak.
\n
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.highest_ss_compound", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.highest_ss_compound", "kind": "variable", "doc": "Returns the compound with the highest spectral similarity score.
\n\nReturns
\n\n\n- LowResCompoundRef or None: The compound with the highest spectral similarity score.
\n
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.highest_score_compound", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.highest_score_compound", "kind": "variable", "doc": "Returns the compound with the highest similarity score.
\n\nReturns
\n\n\n- LowResCompoundRef or None: The compound with the highest similarity score.
\n
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.compound_names", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.compound_names", "kind": "variable", "doc": "Returns a list of names of compounds associated with the peak.
\n\nReturns
\n\n\n- list: List of names of compounds associated with the peak.
\n
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeakDeconvolved", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeakDeconvolved", "kind": "class", "doc": "Represents a deconvolved peak in a chromatogram.
\n\nParameters
\n\n\n- chromatogram_parent (Chromatogram):\nThe parent chromatogram object.
\n- mass_spectra (list):\nList of mass spectra associated with the peak.
\n- apex_index (int):\nIndex of the apex mass spectrum in the
mass_spectra list. \n- rt_list (list):\nList of retention times.
\n- tic_list (list):\nList of total ion currents.
\n
\n", "bases": "GCPeak"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeakDeconvolved.__init__", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeakDeconvolved.__init__", "kind": "function", "doc": "\n", "signature": "(chromatogram_parent, mass_spectra, apex_index, rt_list, tic_list)"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeakDeconvolved.mass_spectra", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeakDeconvolved.mass_spectra", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeakDeconvolved.rt_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeakDeconvolved.rt_list", "kind": "variable", "doc": "Get the list of retention times.
\n\nReturns
\n\n\n- list: The list of retention times.
\n
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeakDeconvolved.tic_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeakDeconvolved.tic_list", "kind": "variable", "doc": "Get the list of total ion currents.
\n\nReturns
\n\n\n- list: The list of total ion currents.
\n
\n"}, {"fullname": "corems.collection", "modulename": "corems.collection", "kind": "module", "doc": "\n"}, {"fullname": "corems.collection.factory", "modulename": "corems.collection.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.collection.input", "modulename": "corems.collection.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.collection.output", "modulename": "corems.collection.output", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation", "modulename": "corems.encapsulation", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.constant", "modulename": "corems.encapsulation.constant", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.constant.Labels", "modulename": "corems.encapsulation.constant", "qualname": "Labels", "kind": "class", "doc": "Class for Labels used in CoreMS
\n\nThese labels are used to define:
\n\n\n- types of columns in plaintext data inputs,
\n- types of data/mass spectra
\n- types of assignment for ions
\n
\n"}, {"fullname": "corems.encapsulation.constant.Labels.mz", "modulename": "corems.encapsulation.constant", "qualname": "Labels.mz", "kind": "variable", "doc": "\n", "default_value": "'m/z'"}, {"fullname": "corems.encapsulation.constant.Labels.abundance", "modulename": "corems.encapsulation.constant", "qualname": "Labels.abundance", "kind": "variable", "doc": "\n", "default_value": "'Peak Height'"}, {"fullname": "corems.encapsulation.constant.Labels.rp", "modulename": "corems.encapsulation.constant", "qualname": "Labels.rp", "kind": "variable", "doc": "\n", "default_value": "'Resolving Power'"}, {"fullname": "corems.encapsulation.constant.Labels.s2n", "modulename": "corems.encapsulation.constant", "qualname": "Labels.s2n", "kind": "variable", "doc": "\n", "default_value": "'S/N'"}, {"fullname": "corems.encapsulation.constant.Labels.label", "modulename": "corems.encapsulation.constant", "qualname": "Labels.label", "kind": "variable", "doc": "\n", "default_value": "'label'"}, {"fullname": "corems.encapsulation.constant.Labels.bruker_profile", "modulename": "corems.encapsulation.constant", "qualname": "Labels.bruker_profile", "kind": "variable", "doc": "\n", "default_value": "'Bruker_Profile'"}, {"fullname": "corems.encapsulation.constant.Labels.thermo_profile", "modulename": "corems.encapsulation.constant", "qualname": "Labels.thermo_profile", "kind": "variable", "doc": "\n", "default_value": "'Thermo_Profile'"}, {"fullname": "corems.encapsulation.constant.Labels.simulated_profile", "modulename": "corems.encapsulation.constant", "qualname": "Labels.simulated_profile", "kind": "variable", "doc": "\n", "default_value": "'Simulated Profile'"}, {"fullname": "corems.encapsulation.constant.Labels.booster_profile", "modulename": "corems.encapsulation.constant", "qualname": "Labels.booster_profile", "kind": "variable", "doc": "\n", "default_value": "'Booster Profile'"}, {"fullname": "corems.encapsulation.constant.Labels.bruker_frequency", "modulename": "corems.encapsulation.constant", "qualname": "Labels.bruker_frequency", "kind": "variable", "doc": "\n", "default_value": "'Bruker_Frequency'"}, {"fullname": "corems.encapsulation.constant.Labels.midas_frequency", "modulename": "corems.encapsulation.constant", "qualname": "Labels.midas_frequency", "kind": "variable", "doc": "\n", "default_value": "'Midas_Frequency'"}, {"fullname": "corems.encapsulation.constant.Labels.thermo_centroid", "modulename": "corems.encapsulation.constant", "qualname": "Labels.thermo_centroid", "kind": "variable", "doc": "\n", "default_value": "'Thermo_Centroid'"}, {"fullname": "corems.encapsulation.constant.Labels.corems_centroid", "modulename": "corems.encapsulation.constant", "qualname": "Labels.corems_centroid", "kind": "variable", "doc": "\n", "default_value": "'CoreMS_Centroid'"}, {"fullname": "corems.encapsulation.constant.Labels.gcms_centroid", "modulename": "corems.encapsulation.constant", "qualname": "Labels.gcms_centroid", "kind": "variable", "doc": "\n", "default_value": "'Thermo_Centroid'"}, {"fullname": "corems.encapsulation.constant.Labels.unassigned", "modulename": "corems.encapsulation.constant", "qualname": "Labels.unassigned", "kind": "variable", "doc": "\n", "default_value": "'unassigned'"}, {"fullname": "corems.encapsulation.constant.Labels.radical_ion", "modulename": "corems.encapsulation.constant", "qualname": "Labels.radical_ion", "kind": "variable", "doc": "\n", "default_value": "'RADICAL'"}, {"fullname": "corems.encapsulation.constant.Labels.protonated_de_ion", "modulename": "corems.encapsulation.constant", "qualname": "Labels.protonated_de_ion", "kind": "variable", "doc": "\n", "default_value": "'DE_OR_PROTONATED'"}, {"fullname": "corems.encapsulation.constant.Labels.protonated", "modulename": "corems.encapsulation.constant", "qualname": "Labels.protonated", "kind": "variable", "doc": "\n", "default_value": "'protonated'"}, {"fullname": "corems.encapsulation.constant.Labels.de_protonated", "modulename": "corems.encapsulation.constant", "qualname": "Labels.de_protonated", "kind": "variable", "doc": "\n", "default_value": "'de-protonated'"}, {"fullname": "corems.encapsulation.constant.Labels.adduct_ion", "modulename": "corems.encapsulation.constant", "qualname": "Labels.adduct_ion", "kind": "variable", "doc": "\n", "default_value": "'ADDUCT'"}, {"fullname": "corems.encapsulation.constant.Labels.neutral", "modulename": "corems.encapsulation.constant", "qualname": "Labels.neutral", "kind": "variable", "doc": "\n", "default_value": "'neutral'"}, {"fullname": "corems.encapsulation.constant.Labels.ion_type", "modulename": "corems.encapsulation.constant", "qualname": "Labels.ion_type", "kind": "variable", "doc": "\n", "default_value": "'IonType'"}, {"fullname": "corems.encapsulation.constant.Labels.ion_type_translate", "modulename": "corems.encapsulation.constant", "qualname": "Labels.ion_type_translate", "kind": "variable", "doc": "\n", "default_value": "{'protonated': 'DE_OR_PROTONATED', 'de-protonated': 'DE_OR_PROTONATED', 'radical': 'RADICAL', 'adduct': 'ADDUCT'}"}, {"fullname": "corems.encapsulation.constant.Atoms", "modulename": "corems.encapsulation.constant", "qualname": "Atoms", "kind": "class", "doc": "Class for Atoms in CoreMS
\n\nThis class includes key properties of atoms (and the electron) and isotopes, including their exact masses, relative abundances, and covalences. \nIt also associates which isotopes are for the same element, and provides an ordering of elements.
\n\nReferences
\n\n\n- NIST - Last Accessed 2019-06-12\nhttps://www.nist.gov/pml/atomic-weights-and-isotopic-compositions-relative-atomic-masses
\n
\n"}, {"fullname": "corems.encapsulation.constant.Atoms.electron_mass", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.electron_mass", "kind": "variable", "doc": "\n", "default_value": "0.000548579909065"}, {"fullname": "corems.encapsulation.constant.Atoms.atomic_masses", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.atomic_masses", "kind": "variable", "doc": "\n", "default_value": "{'H': 1.00782503223, 'D': 2.01410177812, 'T': 3.0160492779, '3He': 3.0160293201, 'He': 4.00260325413, '6Li': 6.0151228874, '7Li': 7.0160034366, '9Be': 9.012183065, '10B': 10.01293695, '11B': 11.00930536, 'C': 12.0, '13C': 13.00335483507, '14C': 14.0032419884, 'N': 14.00307400443, '15N': 15.00010889888, 'O': 15.99491461957, '17O': 16.9991317565, '18O': 17.99915961286, 'F': 18.99840316273, '20Ne': 19.9924401762, '21Ne': 20.993846685, '22Ne': 21.991385114, 'Na': 22.989769282, '24Mg': 23.985041697, '25Mg': 24.985836976, '26Mg': 25.982592968, 'Al': 26.98153853, '28Si': 27.97692653465, '29Si': 28.9764946649, '30Si': 29.973770136, 'P': 30.97376199842, 'S': 31.9720711744, '33S': 32.9714589098, '34S': 33.967867004, '36S': 35.96708071, 'Cl': 34.968852682, '37Cl': 36.965902602, '36Ar': 35.967545105, '38Ar': 37.96273211, '40Ar': 39.9623831237, 'K': 38.9637064864, '40K': 39.963998166, '41K': 40.9618252579, 'Ca': 39.962590863, '42Ca': 41.95861783, '43Ca': 42.95876644, '44Ca': 43.95548156, '46Ca': 45.953689, '48Ca': 47.95252276, '45Sc': 44.95590828, '46Ti': 45.95262772, '47Ti': 46.95175879, '48Ti': 47.94794198, '49Ti': 48.94786568, '50Ti': 49.94478689, '50V': 49.94715601, 'V': 50.94395704, '50Cr': 49.94604183, 'Cr': 51.94050623, '53Cr': 52.94064815, '54Cr': 53.93887916, 'Mn': 54.93804391, '54Fe': 53.93960899, 'Fe': 55.93493633, '57Fe': 56.93539284, '58Fe': 57.93327443, 'Co': 58.93319429, 'Ni': 57.93534241, '60Ni': 59.93078588, '61Ni': 60.93105557, '62Ni': 61.92834537, '64Ni': 63.92796682, 'Cu': 62.92959772, '65Cu': 64.9277897, 'Zn': 63.92914201, '66Zn': 65.92603381, '67Zn': 66.92712775, '68Zn': 67.92484455, '70Zn': 69.9253192, '69Ga': 68.9255735, '71Ga': 70.92470258, '70Ge': 69.92424875, '72Ge': 71.922075826, '73Ge': 72.923458956, '74Ge': 73.921177761, '76Ge': 75.921402726, 'As': 74.92159457, '74Se': 73.922475934, '76Se': 75.919213704, '77Se': 76.919914154, '78Se': 77.91730928, 'Se': 79.9165218, '82Se': 81.9166995, 'Br': 78.9183376, '81Br': 80.9162897, '78Kr': 77.92036494, '80Kr': 79.91637808, '82Kr': 81.91348273, '83Kr': 82.91412716, '84Kr': 83.9114977282, '86Kr': 85.9106106269, '85Rb': 84.9117897379, '87Rb': 86.909180531, '84Sr': 83.9134191, '86Sr': 85.9092606, '87Sr': 86.9088775, '88Sr': 87.9056125, '89Y': 88.9058403, '90Zr': 89.9046977, '91Zr': 90.9056396, '92Zr': 91.9050347, '94Zr': 93.9063108, '96Zr': 95.9082714, '93Nb': 92.906373, '92Mo': 91.90680796, '94Mo': 93.9050849, '95Mo': 94.90583877, '96Mo': 95.90467612, '97Mo': 96.90601812, 'Mo': 97.90540482, '100Mo': 99.9074718, '97Tc': 96.9063667, '98Tc': 97.9072124, '99Tc': 98.9062508, '96Ru': 95.90759025, '98Ru': 97.9052868, '99Ru': 98.9059341, '100Ru': 99.9042143, '101Ru': 100.9055769, '102Ru': 101.9043441, '104Ru': 103.9054275, '103Rh': 102.905498, '102Pd': 101.9056022, '104Pd': 103.9040305, '105Pd': 104.9050796, '106Pd': 105.9034804, '108Pd': 107.9038916, '110Pd': 109.9051722, '107Ag': 106.9050916, '109Ag': 108.9047553, '106Cd': 105.9064599, '108Cd': 107.9041834, '110Cd': 109.90300661, '111Cd': 110.90418287, 'Cd': 111.90276287, '113Cd': 112.90440813, '114Cd': 113.90336509, '116Cd': 115.90476315, '113In': 112.90406184, 'In': 114.903878776, '112Sn': 111.90482387, '114Sn': 113.9027827, '115Sn': 114.903344699, '116Sn': 115.9017428, '117Sn': 116.90295398, '118Sn': 117.90160657, '119Sn': 118.90331117, '120Sn': 119.90220163, '122Sn': 121.9034438, '124Sn': 123.9052766, '121Sb': 120.903812, '123Sb': 122.9042132, '120Te': 119.9040593, '122Te': 121.9030435, '123Te': 122.9042698, '124Te': 123.9028171, '125Te': 124.9044299, '126Te': 125.9033109, '128Te': 127.90446128, '130Te': 129.906222748, 'I': 126.9044719, '124Xe': 123.905892, '126Xe': 125.9042983, '128Xe': 127.903531, '129Xe': 128.9047808611, '130Xe': 129.903509349, '131Xe': 130.90508406, '132Xe': 131.9041550856, '134Xe': 133.90539466, '136Xe': 135.907214484, '133Cs': 132.905451961, '130Ba': 129.9063207, '132Ba': 131.9050611, '134Ba': 133.90450818, '135Ba': 134.90568838, '136Ba': 135.90457573, '137Ba': 136.90582714, '138Ba': 137.905247, '138La': 137.9071149, '139La': 138.9063563, '136Ce': 135.90712921, '138Ce': 137.905991, '140Ce': 139.9054431, '142Ce': 141.9092504, '141Pr': 140.9076576, '142Nd': 141.907729, '143Nd': 142.90982, '144Nd': 143.910093, '145Nd': 144.9125793, '146Nd': 145.9131226, '148Nd': 147.9168993, '150Nd': 149.9209022, '145Pm': 144.9127559, '147Pm': 146.915145, '144Sm': 143.9120065, '147Sm': 146.9149044, '148Sm': 147.9148292, '149Sm': 148.9171921, '150Sm': 149.9172829, '152Sm': 151.9197397, '154Sm': 153.9222169, '151Eu': 150.9198578, '153Eu': 152.921238, '152Gd': 151.9197995, '154Gd': 153.9208741, '155Gd': 154.9226305, '156Gd': 155.9221312, '157Gd': 156.9239686, '158Gd': 157.9241123, '160Gd': 159.9270624, '159Tb': 158.9253547, '156Dy': 155.9242847, '158Dy': 157.9244159, '160Dy': 159.9252046, '161Dy': 160.9269405, '162Dy': 161.9268056, '163Dy': 162.9287383, '164Dy': 163.9291819, '165Ho': 164.9303288, '162Er': 161.9287884, '164Er': 163.9292088, '166Er': 165.9302995, '167Er': 166.9320546, '168Er': 167.9323767, '170Er': 169.9354702, '169Tm': 168.9342179, '168Yb': 167.9338896, '170Yb': 169.9347664, '171Yb': 170.9363302, '172Yb': 171.9363859, '173Yb': 172.9382151, '174Yb': 173.9388664, '176Yb': 175.9425764, '175Lu': 174.9407752, '176Lu': 175.9426897, '174Hf': 173.9400461, '176Hf': 175.9414076, '177Hf': 176.9432277, '178Hf': 177.9437058, '179Hf': 178.9458232, '180Hf': 179.946557, '180Ta': 179.9474648, '181Ta': 180.9479958, '180W': 179.9467108, '182W': 181.94820394, '183W': 182.95022275, '184W': 183.95093092, '186W': 185.9543628, '185Re': 184.9529545, '187Re': 186.9557501, '184Os': 183.9524885, '186Os': 185.953835, '187Os': 186.9557474, '188Os': 187.9558352, '189Os': 188.9581442, '190Os': 189.9584437, '192Os': 191.961477, '191Ir': 190.9605893, '193Ir': 192.9629216, '190Pt': 189.9599297, '192Pt': 191.9610387, '194Pt': 193.9626809, '195Pt': 194.9647917, '196Pt': 195.96495209, '198Pt': 197.9678949, '197Au': 196.96656879, '196Hg': 195.9658326, '198Hg': 197.9667686, '199Hg': 198.96828064, '200Hg': 199.96832659, '201Hg': 200.97030284, '202Hg': 201.9706434, '204Hg': 203.97349398, '203Tl': 202.9723446, '205Tl': 204.9744278, '204Pb': 203.973044, '206Pb': 205.9744657, '207Pb': 206.9758973, 'Pb': 207.9766525, '209Bi': 208.9803991, '209Po': 208.9824308, '210Po': 209.9828741, '210At': 209.9871479, '211At': 210.9874966, '211Rn': 210.9906011, '220Rn': 220.0113941, '222Rn': 222.0175782, '223Fr': 223.019736, '223Ra': 223.0185023, '224Ra': 224.020212, '226Ra': 226.0254103, '228Ra': 228.0310707, '227Ac': 227.0277523, '230Th': 230.0331341, '232Th': 232.0380558, '231Pa': 231.0358842, '233U': 233.0396355, '234U': 234.0409523, '235U': 235.0439301, '236U': 236.0455682, '238U': 238.0507884, '236Np': 236.04657, '237Np': 237.0481736, '238Pu': 238.0495601, '239Pu': 239.0521636, '240Pu': 240.0538138, '241Pu': 241.0568517, '242Pu': 242.0587428, '244Pu': 244.0642053, '241Am': 241.0568293, '243Am': 243.0613813, '243Cm': 243.0613893, '244Cm': 244.0627528, '245Cm': 245.0654915, '246Cm': 246.0672238, '247Cm': 247.0703541, '248Cm': 248.0723499, '247Bk': 247.0703073, '249Bk': 249.0749877, '249Cf': 249.0748539, '250Cf': 250.0764062, '251Cf': 251.0795886, '252Cf': 252.0816272, '252Es': 252.08298, '257Fm': 257.0951061, '258Md': 258.0984315, '260Md': 260.10365, '259No': 259.10103, '262Lr': 262.10961, '267Rf': 267.12179, '268Db': 268.12567, '271Sg': 271.13393, '272Bh': 272.13826, '270Hs': 270.13429, '276Mt': 276.15159, '281Ds': 281.16451, '280Rg': 280.16514, '285Cn': 285.17712, '284Nh': 284.17873, '289Fl': 289.19042, '288Mc': 288.19274, '293Lv': 293.20449, '292Ts': 292.20746, '294Og': 294.21392}"}, {"fullname": "corems.encapsulation.constant.Atoms.atoms_order", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.atoms_order", "kind": "variable", "doc": "\n", "default_value": "['C', 'H', 'O', 'Cl', 'Na', 'S', 'N', '13C', '34S', '37Cl', 'Fe', 'Ca', 'P', 'V', 'I', 'Ac', 'Al', 'Ar', 'As', 'At', 'Au', 'Co', 'Cs', 'D', 'F', 'Fr', '18O', '17O', 'He', 'Po', 'Ra', 'Rh', 'Rn', 'Be', 'Bi', 'Nb, 54Fe', '57Fe', 'Ni', '60Ni', '61Ni', '62Ni', '10B', '11B', '6Li', '7Li', 'La', 'Mn', '107Ag', '109Ag', '100Mo', '100Ru', '101Ru', '102Pd', '102Ru', '104Pd', '104Ru', '105Pd', 'Cd', '106Cd', '106Pd', '108Cd', '108Pd', '110Cd', '110Pd', '111Cd', '112Cd', '112Sn', '113Cd', '113In', '114Cd', '114Sn', 'In', '115In', '115Sn', '116Cd', '116Sn', '117Sn', '118Sn', '119Sn', '120Sn', '120Te', '121Sb', '122Sn', '122Te', '123Sb', '123Te', '124Sn', '124Te', '124Xe', '125Te', '126Te', '126Xe', '128Te', '128Xe', '129Xe', '130Ba', '130Te', '130Xe', '131Xe', '132Ba', '132Xe', '134Ba', '134Xe', '135Ba', '136Ba', '136Xe', '137Ba', '138Ba', '15N', '174Hf', '176Hf', '177Hf', '178Hf', '179Hf', '180Hf', '180W', '182W', '183W', '184Os', '184W', '185Re', '186Os', '186W', '187Os', '187Re', '188Os', '189Os', '190Os', '190Pt', '191Ir', '192Ir', '192Os', '192Pt', '194Pt', '195Pt', '196Hg', '196Pt', '198Hg', '198Pt', '199Hg', '200Hg', '201Hg', '202Hg', '203Tl', '204Hg', '204Pb', '205Tl', '206Pb', '207Pb', '208Pb', 'Pb', '20Ne', '22Ne', '24Mg', '25Mg', '26Mg', '28Si', '29Si', '30Si', 'K', '40Ca', '41K', '44Ca', '46Ti', '47Ti', '48Ti', '49Ti', '50Cr', '50Ti', '50V', '51V', 'Cr', '52Cr', '53Cr', '54Cr', 'Cu', 'Zn', '65Cu', '66Zn', '67Zn', '68Zn', '69Ga', '70Ge', '71Ga', '72Ge', '73Ge', '74Ge', '76Ge', '76Se', '77Se', '78Se', 'Br', '81Br', '80Kr', 'Se', '82Kr', '82Se', '83Kr', '84Kr', '85Rb', '86Kr', '86Sr', '87Rb', '87Sr', '88Sr', '90Zr', '91Zr', '92Mo', '92Zr', '94Mo', '94Zr', '95Mo', '96Mo', '96Ru', '96Zr', '97Mo', 'Mo', '98Ru', '99Ru']"}, {"fullname": "corems.encapsulation.constant.Atoms.atoms_covalence", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.atoms_covalence", "kind": "variable", "doc": "\n", "default_value": "{'C': 4, '13C': 4, 'N': 3, 'O': 2, 'S': 2, 'H': 1, 'F': (1, 0), 'Cl': (1, 0), 'Br': (1, 0), 'I': (1, 0), 'At': 1, 'Li': (1, 0), 'Na': (1, 0), 'K': (1, 0), 'Rb': 1, 'Cs': 1, 'Fr': 1, 'B': (4, 3, 2, 1), 'In': (3, 2, 1), 'Al': (3, 1, 2), 'P': (3, 5, 4, 2, 1), 'Ga': (3, 1, 2), 'Mg': (2, 1), 'Be': (2, 1), 'Ca': (2, 1), 'Sr': (2, 1), 'Ba': 2, 'Ra': 2, 'V': (5, 4, 3, 2, 1), 'Fe': (3, 2, 4, 5, 6), 'Si': (4, 3, 2), 'Sc': (3, 2, 1), 'Ti': (4, 3, 2, 1), 'Cr': (1, 2, 3, 4, 5, 6), 'Mn': (1, 2, 3, 4, 5, 6, 7), 'Co': (1, 2, 3, 4, 5), 'Ni': (1, 2, 3, 4), 'Cu': (2, 1, 3, 4), 'Zn': (2, 1), 'Ge': (4, 3, 2, 1), 'As': (5, 3, 2, 1), 'Se': (6, 4, 2, 1), 'Y': (3, 2, 1), 'Zr': (4, 3, 2, 1), 'Nb': (5, 4, 3, 2, 1), 'Mo': (6, 5, 4, 3, 2, 1), 'Tc': (7, 6, 5, 4, 3, 2, 1), 'Ru': (8, 7, 6, 5, 4, 3, 2, 1), 'Rh': (6, 5, 4, 3, 2, 1), 'Pd': (4, 2, 1), 'Ag': (0, 1, 2, 3, 4), 'Cd': (2, 1), 'Sn': (4, 2), 'Sb': (5, 3), 'Te': (6, 5, 4, 2), 'La': (3, 2), 'Hf': (4, 3, 2), 'Ta': (5, 4, 3, 2), 'W': (6, 5, 4, 3, 2, 1), 'Re': (4, 7, 6, 5, 3, 2, 1), 'Os': (4, 8, 7, 6, 5, 3, 2, 1), 'Ir': (4, 8, 6, 5, 3, 2, 1), 'Pt': (4, 6, 5, 3, 2, 1), 'Au': (3, 5, 2, 1), 'Hg': (1, 2, 4), 'Tl': (3, 1), 'Pb': (4, 2), 'Bi': (3, 1, 5), 'Po': (2, 4, 6), 'Ac': (3, 2)}"}, {"fullname": "corems.encapsulation.constant.Atoms.isotopic_abundance", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.isotopic_abundance", "kind": "variable", "doc": "\n", "default_value": "{'H': 0.999885, 'D': 0.000115, 'T': 0, '3He': 1.34e-06, 'He': 0.99999866, '6Li': 0.0759, 'Li': 0.9241, '9Be': 1.0, '10B': 0.199, '11B': 0.801, 'C': 0.9893, '13C': 0.0107, '14C': 0, 'N': 0.99636, '15N': 0.00364, 'O': 0.99757, '17O': 0.00038, '18O': 0.00205, 'F': 1.0, '20Ne': 0.9048, '21Ne': 0.0027, '22Ne': 0.0925, 'Na': 1.0, '24Mg': 0.7899, '25Mg': 0.1, '26Mg': 0.1101, 'Al': 1.0, '28Si': 0.92223, '29Si': 0.04685, '30Si': 0.03092, 'P': 1.0, 'S': 0.9499, '33S': 0.0075, '34S': 0.0425, '36S': 0.0001, 'Cl': 0.7576, '37Cl': 0.2424, '36Ar': 0.003336, '38Ar': 0.000629, '40Ar': 0.996035, 'K': 0.932581, '40K': 0.000117, '41K': 0.067302, 'Ca': 0.96941, '42Ca': 0.00647, '43Ca': 0.00135, '44Ca': 0.02086, '46Ca': 4e-05, '48Ca': 0.001872, '45Sc': 1.0, '46Ti': 0.0825, '47Ti': 0.0744, '48Ti': 0.7372, '49Ti': 0.0541, '50Ti': 0.0518, '50V': 0.0025, 'V': 0.9975, '50Cr': 0.04345, 'Cr': 0.83789, '53Cr': 0.09501, '54Cr': 0.02365, 'Mn': 1.0, '54Fe': 0.05845, 'Fe': 0.91754, '57Fe': 0.02119, '58Fe': 0.00282, 'Co': 1.0, 'Ni': 0.68077, '60Ni': 0.26223, '61Ni': 0.011399, '62Ni': 0.036346, '64Ni': 0.009255, 'Cu': 0.6915, '65Cu': 0.3085, 'Zn': 0.4917, '66Zn': 0.2773, '67Zn': 0.0404, '68Zn': 0.1845, '70Zn': 0.0061, '69Ga': 0.60108, '71Ga': 0.39892, '70Ge': 0.2057, '72Ge': 0.2745, '73Ge': 0.0775, '74Ge': 0.365, '76Ge': 0.0773, 'As': 1.0, '74Se': 0.0089, '76Se': 0.0937, '77Se': 0.0763, '78Se': 0.2377, 'Se': 0.4961, '82Se': 0.0873, 'Br': 0.5069, '81Br': 0.4931, '78Kr': 0.00355, '80Kr': 0.02286, '82Kr': 0.11593, '83Kr': 0.115, '84Kr': 0.56987, '86Kr': 0.17279, '85Rb': 0.7217, '87Rb': 0.2783, '84Sr': 0.0056, '86Sr': 0.0986, '87Sr': 0.07, '88Sr': 0.8258, '89Y': 1.0, '90Zr': 0.5145, '91Zr': 0.1122, '92Zr': 0.1715, '94Zr': 0.1738, '96Zr': 0.028, '93Nb': 1.0, '92Mo': 0.1453, '94Mo': 0.0915, '95Mo': 0.1584, '96Mo': 0.1667, '97Mo': 0.096, 'Mo': 0.2439, '100Mo': 0.0982, '97Tc': 0, '98Tc': 0, '99Tc': 0, '96Ru': 0.0554, '98Ru': 0.0187, '99Ru': 0.1276, '100Ru': 0.126, '101Ru': 0.1706, '102Ru': 0.3155, '104Ru': 0.1862, '103Rh': 1.0, '102Pd': 0.0102, '104Pd': 0.1114, '105Pd': 0.2233, '106Pd': 0.2733, '108Pd': 0.2646, '110Pd': 0.1172, '107Ag': 0.51839, '109Ag': 0.48161, '106Cd': 0.0125, '108Cd': 0.0089, '110Cd': 0.1249, '111Cd': 0.128, 'Cd': 0.2413, '113Cd': 0.1222, '114Cd': 0.2873, '116Cd': 0.0749, '113In': 0.0429, 'In': 0.9571, '112Sn': 0.0097, '114Sn': 0.0066, '115Sn': 0.0034, '116Sn': 0.1454, '117Sn': 0.0768, '118Sn': 0.2422, '119Sn': 0.0859, '120Sn': 0.3258, '122Sn': 0.0463, '124Sn': 0.0579, '121Sb': 0.5721, '123Sb': 0.4279, '120Te': 0.0009, '122Te': 0.0255, '123Te': 0.0089, '124Te': 0.0474, '125Te': 0.0707, '126Te': 0.1884, '128Te': 0.3174, '130Te': 0.3408, '127I': 1.0, 'I': 1.0, '124Xe': 0.000952, '126Xe': 0.00089, '128Xe': 0.019102, '129Xe': 0.264006, '130Xe': 0.04071, '131Xe': 0.212324, '132Xe': 0.269086, '134Xe': 0.104357, '136Xe': 0.088573, '133Cs': 1.0, '130Ba': 0.00106, '132Ba': 0.00101, '134Ba': 0.02417, '135Ba': 0.06592, '136Ba': 0.07854, '137Ba': 0.11232, '138Ba': 0.71698, '138La': 0.0008881, '139La': 0.9991119, '136Ce': 0.00185, '138Ce': 0.00251, '140Ce': 0.8845, '142Ce': 0.11114, '141Pr': 1.0, '142Nd': 0.27152, '143Nd': 0.12174, '144Nd': 0.23798, '145Nd': 0.08293, '146Nd': 0.17189, '148Nd': 0.05756, '150Nd': 0.05638, '145Pm': 0, '147Pm': 0, '144Sm': 0.0307, '147Sm': 0.1499, '148Sm': 0.1124, '149Sm': 0.1382, '150Sm': 0.0738, '152Sm': 0.2675, '154Sm': 0.2275, '151Eu': 0.4781, '153Eu': 0.5219, '152Gd': 0.002, '154Gd': 0.0218, '155Gd': 0.148, '156Gd': 0.2047, '157Gd': 0.1565, '158Gd': 0.2484, '160Gd': 0.2186, '159Tb': 1.0, '156Dy': 0.00056, '158Dy': 0.00095, '160Dy': 0.02329, '161Dy': 0.18889, '162Dy': 0.25475, '163Dy': 0.24896, '164Dy': 0.2826, '165Ho': 1.0, '162Er': 0.00139, '164Er': 0.01601, '166Er': 0.33503, '167Er': 0.22869, '168Er': 0.26978, '170Er': 0.1491, '169Tm': 1.0, '168Yb': 0.00123, '170Yb': 0.02982, '171Yb': 0.1409, '172Yb': 0.2168, '173Yb': 0.16103, '174Yb': 0.32026, '176Yb': 0.12996, '175Lu': 0.97401, '176Lu': 0.02599, '174Hf': 0.0016, '176Hf': 0.0526, '177Hf': 0.186, '178Hf': 0.2728, '179Hf': 0.1362, '180Hf': 0.3508, '180Ta': 0.0001201, '181Ta': 0.9998799, '180W': 0.0012, '182W': 0.265, '183W': 0.1431, '184W': 0.3064, '186W': 0.2843, '185Re': 0.374, '187Re': 0.626, '184Os': 0.0002, '186Os': 0.0159, '187Os': 0.0196, '188Os': 0.1324, '189Os': 0.1615, '190Os': 0.2626, '192Os': 0.4078, '191Ir': 0.373, '193Ir': 0.627, '190Pt': 0.00012, '192Pt': 0.00782, '194Pt': 0.3286, '195Pt': 0.3378, '196Pt': 0.2521, '198Pt': 0.07356, '197Au': 1.0, '196Hg': 0.0015, '198Hg': 0.0997, '199Hg': 0.16872, '200Hg': 0.231, '201Hg': 0.1318, '202Hg': 0.2986, '204Hg': 0.0687, '203Tl': 0.2952, '205Tl': 0.7048, '204Pb': 0.014, '206Pb': 0.241, '207Pb': 0.221, 'Pb': 0.524, '209Bi': 1.0, '209Po': 0, '210Po': 0, '210At': 0, '211At': 0, '211Rn': 0, '220Rn': 0, '222Rn': 0, '223Fr': 0, '223Ra': 0, '224Ra': 0, '226Ra': 0, '228Ra': 0, '227Ac': 0, '230Th': 0, '232Th': 1.0, '231Pa': 1.0, '233U': 0, '234U': 5.4e-05, '235U': 0.007204, '236U': 0, '238U': 0.992742, '236Np': 0, '237Np': 0, '238Pu': 0, '239Pu': 0, '240Pu': 0, '241Pu': 0, '242Pu': 0, '244Pu': 0, '241Am': 0, '243Am': 0, '243Cm': 0, '244Cm': 0, '245Cm': 0, '246Cm': 0, '247Cm': 0, '248Cm': 0, '247Bk': 0, '249Bk': 0, '249Cf': 0, '250Cf': 0, '251Cf': 0, '252Cf': 0, '252Es': 0, '257Fm': 0, '258Md': 0, '260Md': 0, '259No': 0, '262Lr': 0, '267Rf': 0, '268Db': 0, '271Sg': 0, '272Bh': 0, '270Hs': 0, '276Mt': 0, '281Ds': 0, '280Rg': 0, '285Cn': 0, '284Nh': 0, '289Fl': 0, '288Mc': 0, '293Lv': 0, '292Ts': 0, '294Og': 0}"}, {"fullname": "corems.encapsulation.constant.Atoms.isotopes", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.isotopes", "kind": "variable", "doc": "\n", "default_value": "{'F': ['Flourine'], 'Na': ['Sodium'], 'Al': ['Aluminum'], 'P': ['Phosphorus'], 'Sc': ['Scandium'], 'Co': ['Cobalt'], 'He': ['Helium'], 'Ar': ['Argon'], 'H': ['Hydrogen', ['D']], 'Cl': ['Chlorine', ['37Cl']], 'Li': ['Lithium', ['6Li']], 'Be': ['Beryllium'], 'B': ['Boron', ['11B']], 'C': ['Carbon', ['13C']], 'O': ['Oxygen', ['18O', '17O']], 'S': ['Sulfur', ['34S']], 'N': ['Nitrogen', ['15N']], 'V': ['Vanadium', ['50V']], 'Ne': ['Neon', ['20Ne', '22Ne']], 'Mg': ['Magnesium', ['24Mg', '26Mg', '25Mg']], 'Si': ['Silicon', ['28Si', '29Si', '30Si']], 'K': ['Potassium', ['40K', '41K']], 'Ca': ['Calcium', ['43Ca', '44Ca']], 'Ti': ['Titanium', ['48Ti', '46Ti', '47Ti', '49Ti', '50Ti']], 'Cr': ['Chromium', ['53Cr', '50Cr', '54Cr']], 'Fe': ['Iron', ['54Fe', '57Fe', '58Fe']], 'Mn': ['Manganese'], 'Ni': ['Nickel', ['60Ni', '62Ni', '61Ni']], 'Cu': ['Copper', ['65Cu']], 'Zn': ['Zinc', ['66Zn', '68Zn', '67Zn', '70Zn']], 'Ga': ['Gallium', ['69Ga', '71Ga']], 'Ge': ['Germanium', ['74Ge', '72Ge', '70Ge', '73Ge', '76Ge']], 'As': ['Arsenic'], 'Se': ['Selenium', ['78Se', '76Se', '82Se', '77Se']], 'Br': ['Bromine', ['81Br']], 'Kr': ['Krypton', ['84Kr', '86Kr', '82Kr', '83Kr', '80Kr']], 'Rb': ['Rubidium', ['85Rb', '87Rb']], 'Sr': ['Strontium', ['88Sr', '86Sr', '87Sr']], 'Y': ['Yttrium'], 'Zr': ['Zironium', ['90Zr', '94Zr', '92Zr', '91Zr', '96Zr']], 'Nb': ['Niobium'], 'Mo': ['Molybdenum', ['96Mo', '95Mo', '92Mo', '100Mo', '97Mo', '94Mo']], 'Tc': ['Technetium'], 'Ru': ['Ruthenium', ['102Ru', '104Ru', '101Ru', '99Ru', '100Ru', '96Ru', '98Ru']], 'Rh': ['Rhodium'], 'Pd': ['Palladium', ['106Pd', '108Pd', '105Pd', '110Pd', '104Pd', '102Pd']], 'Ag': ['Silver', ['107Ag', '109Ag']], 'Cd': ['Cadmium', ['114Cd', '111Cd', '110Cd', '113Cd', '116Cd', '106Cd', '108Cd']], 'In': ['Indium', ['113In']], 'Sn': ['Tin', ['120Sn', '118Sn', '116Sn', '119Sn', '117Sn', '124Sn', '122Sn', '112Sn']], 'Sb': ['Antimony', ['121Sb', '123Sb']], 'Te': ['Tellurium', ['130Te', '128Te', '126Te', '125Te', '124Te', '122Te']], 'I': ['Iodine'], 'Xe': ['Xenon', ['132Xe', '129Xe', '131Xe', '134Xe', '136Xe', '130Xe', '128Xe']], 'Cs': ['Cesium'], 'Ba': ['Barium', ['138Ba', '137Ba', '136Ba', '135Ba', '134Ba']], 'La': ['Lanthanum'], 'Hf': ['Hafnium', ['180Hf', '178Hf', '177Hf', '179Hf', '176Hf']], 'Ta': ['Tantalum'], 'W': ['Tungsten', ['184W', '186W', '182W', '183W']], 'Re': ['Rhenium', ['187Re', '185Re']], 'Os': ['Osmium', ['192Os', '190Os', '189Os', '188Os', '187Os', '186Os']], 'Ir': ['Iridium', ['193Ir', '191Ir']], 'Pt': ['Platinum', ['195Pt', '194Pt', '196Pt', '198Pt', '192Pt']], 'Au': ['Gold'], 'Hg': ['Mercury', ['202Hg', '200Hg', '199Hg', '201Hg', '198Hg', '204Hg']], 'Tl': ['Thallium', ['205Tl', '203Tl']], 'Pb': ['Lead', ['206Pb', '207Pb', '204Pb']], 'Bi': ['Bismuth'], 'Po': ['Polonium'], 'At': ['Aslatine'], 'Rn': ['Radon'], 'Fr': ['Francium'], 'Ra': ['Radium'], 'Ac': ['Actinium']}"}, {"fullname": "corems.encapsulation.factory", "modulename": "corems.encapsulation.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.parameters", "modulename": "corems.encapsulation.factory.parameters", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters", "kind": "class", "doc": "MSParameters class is used to store the parameters used for the processing of the mass spectrum
\n\nEach attibute is a class that contains the parameters for the processing of the mass spectrum, see the corems.encapsulation.factory.processingSetting module for more details.
\n\nAttributes
\n\n\n- molecular_search (MolecularFormulaSearchSettings):\nMolecularFormulaSearchSettings object
\n- transient (TransientSetting):\nTransientSetting object
\n- mass_spectrum (MassSpectrumSetting):\nMassSpectrumSetting object
\n- ms_peak (MassSpecPeakSetting):\nMassSpecPeakSetting object
\n- data_input (DataInputSetting):\nDataInputSetting object
\n
\n"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters.molecular_search", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters.molecular_search", "kind": "variable", "doc": "\n", "default_value": "MolecularFormulaSearchSettings(use_isotopologue_filter=False, isotopologue_filter_threshold=33.0, isotopologue_filter_atoms=('Cl', 'Br'), use_runtime_kendrick_filter=False, use_min_peaks_filter=True, min_peaks_per_class=15, url_database='postgresql+psycopg2://coremsappdb:coremsapppnnl@molformdb:5432/coremsapp', db_jobs=3, db_chunk_size=300, ion_charge=-1, min_hc_filter=0.3, max_hc_filter=3.0, min_oc_filter=0.0, max_oc_filter=1.2, min_op_filter=2.0, use_pah_line_rule=False, min_dbe=0.0, max_dbe=40.0, mz_error_score_weight=0.6, isotopologue_score_weight=0.4, adduct_atoms_neg=('Cl', 'Br'), adduct_atoms_pos=('Na', 'K'), score_methods=('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error'), score_method='prob_score', output_min_score=0.1, output_score_method='All Candidates', isRadical=False, isProtonated=True, isAdduct=False, usedAtoms={'C': (1, 100), 'H': (1, 200)}, ionization_type='ESI', min_ppm_error=-10.0, max_ppm_error=10.0, min_abun_error=-100.0, max_abun_error=100.0, mz_error_range=1.5, error_method='None', mz_error_average=0.0, used_atom_valences={'C': 4, '13C': 4, 'N': 3, 'O': 2, 'S': 2, 'H': 1, 'F': (1, 0), 'Cl': (1, 0), 'Br': (1, 0), 'I': (1, 0), 'At': 1, 'Li': (1, 0), 'Na': (1, 0), 'K': (1, 0), 'Rb': 1, 'Cs': 1, 'Fr': 1, 'B': (4, 3, 2, 1), 'In': (3, 2, 1), 'Al': (3, 1, 2), 'P': (3, 5, 4, 2, 1), 'Ga': (3, 1, 2), 'Mg': (2, 1), 'Be': (2, 1), 'Ca': (2, 1), 'Sr': (2, 1), 'Ba': 2, 'Ra': 2, 'V': (5, 4, 3, 2, 1), 'Fe': (3, 2, 4, 5, 6), 'Si': (4, 3, 2), 'Sc': (3, 2, 1), 'Ti': (4, 3, 2, 1), 'Cr': (1, 2, 3, 4, 5, 6), 'Mn': (1, 2, 3, 4, 5, 6, 7), 'Co': (1, 2, 3, 4, 5), 'Ni': (1, 2, 3, 4), 'Cu': (2, 1, 3, 4), 'Zn': (2, 1), 'Ge': (4, 3, 2, 1), 'As': (5, 3, 2, 1), 'Se': (6, 4, 2, 1), 'Y': (3, 2, 1), 'Zr': (4, 3, 2, 1), 'Nb': (5, 4, 3, 2, 1), 'Mo': (6, 5, 4, 3, 2, 1), 'Tc': (7, 6, 5, 4, 3, 2, 1), 'Ru': (8, 7, 6, 5, 4, 3, 2, 1), 'Rh': (6, 5, 4, 3, 2, 1), 'Pd': (4, 2, 1), 'Ag': (0, 1, 2, 3, 4), 'Cd': (2, 1), 'Sn': (4, 2), 'Sb': (5, 3), 'Te': (6, 5, 4, 2), 'La': (3, 2), 'Hf': (4, 3, 2), 'Ta': (5, 4, 3, 2), 'W': (6, 5, 4, 3, 2, 1), 'Re': (4, 7, 6, 5, 3, 2, 1), 'Os': (4, 8, 7, 6, 5, 3, 2, 1), 'Ir': (4, 8, 6, 5, 3, 2, 1), 'Pt': (4, 6, 5, 3, 2, 1), 'Au': (3, 5, 2, 1), 'Hg': (1, 2, 4), 'Tl': (3, 1), 'Pb': (4, 2), 'Bi': (3, 1, 5), 'Po': (2, 4, 6), 'Ac': (3, 2)})"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters.transient", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters.transient", "kind": "variable", "doc": "\n", "default_value": "TransientSetting(implemented_apodization_function=('Hamming', 'Hanning', 'Blackman', 'Full-Sine', 'Half-Sine', 'Kaiser', 'Half-Kaiser'), apodization_method='Hanning', number_of_truncations=0, number_of_zero_fills=1, next_power_of_two=False, kaiser_beta=8.6)"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters.mass_spectrum", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters.mass_spectrum", "kind": "variable", "doc": "\n", "default_value": "MassSpectrumSetting(noise_threshold_method='log', noise_threshold_methods_implemented=('minima', 'signal_noise', 'relative_abundance', 'absolute_abundance', 'log'), noise_threshold_min_std=6, noise_threshold_min_s2n=4.0, noise_threshold_min_relative_abundance=6.0, noise_threshold_absolute_abundance=1000000.0, noise_threshold_log_nsigma=6, noise_threshold_log_nsigma_corr_factor=0.463, noise_threshold_log_nsigma_bins=500, noise_min_mz=50.0, noise_max_mz=1200.0, min_picking_mz=50.0, max_picking_mz=1200.0, picking_point_extrapolate=3, calib_minimize_method='Powell', calib_pol_order=2, max_calib_ppm_error=1.0, min_calib_ppm_error=-1.0, calib_sn_threshold=2.0, do_calibration=True)"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters.ms_peak", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters.ms_peak", "kind": "variable", "doc": "\n", "default_value": "MassSpecPeakSetting(kendrick_base={'C': 1, 'H': 2}, kendrick_rounding_method='floor', implemented_kendrick_rounding_methods=('floor', 'ceil', 'round'), peak_derivative_threshold=0.0, peak_min_prominence_percent=0.1, min_peak_datapoints=5.0, peak_max_prominence_percent=0.1, peak_height_max_percent=10.0, legacy_resolving_power=True)"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters.data_input", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters.data_input", "kind": "variable", "doc": "\n", "default_value": "DataInputSetting(header_translate={'m/z': 'm/z', 'mOz': 'm/z', 'Mass': 'm/z', 'Resolving Power': 'Resolving Power', 'Res.': 'Resolving Power', 'Intensity': 'Peak Height', 'I': 'Peak Height', 'Abundance': 'Peak Height', 'Signal/Noise': 'S/N', 'S/N': 'S/N', 'abs_abu': 'Peak Height', 'sn': 'S/N', 'resolution': 'Resolving Power'})"}, {"fullname": "corems.encapsulation.factory.parameters.GCMSParameters", "modulename": "corems.encapsulation.factory.parameters", "qualname": "GCMSParameters", "kind": "class", "doc": "GCMSParameters class is used to store the parameters used for the processing of the gas chromatograph mass spectrum
\n\nEach attibute is a class that contains the parameters for the processing of the data, see the corems.encapsulation.factory.processingSetting module for more details.
\n\nAttributes
\n\n\n- molecular_search (MolecularFormulaSearchSettings):\nMolecularFormulaSearchSettings object
\n- gc_ms (GasChromatographSetting):\nGasChromatographSetting object
\n
\n"}, {"fullname": "corems.encapsulation.factory.parameters.GCMSParameters.molecular_search", "modulename": "corems.encapsulation.factory.parameters", "qualname": "GCMSParameters.molecular_search", "kind": "variable", "doc": "\n", "default_value": "CompoundSearchSettings(url_database='sqlite:///db/pnnl_lowres_gcms_compounds.sqlite', ri_search_range=35.0, rt_search_range=1.0, correlation_threshold=0.5, score_threshold=0.0, ri_spacing=200.0, ri_std=3.0, ri_calibration_compound_names=['Methyl Caprylate', 'Methyl Caprate', 'Methyl Pelargonate', 'Methyl Laurate', 'Methyl Myristate', 'Methyl Palmitate', 'Methyl Stearate', 'Methyl Eicosanoate', 'Methyl Docosanoate', 'Methyl Linocerate', 'Methyl Hexacosanoate', 'Methyl Octacosanoate', 'Methyl Triacontanoate'], exploratory_mode=False, score_methods=('highest_sim_score', 'highest_ss'), output_score_method='All')"}, {"fullname": "corems.encapsulation.factory.parameters.GCMSParameters.gc_ms", "modulename": "corems.encapsulation.factory.parameters", "qualname": "GCMSParameters.gc_ms", "kind": "variable", "doc": "\n", "default_value": "GasChromatographSetting(use_deconvolution=False, implemented_smooth_method=('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'), smooth_window=5, smooth_method='savgol', savgol_pol_order=2, peak_derivative_threshold=0.0005, peak_height_max_percent=10.0, peak_max_prominence_percent=1.0, min_peak_datapoints=5.0, max_peak_width=0.1, noise_threshold_method='manual_relative_abundance', noise_threshold_methods_implemented=('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative'), std_noise_threshold=3, peak_height_min_percent=0.1, peak_min_prominence_percent=0.1, eic_signal_threshold=0.01, max_rt_distance=0.025)"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters", "kind": "class", "doc": "LCMSParameters class is used to store the parameters used for the processing of the liquid chromatograph mass spectrum
\n\nEach attibute is a class that contains the parameters for the processing of the data, see the corems.encapsulation.factory.processingSetting module for more details.
\n\nAttributes
\n\n\n- lc_ms (LiquidChromatographSetting):\nLiquidChromatographSetting object
\n- mass_spectrum (MassSpectrumSetting):\nMassSpectrumSetting object
\n- ms_peak (MassSpecPeakSetting):\nMassSpecPeakSetting object
\n- ms1_molecular_search (MolecularFormulaSearchSettings):\nMolecularFormulaSearchSettings object
\n- ms2_molecular_search (MolecularFormulaSearchSettings):\nMolecularFormulaSearchSettings object
\n
\n"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters.lc_ms", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters.lc_ms", "kind": "variable", "doc": "\n", "default_value": "LiquidChromatographSetting(scans=(0, 1), eic_tolerance_ppm=5.0, enforce_target_ms2=True, average_target_mz=True, smooth_window=5, smooth_method='savgol', implemented_smooth_method=('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'), savgol_pol_order=2, peak_height_max_percent=10.0, peak_max_prominence_percent=1.0, peak_derivative_threshold=0.0005, min_peak_datapoints=5.0, noise_threshold_method='manual_relative_abundance', noise_threshold_methods_implemented=('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative'), std_noise_threshold=3, peak_height_min_percent=0.1, eic_signal_threshold=0.01)"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters.mass_spectrum", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters.mass_spectrum", "kind": "variable", "doc": "\n", "default_value": "MassSpectrumSetting(noise_threshold_method='log', noise_threshold_methods_implemented=('minima', 'signal_noise', 'relative_abundance', 'absolute_abundance', 'log'), noise_threshold_min_std=6, noise_threshold_min_s2n=4.0, noise_threshold_min_relative_abundance=6.0, noise_threshold_absolute_abundance=1000000.0, noise_threshold_log_nsigma=6, noise_threshold_log_nsigma_corr_factor=0.463, noise_threshold_log_nsigma_bins=500, noise_min_mz=50.0, noise_max_mz=1200.0, min_picking_mz=50.0, max_picking_mz=1200.0, picking_point_extrapolate=3, calib_minimize_method='Powell', calib_pol_order=2, max_calib_ppm_error=1.0, min_calib_ppm_error=-1.0, calib_sn_threshold=2.0, do_calibration=True)"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters.ms_peak", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters.ms_peak", "kind": "variable", "doc": "\n", "default_value": "MassSpecPeakSetting(kendrick_base={'C': 1, 'H': 2}, kendrick_rounding_method='floor', implemented_kendrick_rounding_methods=('floor', 'ceil', 'round'), peak_derivative_threshold=0.0, peak_min_prominence_percent=0.1, min_peak_datapoints=5.0, peak_max_prominence_percent=0.1, peak_height_max_percent=10.0, legacy_resolving_power=True)"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters.ms1_molecular_search", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters.ms1_molecular_search", "kind": "variable", "doc": "\n", "default_value": "MolecularFormulaSearchSettings(use_isotopologue_filter=False, isotopologue_filter_threshold=33.0, isotopologue_filter_atoms=('Cl', 'Br'), use_runtime_kendrick_filter=False, use_min_peaks_filter=True, min_peaks_per_class=15, url_database='postgresql+psycopg2://coremsappdb:coremsapppnnl@molformdb:5432/coremsapp', db_jobs=3, db_chunk_size=300, ion_charge=-1, min_hc_filter=0.3, max_hc_filter=3.0, min_oc_filter=0.0, max_oc_filter=1.2, min_op_filter=2.0, use_pah_line_rule=False, min_dbe=0.0, max_dbe=40.0, mz_error_score_weight=0.6, isotopologue_score_weight=0.4, adduct_atoms_neg=('Cl', 'Br'), adduct_atoms_pos=('Na', 'K'), score_methods=('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error'), score_method='prob_score', output_min_score=0.1, output_score_method='All Candidates', isRadical=False, isProtonated=True, isAdduct=False, usedAtoms={'C': (1, 100), 'H': (1, 200)}, ionization_type='ESI', min_ppm_error=-10.0, max_ppm_error=10.0, min_abun_error=-100.0, max_abun_error=100.0, mz_error_range=1.5, error_method='None', mz_error_average=0.0, used_atom_valences={'C': 4, '13C': 4, 'N': 3, 'O': 2, 'S': 2, 'H': 1, 'F': (1, 0), 'Cl': (1, 0), 'Br': (1, 0), 'I': (1, 0), 'At': 1, 'Li': (1, 0), 'Na': (1, 0), 'K': (1, 0), 'Rb': 1, 'Cs': 1, 'Fr': 1, 'B': (4, 3, 2, 1), 'In': (3, 2, 1), 'Al': (3, 1, 2), 'P': (3, 5, 4, 2, 1), 'Ga': (3, 1, 2), 'Mg': (2, 1), 'Be': (2, 1), 'Ca': (2, 1), 'Sr': (2, 1), 'Ba': 2, 'Ra': 2, 'V': (5, 4, 3, 2, 1), 'Fe': (3, 2, 4, 5, 6), 'Si': (4, 3, 2), 'Sc': (3, 2, 1), 'Ti': (4, 3, 2, 1), 'Cr': (1, 2, 3, 4, 5, 6), 'Mn': (1, 2, 3, 4, 5, 6, 7), 'Co': (1, 2, 3, 4, 5), 'Ni': (1, 2, 3, 4), 'Cu': (2, 1, 3, 4), 'Zn': (2, 1), 'Ge': (4, 3, 2, 1), 'As': (5, 3, 2, 1), 'Se': (6, 4, 2, 1), 'Y': (3, 2, 1), 'Zr': (4, 3, 2, 1), 'Nb': (5, 4, 3, 2, 1), 'Mo': (6, 5, 4, 3, 2, 1), 'Tc': (7, 6, 5, 4, 3, 2, 1), 'Ru': (8, 7, 6, 5, 4, 3, 2, 1), 'Rh': (6, 5, 4, 3, 2, 1), 'Pd': (4, 2, 1), 'Ag': (0, 1, 2, 3, 4), 'Cd': (2, 1), 'Sn': (4, 2), 'Sb': (5, 3), 'Te': (6, 5, 4, 2), 'La': (3, 2), 'Hf': (4, 3, 2), 'Ta': (5, 4, 3, 2), 'W': (6, 5, 4, 3, 2, 1), 'Re': (4, 7, 6, 5, 3, 2, 1), 'Os': (4, 8, 7, 6, 5, 3, 2, 1), 'Ir': (4, 8, 6, 5, 3, 2, 1), 'Pt': (4, 6, 5, 3, 2, 1), 'Au': (3, 5, 2, 1), 'Hg': (1, 2, 4), 'Tl': (3, 1), 'Pb': (4, 2), 'Bi': (3, 1, 5), 'Po': (2, 4, 6), 'Ac': (3, 2)})"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters.ms2_molecular_search", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters.ms2_molecular_search", "kind": "variable", "doc": "\n", "default_value": "MolecularFormulaSearchSettings(use_isotopologue_filter=False, isotopologue_filter_threshold=33.0, isotopologue_filter_atoms=('Cl', 'Br'), use_runtime_kendrick_filter=False, use_min_peaks_filter=True, min_peaks_per_class=15, url_database='postgresql+psycopg2://coremsappdb:coremsapppnnl@molformdb:5432/coremsapp', db_jobs=3, db_chunk_size=300, ion_charge=-1, min_hc_filter=0.3, max_hc_filter=3.0, min_oc_filter=0.0, max_oc_filter=1.2, min_op_filter=2.0, use_pah_line_rule=False, min_dbe=0.0, max_dbe=40.0, mz_error_score_weight=0.6, isotopologue_score_weight=0.4, adduct_atoms_neg=('Cl', 'Br'), adduct_atoms_pos=('Na', 'K'), score_methods=('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error'), score_method='prob_score', output_min_score=0.1, output_score_method='All Candidates', isRadical=False, isProtonated=True, isAdduct=False, usedAtoms={'C': (1, 100), 'H': (1, 200)}, ionization_type='ESI', min_ppm_error=-10.0, max_ppm_error=10.0, min_abun_error=-100.0, max_abun_error=100.0, mz_error_range=1.5, error_method='None', mz_error_average=0.0, used_atom_valences={'C': 4, '13C': 4, 'N': 3, 'O': 2, 'S': 2, 'H': 1, 'F': (1, 0), 'Cl': (1, 0), 'Br': (1, 0), 'I': (1, 0), 'At': 1, 'Li': (1, 0), 'Na': (1, 0), 'K': (1, 0), 'Rb': 1, 'Cs': 1, 'Fr': 1, 'B': (4, 3, 2, 1), 'In': (3, 2, 1), 'Al': (3, 1, 2), 'P': (3, 5, 4, 2, 1), 'Ga': (3, 1, 2), 'Mg': (2, 1), 'Be': (2, 1), 'Ca': (2, 1), 'Sr': (2, 1), 'Ba': 2, 'Ra': 2, 'V': (5, 4, 3, 2, 1), 'Fe': (3, 2, 4, 5, 6), 'Si': (4, 3, 2), 'Sc': (3, 2, 1), 'Ti': (4, 3, 2, 1), 'Cr': (1, 2, 3, 4, 5, 6), 'Mn': (1, 2, 3, 4, 5, 6, 7), 'Co': (1, 2, 3, 4, 5), 'Ni': (1, 2, 3, 4), 'Cu': (2, 1, 3, 4), 'Zn': (2, 1), 'Ge': (4, 3, 2, 1), 'As': (5, 3, 2, 1), 'Se': (6, 4, 2, 1), 'Y': (3, 2, 1), 'Zr': (4, 3, 2, 1), 'Nb': (5, 4, 3, 2, 1), 'Mo': (6, 5, 4, 3, 2, 1), 'Tc': (7, 6, 5, 4, 3, 2, 1), 'Ru': (8, 7, 6, 5, 4, 3, 2, 1), 'Rh': (6, 5, 4, 3, 2, 1), 'Pd': (4, 2, 1), 'Ag': (0, 1, 2, 3, 4), 'Cd': (2, 1), 'Sn': (4, 2), 'Sb': (5, 3), 'Te': (6, 5, 4, 2), 'La': (3, 2), 'Hf': (4, 3, 2), 'Ta': (5, 4, 3, 2), 'W': (6, 5, 4, 3, 2, 1), 'Re': (4, 7, 6, 5, 3, 2, 1), 'Os': (4, 8, 7, 6, 5, 3, 2, 1), 'Ir': (4, 8, 6, 5, 3, 2, 1), 'Pt': (4, 6, 5, 3, 2, 1), 'Au': (3, 5, 2, 1), 'Hg': (1, 2, 4), 'Tl': (3, 1), 'Pb': (4, 2), 'Bi': (3, 1, 5), 'Po': (2, 4, 6), 'Ac': (3, 2)})"}, {"fullname": "corems.encapsulation.factory.parameters.default_parameters", "modulename": "corems.encapsulation.factory.parameters", "qualname": "default_parameters", "kind": "function", "doc": "Generate parameters dictionary with the default parameters for data processing\n To gather parameters from instrument data during the data parsing step, a parameters dictionary with the default parameters needs to be generated.\n This dictionary acts as a placeholder and is later used as an argument for all the class constructor methods during instantiation. \n The data gathered from the instrument is added to the class properties.
\n\nParameters
\n\n\n- file_location (str):\npath to the file
\n
\n\nReturns
\n\n\n- parameters (dict):\ndictionary with the default parameters for data processing
\n
\n", "signature": "(file_location):", "funcdef": "def"}, {"fullname": "corems.encapsulation.factory.processingSetting", "modulename": "corems.encapsulation.factory.processingSetting", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting", "kind": "class", "doc": "Transient processing settings class
\n\nAttributes
\n\n\n- implemented_apodization_function (tuple):\nAvailable apodization functions
\n- apodization_method (str):\nApodization function to use. Hanning is a good default for Fourier transform magnitude mode. For absorption mode processing, Half-Sine or Half-Kaiser may be more appropriate.
\n- number_of_truncations (int):\nHow many times to truncate the transient prior to Fourier transform
\n- number_of_zero_fills (int):\nHow many times to zero fille the transient prior to Fourier transform.
\n- next_power_of_two (bool):\nIf True, zero fill to the next power of two after the new length of len(transient)+(number_of_zero_fills*len(transient)).
\n- kaiser_beta (float):\nBeta parameter for Kaiser or Half-Kaiser apodisation function. 0 is rectangular, 5 is similar to Hamming,\n6 is similar to hanning, and 8.6 is similar to Blackman (from numpy docs)
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.__init__", "kind": "function", "doc": "\n", "signature": "(\timplemented_apodization_function: tuple = ('Hamming', 'Hanning', 'Blackman', 'Full-Sine', 'Half-Sine', 'Kaiser', 'Half-Kaiser'),\tapodization_method: str = 'Hanning',\tnumber_of_truncations: int = 0,\tnumber_of_zero_fills: int = 1,\tnext_power_of_two: bool = False,\tkaiser_beta: float = 8.6)"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.implemented_apodization_function", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.implemented_apodization_function", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('Hamming', 'Hanning', 'Blackman', 'Full-Sine', 'Half-Sine', 'Kaiser', 'Half-Kaiser')"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.apodization_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.apodization_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'Hanning'"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.number_of_truncations", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.number_of_truncations", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "0"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.number_of_zero_fills", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.number_of_zero_fills", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "1"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.next_power_of_two", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.next_power_of_two", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.kaiser_beta", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.kaiser_beta", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "8.6"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting", "kind": "class", "doc": "Data input settings class
\n\nAttributes
\n\n\n- header_translate (dict):\nDictionary with the header labels to be translated to the corems labels. For example, {'m/z':'m/z', 'Resolving Power':'Resolving Power', 'Abundance':'Abundance' , 'S/N':'S/N'}
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.__init__", "kind": "function", "doc": "\n", "signature": "(header_translate: dict = <factory>)"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.header_translate", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.header_translate", "kind": "variable", "doc": "\n", "annotation": ": dict"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.add_mz_label", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.add_mz_label", "kind": "function", "doc": "Add a label to the header_translate dictionary to be translated to the corems label for mz.
\n", "signature": "(self, label):", "funcdef": "def"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.add_peak_height_label", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.add_peak_height_label", "kind": "function", "doc": "Add a label to the header_translate dictionary to be translated to the corems label for peak height.
\n", "signature": "(self, label):", "funcdef": "def"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.add_sn_label", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.add_sn_label", "kind": "function", "doc": "Add a label to the header_translate dictionary to be translated to the corems label for signal to noise.
\n", "signature": "(self, label):", "funcdef": "def"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.add_resolving_power_label", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.add_resolving_power_label", "kind": "function", "doc": "Add a label to the header_translate dictionary to be translated to the corems label for resolving power.
\n", "signature": "(self, label):", "funcdef": "def"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting", "kind": "class", "doc": "Liquid chromatograph processing settings class
\n\nAttributes
\n\n\n- scans (list or tuple, optional):\nList of select scan to average or a tuple containing the range to average. Default is (0, 1).
\n- eic_tolerance_ppm (float, optional):\nMass tolerance in ppm for extracted ion chromatogram peak detection. Default is 5.
\n- correct_eic_baseline (bool, optional):\nIf True, correct the baseline of the extracted ion chromatogram. Default is True.
\n- enforce_target_ms2 (bool, optional):\nOnly extract EICs for target_mz if the m/z was selected as precursor for ms2. Default is True.
\n- average_target_mz (bool, optional):\nIf True, average the target_mz EICs. Default is True.
\n- smooth_window (int, optional):\nWindow size for smoothing the ion chromatogram. Default is 5.
\n- smooth_method (str, optional):\nSmoothing method to use. Default is 'savgol'. Other options are 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'.
\n- implemented_smooth_method (tuple, optional):\nSmoothing methods that can be implemented. Values are ('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar').
\n- savgol_pol_order (int, optional):\nPolynomial order for Savitzky-Golay smoothing. Default is 2.
\n- peak_height_max_percent (float, optional):\n1-100 % used for baseline detection use 0.1 for second_derivative and 10 for other methods. Default is 10.
\n- peak_max_prominence_percent (float, optional):\n1-100 % used for baseline detection. Default is 1.
\n- peak_derivative_threshold (float, optional):\nThreshold for defining derivative crossing. Default is 0.0005.
\n- min_peak_datapoints (float, optional):\nminimum data point to define a chromatografic peak. Default is 5.
\n- noise_threshold_method (str, optional):\nMethod for detecting noise threshold. Default is 'manual_relative_abundance'.
\n- noise_threshold_methods_implemented (tuple, optional):\nMethods for detected noise threshold that can be implemented. Default is ('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative').
\n- std_noise_threshold (int, optional):\nthe amount of standard deviations used to calculate noise thresould, average + (std_noise_threshold * noise). Default is 3.
\n- peak_height_min_percent (float, optional):\n0-100 % used for peak detection. Default is 0.1.
\n- eic_signal_threshold (float, optional):\n0-100 % used for extracted ion chromatogram peak detection. Default is 0.01.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.__init__", "kind": "function", "doc": "\n", "signature": "(\tscans: list | tuple = (0, 1),\teic_tolerance_ppm: float = 5,\tenforce_target_ms2: bool = True,\taverage_target_mz: bool = True,\tsmooth_window: int = 5,\tsmooth_method: str = 'savgol',\timplemented_smooth_method: tuple = ('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'),\tsavgol_pol_order: int = 2,\tpeak_height_max_percent: float = 10,\tpeak_max_prominence_percent: float = 1,\tpeak_derivative_threshold: float = 0.0005,\tmin_peak_datapoints: float = 5,\tnoise_threshold_method: str = 'manual_relative_abundance',\tnoise_threshold_methods_implemented: tuple = ('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative'),\tstd_noise_threshold: int = 3,\tpeak_height_min_percent: float = 0.1,\teic_signal_threshold: float = 0.01)"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.scans", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.scans", "kind": "variable", "doc": "\n", "annotation": ": list | tuple", "default_value": "(0, 1)"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.eic_tolerance_ppm", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.eic_tolerance_ppm", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.correct_eic_baseline", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.correct_eic_baseline", "kind": "variable", "doc": "\n", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.enforce_target_ms2", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.enforce_target_ms2", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.average_target_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.average_target_mz", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.smooth_window", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.smooth_window", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.smooth_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.smooth_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'savgol'"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.implemented_smooth_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.implemented_smooth_method", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar')"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.savgol_pol_order", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.savgol_pol_order", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "2"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.peak_height_max_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.peak_height_max_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "10"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.peak_max_prominence_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.peak_max_prominence_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.peak_derivative_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.peak_derivative_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0005"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.min_peak_datapoints", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.min_peak_datapoints", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.noise_threshold_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.noise_threshold_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'manual_relative_abundance'"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.noise_threshold_methods_implemented", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.noise_threshold_methods_implemented", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative')"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.std_noise_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.std_noise_threshold", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.peak_height_min_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.peak_height_min_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.eic_signal_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.eic_signal_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.01"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting", "kind": "class", "doc": "Mass spectrum processing settings class
\n\nAttributes
\n\n\n- noise_threshold_method (str, optional):\nMethod for detecting noise threshold. Default is 'log'.
\n- noise_threshold_methods_implemented (tuple, optional):\nMethods for detected noise threshold that can be implemented. Default is ('minima', 'signal_noise', 'relative_abundance', 'absolute_abundance', 'log').
\n- noise_threshold_min_std (int, optional):\nMinumum value for noise thresholding when using 'minima' noise threshold method. Default is 6.
\n- noise_threshold_min_s2n (float, optional):\nMinimum value for noise thresholding when using 'signal_noise' noise threshold method. Default is 4.
\n- noise_threshold_min_relative_abundance (float, optional):\nMinimum value for noise thresholding when using 'relative_abundance' noise threshold method. Default is 6.
\n- noise_threshold_absolute_abundance (float, optional):\nMinimum value for noise thresholding when using 'absolute_abundance' noise threshold method. Default is 1_000_000.
\n- noise_threshold_log_nsigma (int, optional):\nNumber of standard deviations to use when using 'log' noise threshold method. Default is 6.
\n- noise_threshold_log_nsigma_corr_factor (float, optional):\nCorrection factor for log noise threshold method. Default is 0.463.
\n- noise_threshold_log_nsigma_bins (int, optional):\nNumber of bins to use for histogram when using 'log' noise threshold method. Default is 500.
\n- noise_min_mz (float, optional):\nMinimum m/z to use for noise thresholding. Default is 50.0.
\n- noise_max_mz (float, optional):\nMaximum m/z to use for noise thresholding. Default is 1200.0.
\n- min_picking_mz (float, optional):\nMinimum m/z to use for peak picking. Default is 50.0.
\n- max_picking_mz (float, optional):\nMaximum m/z to use for peak picking. Default is 1200.0.
\n- picking_point_extrapolate (int, optional):\nHow many data points (in each direction) to extrapolate the mz axis and 0 pad the abundance axis. Default is 3.
\n- calib_minimize_method (str, optional):\nMinimization method to use for calibration. Default is 'Powell'.
\n- calib_pol_order (int, optional):\nPolynomial order to use for calibration. Default is 2.
\n- max_calib_ppm_error (float, optional):\nMaximum ppm error to use for calibration. Default is 1.0.
\n- min_calib_ppm_error (float, optional):\nMinimum ppm error to use for calibration. Default is -1.0.
\n- calib_sn_threshold (float, optional):\nSignal to noise threshold to use for calibration. Default is 2.0.
\n- do_calibration (bool, optional):\nIf True, perform calibration. Default is True.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.__init__", "kind": "function", "doc": "\n", "signature": "(\tnoise_threshold_method: str = 'log',\tnoise_threshold_methods_implemented: tuple = ('minima', 'signal_noise', 'relative_abundance', 'absolute_abundance', 'log'),\tnoise_threshold_min_std: int = 6,\tnoise_threshold_min_s2n: float = 4,\tnoise_threshold_min_relative_abundance: float = 6,\tnoise_threshold_absolute_abundance: float = 1000000,\tnoise_threshold_log_nsigma: int = 6,\tnoise_threshold_log_nsigma_corr_factor: float = 0.463,\tnoise_threshold_log_nsigma_bins: int = 500,\tnoise_min_mz: float = 50.0,\tnoise_max_mz: float = 1200.0,\tmin_picking_mz: float = 50.0,\tmax_picking_mz: float = 1200.0,\tpicking_point_extrapolate: int = 3,\tcalib_minimize_method: str = 'Powell',\tcalib_pol_order: int = 2,\tmax_calib_ppm_error: float = 1.0,\tmin_calib_ppm_error: float = -1.0,\tcalib_sn_threshold: float = 2.0,\tdo_calibration: bool = True)"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'log'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_methods_implemented", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_methods_implemented", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('minima', 'signal_noise', 'relative_abundance', 'absolute_abundance', 'log')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_min_std", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_min_std", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "6"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_min_s2n", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_min_s2n", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "4"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_min_relative_abundance", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_min_relative_abundance", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "6"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_absolute_abundance", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_absolute_abundance", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1000000"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_log_nsigma", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_log_nsigma", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "6"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_log_nsigma_corr_factor", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_log_nsigma_corr_factor", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.463"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_log_nsigma_bins", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_log_nsigma_bins", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "500"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_min_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_min_mz", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "50.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_max_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_max_mz", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1200.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.min_picking_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.min_picking_mz", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "50.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.max_picking_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.max_picking_mz", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1200.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.picking_point_extrapolate", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.picking_point_extrapolate", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.calib_minimize_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.calib_minimize_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'Powell'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.calib_pol_order", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.calib_pol_order", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "2"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.max_calib_ppm_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.max_calib_ppm_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.min_calib_ppm_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.min_calib_ppm_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "-1.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.calib_sn_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.calib_sn_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "2.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.do_calibration", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.do_calibration", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting", "kind": "class", "doc": "Mass spectrum peak processing settings class
\n\nAttributes
\n\n\n- kendrick_base (Dict, optional):\nDictionary specifying the elements and their counts in the Kendrick base.\nDefaults to {'C': 1, 'H': 2}.
\n- kendrick_rounding_method (str, optional):\nMethod for calculating the nominal Kendrick mass. Valid values are 'floor', 'ceil', or 'round'.\nDefaults to 'floor'.
\n- implemented_kendrick_rounding_methods (tuple):\nTuple of valid rounding methods for calculating the nominal Kendrick mass.\nDefaults to ('floor', 'ceil', 'round').
\n- peak_derivative_threshold (float, optional):\nThreshold for defining derivative crossing. Should be a value between 0 and 1.\nDefaults to 0.0.
\n- peak_min_prominence_percent (float, optional):\nMinimum prominence percentage used for peak detection. Should be a value between 1 and 100.\nDefaults to 0.1.
\n- min_peak_datapoints (float, optional):\nMinimum number of data points used for peak detection. Should be a value between 0 and infinity.\nDefaults to 5.
\n- peak_max_prominence_percent (float, optional):\nMaximum prominence percentage used for baseline detection. Should be a value between 1 and 100.\nDefaults to 0.1.
\n- peak_height_max_percent (float, optional):\nMaximum height percentage used for baseline detection. Should be a value between 1 and 100.\nDefaults to 10.
\n- legacy_resolving_power (bool, optional):\nFlag indicating whether to use the legacy (CoreMS v1) resolving power calculation.\nDefaults to True.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.__init__", "kind": "function", "doc": "\n", "signature": "(\tkendrick_base: Dict = <factory>,\tkendrick_rounding_method: str = 'floor',\timplemented_kendrick_rounding_methods: tuple = ('floor', 'ceil', 'round'),\tpeak_derivative_threshold: float = 0.0,\tpeak_min_prominence_percent: float = 0.1,\tmin_peak_datapoints: float = 5,\tpeak_max_prominence_percent: float = 0.1,\tpeak_height_max_percent: float = 10,\tlegacy_resolving_power: bool = True)"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.kendrick_base", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.kendrick_base", "kind": "variable", "doc": "\n", "annotation": ": Dict"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.kendrick_rounding_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.kendrick_rounding_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'floor'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.implemented_kendrick_rounding_methods", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.implemented_kendrick_rounding_methods", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('floor', 'ceil', 'round')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.peak_derivative_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.peak_derivative_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.peak_min_prominence_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.peak_min_prominence_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.min_peak_datapoints", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.min_peak_datapoints", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.peak_max_prominence_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.peak_max_prominence_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.peak_height_max_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.peak_height_max_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "10"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.legacy_resolving_power", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.legacy_resolving_power", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting", "kind": "class", "doc": "Gas chromatograph processing settings class
\n\nAttributes
\n\n\n- use_deconvolution (bool, optional):\nIf True, use deconvolution. Default is False.
\n- implemented_smooth_method (tuple, optional):\nSmoothing methods that can be implemented. Default is ('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar').
\n- smooth_window (int, optional):\nWindow size for smoothing the ion chromatogram. Default is 5.
\n- smooth_method (str, optional):\nSmoothing method to use. Default is 'savgol'. Other options are 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'.
\n- savgol_pol_order (int, optional):\nPolynomial order for Savitzky-Golay smoothing. Default is 2.
\n- peak_derivative_threshold (float, optional):\nThreshold for defining derivative crossing. Should be a value between 0 and 1.\nDefaults to 0.0005.
\n- peak_height_max_percent (float, optional):\nMaximum height percentage used for baseline detection. Should be a value between 1 and 100.\nDefaults to 10.
\n- peak_max_prominence_percent (float, optional):\nMaximum prominence percentage used for baseline detection. Should be a value between 1 and 100.\nDefaults to 1.
\n- min_peak_datapoints (float, optional):\nMinimum number of data points used for peak detection. Should be a value between 0 and infinity.\nDefaults to 5.
\n- max_peak_width (float, optional):\nMaximum peak width used for peak detection. Should be a value between 0 and infinity.\nDefaults to 0.1.
\n- noise_threshold_method (str, optional):\nMethod for detecting noise threshold. Default is 'manual_relative_abundance'.
\n- noise_threshold_methods_implemented (tuple, optional):\nMethods for detected noise threshold that can be implemented. Default is ('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative').
\n- std_noise_threshold (int, optional):\nDefault is 3.
\n- peak_height_min_percent (float, optional):\n0-100 % used for peak detection. Default is 0.1.
\n- peak_min_prominence_percent (float, optional):\n0-100 % used for peak detection. Default is 0.1.
\n- eic_signal_threshold (float, optional):\n0-100 % used for extracted ion chromatogram peak detection. Default is 0.01.
\n- max_rt_distance (float, optional):\nMaximum distance allowance for hierarchical cluster, in minutes. Default is 0.025.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.__init__", "kind": "function", "doc": "\n", "signature": "(\tuse_deconvolution: bool = False,\timplemented_smooth_method: tuple = ('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'),\tsmooth_window: int = 5,\tsmooth_method: str = 'savgol',\tsavgol_pol_order: int = 2,\tpeak_derivative_threshold: float = 0.0005,\tpeak_height_max_percent: float = 10,\tpeak_max_prominence_percent: float = 1,\tmin_peak_datapoints: float = 5,\tmax_peak_width: float = 0.1,\tnoise_threshold_method: str = 'manual_relative_abundance',\tnoise_threshold_methods_implemented: tuple = ('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative'),\tstd_noise_threshold: int = 3,\tpeak_height_min_percent: float = 0.1,\tpeak_min_prominence_percent: float = 0.1,\teic_signal_threshold: float = 0.01,\tmax_rt_distance: float = 0.025)"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.use_deconvolution", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.use_deconvolution", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.implemented_smooth_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.implemented_smooth_method", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar')"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.smooth_window", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.smooth_window", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.smooth_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.smooth_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'savgol'"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.savgol_pol_order", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.savgol_pol_order", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "2"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.peak_derivative_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.peak_derivative_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0005"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.peak_height_max_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.peak_height_max_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "10"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.peak_max_prominence_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.peak_max_prominence_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.min_peak_datapoints", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.min_peak_datapoints", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.max_peak_width", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.max_peak_width", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.noise_threshold_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.noise_threshold_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'manual_relative_abundance'"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.noise_threshold_methods_implemented", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.noise_threshold_methods_implemented", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative')"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.std_noise_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.std_noise_threshold", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.peak_height_min_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.peak_height_min_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.peak_min_prominence_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.peak_min_prominence_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.eic_signal_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.eic_signal_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.01"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.max_rt_distance", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.max_rt_distance", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.025"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings", "kind": "class", "doc": "Settings for compound search
\n\nAttributes
\n\n\n- url_database (str, optional):\nURL for the database. Default is 'sqlite:///db/pnnl_lowres_gcms_compounds.sqlite'.
\n- ri_search_range (float, optional):\nRetention index search range. Default is 35.
\n- rt_search_range (float, optional):\nRetention time search range, in minutes. Default is 1.0.
\n- correlation_threshold (float, optional):\nThreshold for correlation for spectral similarity. Default is 0.5.
\n- score_threshold (float, optional):\nThreshold for compsite score. Default is 0.0.
\n- ri_spacing (float, optional):\nRetention index spacing. Default is 200.
\n- ri_std (float, optional):\nRetention index standard deviation. Default is 3.
\n- ri_calibration_compound_names (list, optional):\nList of compound names to use for retention index calibration. Default is ['Methyl Caprylate', 'Methyl Caprate', 'Methyl Pelargonate', 'Methyl Laurate', 'Methyl Myristate', 'Methyl Palmitate', 'Methyl Stearate', 'Methyl Eicosanoate', 'Methyl Docosanoate', 'Methyl Linocerate', 'Methyl Hexacosanoate', 'Methyl Octacosanoate', 'Methyl Triacontanoate'].
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.__init__", "kind": "function", "doc": "\n", "signature": "(\turl_database: str = 'postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/lowres',\tri_search_range: float = 35,\trt_search_range: float = 1.0,\tcorrelation_threshold: float = 0.5,\tscore_threshold: float = 0.0,\tri_spacing: float = 200,\tri_std: float = 3,\tri_calibration_compound_names: List = <factory>,\texploratory_mode: bool = False,\tscore_methods: tuple = ('highest_sim_score', 'highest_ss'),\toutput_score_method: str = 'All')"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.url_database", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.url_database", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/lowres'"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.ri_search_range", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.ri_search_range", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "35"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.rt_search_range", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.rt_search_range", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.correlation_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.correlation_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.5"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.score_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.score_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.ri_spacing", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.ri_spacing", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "200"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.ri_std", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.ri_std", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.ri_calibration_compound_names", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.ri_calibration_compound_names", "kind": "variable", "doc": "\n", "annotation": ": List"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.exploratory_mode", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.exploratory_mode", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.score_methods", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.score_methods", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('highest_sim_score', 'highest_ss')"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.output_score_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.output_score_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'All'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings", "kind": "class", "doc": "Settings for molecular searching
\n\nThese are used to generate the database entries, do not change.
\n\nAttributes
\n\n\n- usedAtoms (dict, optional):\nDictionary of atoms and ranges. Default is {'C': (1, 90), 'H': (4, 200), 'O': (0, 12), 'N': (0, 0), 'S': (0, 0), 'P': (0, 0), 'Cl': (0, 0)}.
\n- min_mz (float, optional):\nMinimum m/z to use for searching. Default is 50.0.
\n- max_mz (float, optional):\nMaximum m/z to use for searching. Default is 1200.0.
\n- min_dbe (float, optional):\nMinimum double bond equivalent to use for searching. Default is 0.
\n- max_dbe (float, optional):\nMaximum double bond equivalent to use for searching. Default is 50.
\n- use_pah_line_rule (bool, optional):\nIf True, use the PAH line rule. Default is False.
\n- isRadical (bool, optional):\nIf True, search for radical ions. Default is True.
\n- isProtonated (bool, optional):\nIf True, search for protonated ions. Default is True.
\n- min_op_filter (float, optional):\nMinimum oxygen to phosphorous ratio. Default is 2.
\n- min_hc_filter (float, optional):\nMinimum hydrogen to carbon ratio. Default is 0.3.
\n- min_oc_filter (float, optional):\nMinimum oxygen to carbon ratio. Default is 1.2.
\n- max_oc_filter (float, optional):\nMaximum oxygen to carbon ratio. Default is 0.0.
\n- url_database (str, optional):\nURL for the database. Default is None.
\n- db_jobs (int, optional):\nNumber of jobs to use for database queries. Default is 1.
\n- used_atom_valences (dict, optional):\nDictionary of atoms and valences. Default is {'C': 4, '13C': 4, 'H': 1, 'O': 2, '18O': 2, 'N': 3, 'S': 2, '34S': 2, 'P': 3, 'Cl': 1, '37Cl': 1, 'Br': 1, 'Na': 1, 'F': 1, 'K': 0}.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.usedAtoms", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.usedAtoms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.min_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.min_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.max_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.max_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.min_dbe", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.min_dbe", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.max_dbe", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.max_dbe", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.use_pah_line_rule", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.use_pah_line_rule", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.isRadical", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.isRadical", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.isProtonated", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.isProtonated", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.min_op_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.min_op_filter", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.min_hc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.min_hc_filter", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.min_oc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.min_oc_filter", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.max_oc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.max_oc_filter", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.url_database", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.url_database", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.db_jobs", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.db_jobs", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.used_atom_valences", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.used_atom_valences", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings", "kind": "class", "doc": "Settings for molecular searching
\n\nAttributes
\n\n\n- use_isotopologue_filter (bool, optional):\nIf True, use isotopologue filter. Default is False.
\n- isotopologue_filter_threshold (float, optional):\nThreshold for isotopologue filter. Default is 33.
\n- isotopologue_filter_atoms (tuple, optional):\nTuple of atoms to use for isotopologue filter. Default is ('Cl', 'Br').
\n- use_runtime_kendrick_filter (bool, optional):\nIf True, use runtime Kendrick filter. Default is False.
\n- use_min_peaks_filter (bool, optional):\nIf True, use minimum peaks filter. Default is True.
\n- min_peaks_per_class (int, optional):\nMinimum number of peaks per class. Default is 15.
\n- url_database (str, optional):\nURL for the database. Default is 'postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp'.
\n- db_jobs (int, optional):\nNumber of jobs to use for database queries. Default is 3.
\n- db_chunk_size (int, optional):\nChunk size to use for database queries. Default is 300.
\n- ion_charge (int, optional):\nIon charge. Default is -1.
\n- min_hc_filter (float, optional):\nMinimum hydrogen to carbon ratio. Default is 0.3.
\n- max_hc_filter (float, optional):\nMaximum hydrogen to carbon ratio. Default is 3.
\n- min_oc_filter (float, optional):\nMinimum oxygen to carbon ratio. Default is 0.0.
\n- max_oc_filter (float, optional):\nMaximum oxygen to carbon ratio. Default is 1.2.
\n- min_op_filter (float, optional):\nMinimum oxygen to phosphorous ratio. Default is 2.
\n- use_pah_line_rule (bool, optional):\nIf True, use the PAH line rule. Default is False.
\n- min_dbe (float, optional):\nMinimum double bond equivalent to use for searching. Default is 0.
\n- max_dbe (float, optional):\nMaximum double bond equivalent to use for searching. Default is 40.
\n- mz_error_score_weight (float, optional):\nWeight for m/z error score to contribute to composite score. Default is 0.6.
\n- isotopologue_score_weight (float, optional):\nWeight for isotopologue score to contribute to composite score. Default is 0.4.
\n- adduct_atoms_neg (tuple, optional):\nTuple of atoms to use in negative polarity. Default is ('Cl', 'Br').
\n- adduct_atoms_pos (tuple, optional):\nTuple of atoms to use in positive polarity. Default is ('Na', 'K').
\n- score_methods (tuple, optional):\nTuple of score method that can be implemented. \nDefault is ('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error').
\n- score_method (str, optional):\nScore method to use. Default is 'prob_score'. Options are 'S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error'.
\n- output_min_score (float, optional):\nMinimum score for output. Default is 0.1.
\n- output_score_method (str, optional):\nScore method to use for output. Default is 'All Candidates'.
\n- output_min_score (float, optional):\nMinimum score for output. Default is 0.1.
\n- isRadical (bool, optional):\nIf True, search for radical ions. Default is False.
\n- isProtonated (bool, optional):\nIf True, search for protonated ions. Default is True.
\n- isAdduct (bool, optional):\nIf True, search for adduct ions. Default is False.
\n- usedAtoms (dict, optional):\nDictionary of atoms and ranges. Default is {'C': (1, 90), 'H': (4, 200), 'O': (0, 12), 'N': (0, 0), 'S': (0, 0), 'P': (0, 0), 'Cl': (0, 0)}.
\n- ionization_type (str, optional):\nIonization type. Default is 'ESI'.
\n- min_ppm_error (float, optional):\nMinimum ppm error. Default is -10.0.
\n- max_ppm_error (float, optional):\nMaximum ppm error. Default is 10.0.
\n- min_abun_error (float, optional):\nMinimum abundance error for isotolopologue search. Default is -100.0.
\n- max_abun_error (float, optional):\nMaximum abundance error for isotolopologue search. Default is 100.0.
\n- mz_error_range (float, optional):\nm/z error range. Default is 1.5.
\n- error_method (str, optional):\nError method. Default is 'None'. Options are 'distance', 'lowest', 'symmetrical','average' 'None'.
\n- mz_error_average (float, optional):\nm/z error average. Default is 0.0.
\n- used_atom_valences (dict, optional):\nDictionary of atoms and valences. Default is {'C': 4, '13C': 4, 'H': 1, 'O': 2, '18O': 2, 'N': 3, 'S': 2, '34S': 2, 'P': 3, 'Cl': 1, '37Cl': 1, 'Br': 1, 'Na': 1, 'F': 1, 'K': 0}.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.__init__", "kind": "function", "doc": "\n", "signature": "(\tuse_isotopologue_filter: bool = False,\tisotopologue_filter_threshold: float = 33,\tisotopologue_filter_atoms: tuple = ('Cl', 'Br'),\tuse_runtime_kendrick_filter: bool = False,\tuse_min_peaks_filter: bool = True,\tmin_peaks_per_class: int = 15,\turl_database: str = 'postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp',\tdb_jobs: int = 3,\tdb_chunk_size: int = 300,\tion_charge: int = -1,\tmin_hc_filter: float = 0.3,\tmax_hc_filter: float = 3,\tmin_oc_filter: float = 0.0,\tmax_oc_filter: float = 1.2,\tmin_op_filter: float = 2,\tuse_pah_line_rule: bool = False,\tmin_dbe: float = 0,\tmax_dbe: float = 40,\tmz_error_score_weight: float = 0.6,\tisotopologue_score_weight: float = 0.4,\tadduct_atoms_neg: tuple = ('Cl', 'Br'),\tadduct_atoms_pos: tuple = ('Na', 'K'),\tscore_methods: tuple = ('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error'),\tscore_method: str = 'prob_score',\toutput_min_score: float = 0.1,\toutput_score_method: str = 'All Candidates',\tisRadical: bool = False,\tisProtonated: bool = True,\tisAdduct: bool = False,\tusedAtoms: dict = <factory>,\tionization_type: str = 'ESI',\tmin_ppm_error: float = -10.0,\tmax_ppm_error: float = 10.0,\tmin_abun_error: float = -100.0,\tmax_abun_error: float = 100.0,\tmz_error_range: float = 1.5,\terror_method: str = 'None',\tmz_error_average: float = 0.0,\tused_atom_valences: dict = <factory>)"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.use_isotopologue_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.use_isotopologue_filter", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isotopologue_filter_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isotopologue_filter_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "33"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isotopologue_filter_atoms", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isotopologue_filter_atoms", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('Cl', 'Br')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.use_runtime_kendrick_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.use_runtime_kendrick_filter", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.use_min_peaks_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.use_min_peaks_filter", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_peaks_per_class", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_peaks_per_class", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "15"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.url_database", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.url_database", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.db_jobs", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.db_jobs", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.db_chunk_size", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.db_chunk_size", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "300"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.ion_charge", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.ion_charge", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "-1"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_hc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_hc_filter", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.3"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.max_hc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.max_hc_filter", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_oc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_oc_filter", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.max_oc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.max_oc_filter", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1.2"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_op_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_op_filter", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "2"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.use_pah_line_rule", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.use_pah_line_rule", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_dbe", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_dbe", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.max_dbe", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.max_dbe", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "40"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.mz_error_score_weight", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.mz_error_score_weight", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.6"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isotopologue_score_weight", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isotopologue_score_weight", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.4"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.adduct_atoms_neg", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.adduct_atoms_neg", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('Cl', 'Br')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.adduct_atoms_pos", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.adduct_atoms_pos", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('Na', 'K')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.score_methods", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.score_methods", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.score_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.score_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'prob_score'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.output_min_score", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.output_min_score", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.output_score_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.output_score_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'All Candidates'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isRadical", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isRadical", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isProtonated", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isProtonated", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isAdduct", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isAdduct", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.usedAtoms", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.usedAtoms", "kind": "variable", "doc": "\n", "annotation": ": dict"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.ionization_type", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.ionization_type", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'ESI'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_ppm_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_ppm_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "-10.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.max_ppm_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.max_ppm_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "10.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_abun_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_abun_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "-100.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.max_abun_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.max_abun_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "100.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.mz_error_range", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.mz_error_range", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1.5"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.error_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.error_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'None'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.mz_error_average", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.mz_error_average", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.used_atom_valences", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.used_atom_valences", "kind": "variable", "doc": "\n", "annotation": ": dict"}, {"fullname": "corems.encapsulation.input", "modulename": "corems.encapsulation.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.input.parameter_from_json", "modulename": "corems.encapsulation.input.parameter_from_json", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_toml_parameters_ms", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_toml_parameters_ms", "kind": "function", "doc": "Load parameters from a toml file and set the parameters in the mass_spec_obj
\n\nParameters
\n\n\n- mass_spec_obj (MassSpectrum):\ncorems MassSpectrum object
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n", "signature": "(mass_spec_obj, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_parameters_ms", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_parameters_ms", "kind": "function", "doc": "Load parameters from a json file and set the parameters in the mass_spec_obj
\n\nParameters
\n\n\n- mass_spec_obj (MassSpectrum):\ncorems MassSpectrum object
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n", "signature": "(mass_spec_obj, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_toml_parameters_gcms", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_toml_parameters_gcms", "kind": "function", "doc": "Load parameters from a toml file and set the parameters in the GCMS object
\n\nParameters
\n\n\n- gcms_obj (GCMSBase):\ncorems GCMSBase object
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n", "signature": "(gcms_obj, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_parameters_gcms", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_parameters_gcms", "kind": "function", "doc": "Load parameters from a json file and set the parameters in the GCMS object
\n\nParameters
\n\n\n- gcms_obj (GCMSBase):\ncorems GCMSBase object
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n", "signature": "(gcms_obj, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_toml_parameters_class", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_toml_parameters_class", "kind": "function", "doc": "Load parameters from a toml file and set the parameters in the instance_parameters_class
\n\nParameters
\n\n\n- parameter_label (str):\nlabel of the parameters in the toml file
\n- instance_parameters_class (object):\ninstance of the parameters class
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n\nReturns
\n\n\n- object: instance of the parameters class
\n
\n", "signature": "(parameter_label, instance_parameters_class, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_parameters_class", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_parameters_class", "kind": "function", "doc": "Load parameters from a json file and set the parameters in the instance_parameters_class
\n\nParameters
\n\n\n- parameter_label (str):\nlabel of the parameters in the json file
\n- instance_parameters_class (object):\ninstance of the parameters class
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n\nReturns
\n\n\n- object: instance of the parameters class
\n
\n", "signature": "(parameter_label, instance_parameters_class, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output", "modulename": "corems.encapsulation.output", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.output.parameter_to_dict", "modulename": "corems.encapsulation.output.parameter_to_dict", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.output.parameter_to_dict.get_dict_all_default_data", "modulename": "corems.encapsulation.output.parameter_to_dict", "qualname": "get_dict_all_default_data", "kind": "function", "doc": "Return a dictionary with all default parameters for MS and GCMS
\n", "signature": "():", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_dict.get_dict_data_ms", "modulename": "corems.encapsulation.output.parameter_to_dict", "qualname": "get_dict_data_ms", "kind": "function", "doc": "Return a dictionary with all parameters for MS
\n", "signature": "(mass_spec):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_dict.get_dict_ms_default_data", "modulename": "corems.encapsulation.output.parameter_to_dict", "qualname": "get_dict_ms_default_data", "kind": "function", "doc": "Return a dictionary with all default parameters for MS including data input
\n", "signature": "():", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_dict.get_dict_gcms_default_data", "modulename": "corems.encapsulation.output.parameter_to_dict", "qualname": "get_dict_gcms_default_data", "kind": "function", "doc": "Return a dictionary with all default parameters for GCMS
\n", "signature": "():", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_dict.get_dict_data_gcms", "modulename": "corems.encapsulation.output.parameter_to_dict", "qualname": "get_dict_data_gcms", "kind": "function", "doc": "Return a dictionary with all parameters for GCMS
\n", "signature": "(gcms):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json", "modulename": "corems.encapsulation.output.parameter_to_json", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_all_settings_json", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_all_settings_json", "kind": "function", "doc": "Write JSON file into current directory with all the default settings for the CoreMS package.
\n\nParameters:
\n\nfilename : str, optional\n The name of the JSON file to be created. Default is 'SettingsCoreMS.json'.\nfile_path : str or Path, optional\n The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
\n", "signature": "(filename='SettingsCoreMS.json', file_path=None):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_ms_settings_json", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_ms_settings_json", "kind": "function", "doc": "Write JSON file into current directory with all the mass spectrum default settings for the CoreMS package.
\n\nParameters
\n\n\n- filename (str, optional):\nThe name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
\n- file_path (str or Path, optional):\nThe path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
\n
\n", "signature": "(filename='SettingsCoreMS.json', file_path=None):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_gcms_settings_json", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_gcms_settings_json", "kind": "function", "doc": "Write JSON file into current directory containing the default GCMS settings data.
\n\nParameters
\n\n\n- filename (str, optional):\nThe name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
\n- file_path (str or Path-like object, optional):\nThe path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
\n
\n", "signature": "(filename='SettingsCoreMS.json', file_path=None):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_all_settings_toml", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_all_settings_toml", "kind": "function", "doc": "Write TOML file into the specified file path or the current directory with all the default settings for the CoreMS package.
\n\nParameters
\n\n\n- filename (str, optional):\nThe name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
\n- file_path (str or Path, optional):\nThe path where the TOML file will be saved. If not provided, the file will be saved in the current directory.
\n
\n", "signature": "(filename='SettingsCoreMS.toml', file_path=None):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_ms_settings_toml", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_ms_settings_toml", "kind": "function", "doc": "Write TOML file into the current directory with all the mass spectrum default settings for the CoreMS package.
\n\nParameters
\n\n\n- filename (str, optional):\nThe name of the TOML file to be created. Default is 'SettingsCoreMS.toml'.
\n- file_path (str or Path, optional):\nThe path where the TOML file should be saved. If not provided, the file will be saved in the current working directory.
\n
\n", "signature": "(filename='SettingsCoreMS.toml', file_path=None):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_gcms_settings_toml", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_gcms_settings_toml", "kind": "function", "doc": "Write TOML file into current directory containing the default GCMS settings data.
\n\nParameters
\n\n\n- filename (str, optional):\nThe name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
\n- file_path (str or Path, optional):\nThe path where the TOML file will be saved. If not provided, the file will be saved in the current working directory.
\n
\n", "signature": "(filename='SettingsCoreMS.toml', file_path=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectra", "modulename": "corems.mass_spectra", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc", "modulename": "corems.mass_spectra.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_Calc", "modulename": "corems.mass_spectra.calc.GC_Calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_Calc.GC_Calculations", "modulename": "corems.mass_spectra.calc.GC_Calc", "qualname": "GC_Calculations", "kind": "class", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_Calc.GC_Calculations.calibrate_ri", "modulename": "corems.mass_spectra.calc.GC_Calc", "qualname": "GC_Calculations.calibrate_ri", "kind": "function", "doc": "\n", "signature": "(self, ref_dict, cal_file_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Calc.GC_Calculations.smooth_tic", "modulename": "corems.mass_spectra.calc.GC_Calc", "qualname": "GC_Calculations.smooth_tic", "kind": "function", "doc": "\n", "signature": "(self, tic):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Calc.GC_Calculations.centroid_detector", "modulename": "corems.mass_spectra.calc.GC_Calc", "qualname": "GC_Calculations.centroid_detector", "kind": "function", "doc": "\n", "signature": "(self, tic, rt):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Calc.GC_Calculations.remove_outliers", "modulename": "corems.mass_spectra.calc.GC_Calc", "qualname": "GC_Calculations.remove_outliers", "kind": "function", "doc": "\n", "signature": "(self, data):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution", "kind": "class", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.run_deconvolution", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.run_deconvolution", "kind": "function", "doc": "\n", "signature": "(self, plot_res=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.centroid_detector", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.centroid_detector", "kind": "function", "doc": "this function has been replaced with sp.peak_picking_first_derivative\nand it not used
\n", "signature": "(self, tic, rt):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.ion_extracted_chroma", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.ion_extracted_chroma", "kind": "function", "doc": "\n", "signature": "(self, mass_spectra_obj):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.hc", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.hc", "kind": "function", "doc": "\n", "signature": "(self, X, Y, max_rt_distance=0.025):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.find_peaks_entity", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.find_peaks_entity", "kind": "function", "doc": "combine eic with mathing rt apexes
\n", "signature": "(self, eic_dict):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.mass_spec_factory", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.mass_spec_factory", "kind": "function", "doc": "\n", "signature": "(self, rt, datadict):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.smooth_signal", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.smooth_signal", "kind": "function", "doc": "\n", "signature": "(self, signal):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.add_gcpeak", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.add_gcpeak", "kind": "function", "doc": "\n", "signature": "(\tself,\tnew_apex_index,\tstart_rt,\tfinal_rt,\tpeak_rt,\tsmoothed_tic,\tdatadict,\tplot_res):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.deconvolution", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.deconvolution", "kind": "function", "doc": "\n", "signature": "(self, peaks_entity_data, plot_res):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.quadratic_interpolation", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.quadratic_interpolation", "kind": "function", "doc": "\n", "signature": "(self, rt_list, tic_list, apex_index):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_RI_Calibration", "modulename": "corems.mass_spectra.calc.GC_RI_Calibration", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_RI_Calibration.get_rt_ri_pairs", "modulename": "corems.mass_spectra.calc.GC_RI_Calibration", "qualname": "get_rt_ri_pairs", "kind": "function", "doc": "\n", "signature": "(gcms_ref_obj, sql_obj=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LC_Calc", "modulename": "corems.mass_spectra.calc.LC_Calc", "kind": "module", "doc": "Created on Jun 14, 2019
\n\n@author: eber373
\n"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations", "kind": "class", "doc": "classdocs
\n"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations.get_max_eic", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations.get_max_eic", "kind": "function", "doc": "\n", "signature": "(eic_data: dict):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations.smooth_tic", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations.smooth_tic", "kind": "function", "doc": "\n", "signature": "(self, tic):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations.eic_centroid_detector", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations.eic_centroid_detector", "kind": "function", "doc": "\n", "signature": "(self, rt, eic, max_eic):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations.centroid_detector", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations.centroid_detector", "kind": "function", "doc": "\n", "signature": "(self, rt, tic):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations.find_nearest_scan", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations.find_nearest_scan", "kind": "function", "doc": "\n", "signature": "(self, rt):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted", "modulename": "corems.mass_spectra.calc.LF_Targeted", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted", "kind": "class", "doc": "\n", "bases": "corems.mass_spectra.calc.GC_Calc.GC_Calculations"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.__init__", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.__init__", "kind": "function", "doc": "\n", "signature": "(ref_file='Unknown', noise_cutoff='Unknown', tolerance='Unknown')"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.tolerance", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.tolerance", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.noise_cutoff", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.noise_cutoff", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.offset_hits", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.offset_hits", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.mz_filtered", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.mz_filtered", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.abund_filtered", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.abund_filtered", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.mz_count", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.mz_count", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.ms_info_get", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.ms_info_get", "kind": "function", "doc": "\n", "signature": "(self, mass_spectra_obj):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.loss_ref_get", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.loss_ref_get", "kind": "function", "doc": "\n", "signature": "(self, file_location, tolerance):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.threshold_filter", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.threshold_filter", "kind": "function", "doc": "\n", "signature": "(self, mz_dict, Intensity, noise_cutoff):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.mz_pair_checker", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.mz_pair_checker", "kind": "function", "doc": "\n", "signature": "(self, chem, lower, upper, mz1, spectrum, Intensity, scan_number):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.findpeakoffset", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.findpeakoffset", "kind": "function", "doc": "\n", "signature": "(self, range_ref, mz_filtered, abund_filtered):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.LF_out", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.LF_out", "kind": "function", "doc": "\n", "signature": "(self, LF_dict, mz_count):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.plot_offset", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.plot_offset", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch", "modulename": "corems.mass_spectra.calc.MZSearch", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults", "kind": "class", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults.__init__", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults.__init__", "kind": "function", "doc": "\n", "signature": "(calculated_mz: float, exp_mz: float, error: float, tolerance: float)"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults.calculated_mz", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults.calculated_mz", "kind": "variable", "doc": "\n", "annotation": ": float"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults.exp_mz", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults.exp_mz", "kind": "variable", "doc": "\n", "annotation": ": float"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults.error", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults.error", "kind": "variable", "doc": "\n", "annotation": ": float"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults.tolerance", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults.tolerance", "kind": "variable", "doc": "\n", "annotation": ": float"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch", "kind": "class", "doc": "A class that represents a thread of control.
\n\nThis class can be safely subclassed in a limited fashion. There are two ways\nto specify the activity: by passing a callable object to the constructor, or\nby overriding the run() method in a subclass.
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.__init__", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.__init__", "kind": "function", "doc": "Parameters
\n\n\ncalculated_mzs ([float] calculated m/z):
exp_mzs ([float] experimental m/z):
method (string,):\nppm or ppb
- call run to trigger the m/z search algorithm
\n- or start if using it as thread
\n
\n", "signature": "(\texp_mzs: List[float],\tcalculated_mzs: List[float],\ttolerance,\tmethod='ppm',\taverage_target_mz=True)"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.method", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.method", "kind": "variable", "doc": "method: string,\n ppm or ppb
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.results", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.results", "kind": "variable", "doc": "{calculated_mz: [SearchResults]}\ncontains the results of the search
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.averaged_target_mz", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.averaged_target_mz", "kind": "variable", "doc": "[float]\ncontains the average target m/z to be searched against
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.calculated_mzs", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.calculated_mzs", "kind": "variable", "doc": "[float]\ncontains the mz target to be searched against
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.exp_mzs", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.exp_mzs", "kind": "variable", "doc": "[float]\ncontains the exp mz to be searched against
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.tolerance", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.tolerance", "kind": "variable", "doc": "method: string,\n ppm or ppb
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.colapse_calculated", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.colapse_calculated", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.run", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.run", "kind": "function", "doc": "Method representing the thread's activity.
\n\nYou may override this method in a subclass. The standard run() method\ninvokes the callable object passed to the object's constructor as the\ntarget argument, if any, with sequential and keyword arguments taken\nfrom the args and kwargs arguments, respectively.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.calc_mz_error", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.calc_mz_error", "kind": "function", "doc": "Parameters
\n\n\n", "signature": "(calculated_mz, exp_mz, method='ppm'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.check_ppm_error", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.check_ppm_error", "kind": "function", "doc": "\n", "signature": "(tolerance, error):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.get_nominal_exp", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.get_nominal_exp", "kind": "function", "doc": "\n", "signature": "(self, exp_mzs) -> dict:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.search_mz", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.search_mz", "kind": "function", "doc": "\n", "signature": "(self, results, dict_nominal_exp_mz, calculated_mz, offset) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing", "modulename": "corems.mass_spectra.calc.SignalProcessing", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.peak_detector", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "peak_detector", "kind": "function", "doc": "\n", "signature": "(tic, max_tic):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.find_nearest_scan", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "find_nearest_scan", "kind": "function", "doc": "\n", "signature": "(data, nodes):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.peak_picking_first_derivative", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "peak_picking_first_derivative", "kind": "function", "doc": "\n", "signature": "(\tdomain,\tsignal,\tmax_height,\tmax_prominence,\tmax_signal,\tmin_peak_datapoints,\tpeak_derivative_thresould,\tsignal_threshold=0.1,\tcorrect_baseline=True,\tplot_res=False,\tabun_norm=100,\tcheck_abundance=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.find_minima", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "find_minima", "kind": "function", "doc": "\n", "signature": "(index, tic, right=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.derivate", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "derivate", "kind": "function", "doc": "\n", "signature": "(data_array):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.minima_detector", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "minima_detector", "kind": "function", "doc": "\n", "signature": "(tic, max_tic, peak_height_max_percent, peak_max_prominence_percent):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.baseline_detector", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "baseline_detector", "kind": "function", "doc": "\n", "signature": "(\ttic,\trt,\tpeak_height_max_percent,\tpeak_max_prominence_percent,\tdo_interpolation=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.peak_detector_generator", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "peak_detector_generator", "kind": "function", "doc": "\n", "signature": "(\ttic,\tstds,\tmethod,\trt,\tmax_height,\tmin_height,\tmax_prominence,\tmin_datapoints):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.smooth_signal", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "smooth_signal", "kind": "function", "doc": "smooth the data using a window with requested size.
\n\nThis method is based on the convolution of a scaled window with the signal.\nThe signal is prepared by introducing reflected copies of the signal \n(with the window size) in both ends so that transient parts are minimized\nin the begining and end part of the output signal.
\n\noutput:\n the smoothed signal
\n\nsee also:
\n\nnumpy.hanning, numpy.hamming, numpy.bartlett, numpy.blackman, numpy.convolve\nscipy.signal.savgol_filter
\n", "signature": "(x, window_len, window, pol_order, implemented_smooth_method):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.second_derivative_threshold", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "second_derivative_threshold", "kind": "function", "doc": "\n", "signature": "(tic, stds, rt, peak_height_max_percent, peak_max_prominence_percent):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory", "modulename": "corems.mass_spectra.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class", "modulename": "corems.mass_spectra.factory.GC_Class", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase", "kind": "class", "doc": "Base class for GC-MS data processing.
\n\nParameters
\n\n\n- file_location (str, pathlib.Path, or s3path.S3Path):\nPath object containing the file location.
\n- analyzer (str, optional):\nName of the analyzer. Defaults to 'Unknown'.
\n- instrument_label (str, optional):\nLabel of the instrument. Defaults to 'Unknown'.
\n- sample_name (str, optional):\nName of the sample. If not provided, it is derived from the file location.
\n
\n\nAttributes
\n\n\n- file_location (pathlib.Path):\nPath object containing the file location.
\n- sample_name (str):\nName of the sample.
\n- analyzer (str):\nName of the analyzer.
\n- instrument_label (str):\nLabel of the instrument.
\n- gcpeaks (list):\nList of GCPeak objects.
\n- ri_pairs_ref (None):\nReference retention index pairs.
\n- cal_file_path (None):\nCalibration file path.
\n- _parameters (GCMSParameters):\nGC-MS parameters.
\n- _retention_time_list (list):\nList of retention times.
\n- _scans_number_list (list):\nList of scan numbers.
\n- _tic_list (list):\nList of total ion chromatogram values.
\n- _ms (dict):\nDictionary containing all mass spectra.
\n- _processed_tic (list):\nList of processed total ion chromatogram values.
\n
\n\nMethods
\n\n\n- process_chromatogram(plot_res=False). Process the chromatogram.
\n- plot_gc_peaks(ax=None, color='red'). Plot the GC peaks.
\n
\n", "bases": "corems.mass_spectra.calc.GC_Calc.GC_Calculations, corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.__init__", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.__init__", "kind": "function", "doc": "\n", "signature": "(\tfile_location,\tanalyzer='Unknown',\tinstrument_label='Unknown',\tsample_name=None)"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.file_location", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.analyzer", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.analyzer", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.instrument_label", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.instrument_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.gcpeaks", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.gcpeaks", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.ri_pairs_ref", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.ri_pairs_ref", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.cal_file_path", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.cal_file_path", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.process_chromatogram", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.process_chromatogram", "kind": "function", "doc": "Process the chromatogram.
\n\nThis method processes the chromatogram.
\n\nParameters
\n\n\n- plot_res (bool, optional):\nIf True, plot the results. Defaults to False.
\n
\n", "signature": "(self, plot_res=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.add_mass_spectrum", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.add_mass_spectrum", "kind": "function", "doc": "Add a mass spectrum to the GC-MS object.
\n\nThis method adds a mass spectrum to the GC-MS object.
\n\nParameters
\n\n\n- mass_spec (MassSpectrum):\nMass spectrum to be added.
\n
\n", "signature": "(self, mass_spec):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.set_tic_list_from_data", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.set_tic_list_from_data", "kind": "function", "doc": "Set the total ion chromatogram list from the mass spectra data within the GC-MS data object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.set_retention_time_from_data", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.set_retention_time_from_data", "kind": "function", "doc": "Set the retention time list from the mass spectra data within the GC-MS data object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.set_scans_number_from_data", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.set_scans_number_from_data", "kind": "function", "doc": "Set the scan number list from the mass spectra data within the GC-MS data object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.parameter", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.parameter", "kind": "variable", "doc": "GCMS Parameters
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.molecular_search_settings", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.molecular_search_settings", "kind": "variable", "doc": "Molecular Search Settings
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.chromatogram_settings", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.chromatogram_settings", "kind": "variable", "doc": "Chromatogram Settings
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.scans_number", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.scans_number", "kind": "variable", "doc": "Scans Number
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.retention_time", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.retention_time", "kind": "variable", "doc": "Retention Time
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.processed_tic", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.processed_tic", "kind": "variable", "doc": "Processed Total Ion Current
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.tic", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.tic", "kind": "variable", "doc": "Total Ion Current
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.max_tic", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.max_tic", "kind": "variable", "doc": "Maximum Total Ion Current
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.min_tic", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.min_tic", "kind": "variable", "doc": "Minimum Total Ion Current
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.dynamic_range", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.dynamic_range", "kind": "variable", "doc": "Dynamic Range of the Total Ion Current
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.matched_peaks", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.matched_peaks", "kind": "variable", "doc": "Matched Peaks
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.sorted_gcpeaks", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.sorted_gcpeaks", "kind": "variable", "doc": "Sorted GC Peaks, by retention time
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.unique_metabolites", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.unique_metabolites", "kind": "variable", "doc": "Unique Metabolites
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.metabolites_data", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.metabolites_data", "kind": "variable", "doc": "Metabolites Data
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.no_matched_peaks", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.no_matched_peaks", "kind": "variable", "doc": "Peaks with no Matched Metabolites
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_gc_peaks", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_gc_peaks", "kind": "function", "doc": "Plot the GC peaks.
\n\nThis method plots the GC peaks.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the GC peaks. Defaults to None.
\n- color (str, optional):\nColor of the GC peaks. Defaults to 'red'.
\n
\n", "signature": "(self, ax=None, color='red'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_excel", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_excel", "kind": "function", "doc": "Export the GC-MS data to an Excel file.
\n\nThis method exports the GC-MS data to an Excel file.
\n\nParameters
\n\n\n- out_file_path (str, pathlib.Path, or s3path.S3Path):\nPath object containing the file location.
\n- write_mode (str, optional):\nWrite mode. Defaults to 'ab'.
\n- write_metadata (bool, optional):\nIf True, write the metadata. Defaults to True.
\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n
\n", "signature": "(\tself,\tout_file_path,\twrite_mode='ab',\twrite_metadata=True,\tid_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_csv", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_csv", "kind": "function", "doc": "Export the GC-MS data to a CSV file.
\n\nParameters
\n\n\n- out_file_path (str, pathlib.Path, or s3path.S3Path):\nPath object containing the file location.
\n- separate_output (bool, optional):\nIf True, separate the output. Defaults to False.
\n- write_metadata (bool, optional):\nIf True, write the metadata. Defaults to True.
\n
\n", "signature": "(\tself,\tout_file_path,\tseparate_output=False,\twrite_metadata=True,\tid_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_pandas", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_pandas", "kind": "function", "doc": "Export the GC-MS data to a Pandas dataframe.
\n\nParameters
\n\n\n- out_file_path (str, pathlib.Path, or s3path.S3Path):\nPath object containing the file location.
\n- write_metadata (bool, optional):\nIf True, write the metadata. Defaults to True.
\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n
\n", "signature": "(self, out_file_path, write_metadata=True, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_dataframe", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_dataframe", "kind": "function", "doc": "Export the GC-MS data to a Pandas dataframe.
\n\nParameters
\n\n\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n
\n", "signature": "(self, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.processing_stats", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.processing_stats", "kind": "function", "doc": "Return the processing statistics.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.parameters_json", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.parameters_json", "kind": "function", "doc": "Return the parameters in JSON format.
\n\nParameters
\n\n\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n- output_path (str, optional):\nPath object containing the file location. Defaults to \" \".
\n
\n", "signature": "(self, id_label='corems:', output_path=' '):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_json", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_json", "kind": "function", "doc": "Export the GC-MS data to a JSON file.
\n\nParameters
\n\n\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n
\n", "signature": "(self, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_hdf", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_hdf", "kind": "function", "doc": "Export the GC-MS data to a HDF file.
\n\nParameters
\n\n\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n
\n", "signature": "(self, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_chromatogram", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_chromatogram", "kind": "function", "doc": "Plot the chromatogram.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the chromatogram. Defaults to None.
\n- color (str, optional):\nColor of the chromatogram. Defaults to 'blue'.
\n
\n", "signature": "(self, ax=None, color='blue'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_smoothed_chromatogram", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_smoothed_chromatogram", "kind": "function", "doc": "Plot the smoothed chromatogram.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the smoothed chromatogram. Defaults to None.
\n- color (str, optional):\nColor of the smoothed chromatogram. Defaults to 'green'.
\n
\n", "signature": "(self, ax=None, color='green'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_detected_baseline", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_detected_baseline", "kind": "function", "doc": "Plot the detected baseline.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the detected baseline. Defaults to None.
\n- color (str, optional):\nColor of the detected baseline. Defaults to 'blue'.
\n
\n", "signature": "(self, ax=None, color='blue'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_baseline_subtraction", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_baseline_subtraction", "kind": "function", "doc": "Plot the baseline subtraction.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the baseline subtraction. Defaults to None.
\n- color (str, optional):\nColor of the baseline subtraction. Defaults to 'black'.
\n
\n", "signature": "(self, ax=None, color='black'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.peaks_rt_tic", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.peaks_rt_tic", "kind": "function", "doc": "Return the peaks, retention time, and total ion chromatogram.
\n\nParameters
\n\n\n- json_string (bool, optional):\nIf True, return the peaks, retention time, and total ion chromatogram in JSON format. Defaults to False.
\n
\n", "signature": "(self, json_string=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_processed_chromatogram", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_processed_chromatogram", "kind": "function", "doc": "Plot the processed chromatogram.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the processed chromatogram. Defaults to None.
\n- color (str, optional):\nColor of the processed chromatogram. Defaults to 'black'.
\n
\n", "signature": "(self, ax=None, color='black'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class", "modulename": "corems.mass_spectra.factory.LC_Class", "kind": "module", "doc": "Created on Oct 15, 2021
\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase", "kind": "class", "doc": "classdocs
\n", "bases": "collections.abc.Mapping, corems.mass_spectra.calc.LC_Calc.LC_Calculations"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.__init__", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.__init__", "kind": "function", "doc": "Parameters
\n\n ----------\n file_location: text, pathlib.Path(), or s3path.S3Path\n
\n\nPath object from pathlib containing the file location
\n", "signature": "(\tfile_location,\tanalyzer='Unknown',\tinstrument_label='Unknown',\tsample_name=None)"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.file_location", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.analyzer", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.analyzer", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.instrument_label", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.instrument_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.add_mass_spectrum", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.add_mass_spectrum", "kind": "function", "doc": "\n", "signature": "(self, mass_spec):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.set_tic_list_from_data", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.set_tic_list_from_data", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.set_retention_time_from_data", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.set_retention_time_from_data", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.set_scans_number_from_data", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.set_scans_number_from_data", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.scans_number", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.scans_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.retention_time", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.retention_time", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.tic", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.tic", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS", "kind": "class", "doc": "classdocs
\n", "bases": "corems.mass_spectra.calc.LC_Calc.LC_Calculations"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.__init__", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.__init__", "kind": "function", "doc": "\n", "signature": "(\tfile_location,\ttarget_mzs: List[float],\tparser,\tanalyzer: str = 'Unknown',\tinstrument_label: str = 'Unknown',\tsample_name: str = None)"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.file_location", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.add_peak", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.add_peak", "kind": "function", "doc": "\n", "signature": "(self, mass_spectrum, peak_scans, eic_data, possible_molform=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.ms1_molecular_search_settings", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.ms1_molecular_search_settings", "kind": "variable", "doc": "\n", "annotation": ": corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.chromatogram_settings", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.chromatogram_settings", "kind": "variable", "doc": "\n", "annotation": ": corems.encapsulation.factory.processingSetting.LiquidChromatographSetting"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.parameters", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.parameters", "kind": "variable", "doc": "\n", "annotation": ": corems.encapsulation.factory.parameters.LCMSParameters"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.eic_scans_number", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.eic_scans_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.scans_number", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.scans_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.retention_time", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.retention_time", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.tic", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.tic", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.get_tic", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.get_tic", "kind": "function", "doc": "ms_type: str ('MS', MS2')\nstart_scan: int default -1 will select the lowest available\nend_scan: int default -1 will select the highest available\nreturns:\n chroma: dict\n {\n Scan: [int]\n original thermo scan numberMS\n Time: [floats]\n list of retention times\n TIC: [floats]\n total ion chromatogram\n Apexes: [int]
\n original thermo apex scan number after peak picking
\n }
\n", "signature": "(\tself,\tms_type='MS !d',\tpeak_detection=True,\tsmooth=True,\tplot=False,\tax=None) -> Tuple[corems.mass_spectra.factory.LC_Temp.TIC_Data, matplotlib.axes._axes.Axes]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.get_eics", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.get_eics", "kind": "function", "doc": "ms_type: str ('MS', MS2')\nstart_scan: int default -1 will select the lowest available\nend_scan: int default -1 will select the highest available
\n\nreturns:
\n\nchroma: dict{target_mz: EIC_Data(\n Scans: [int]\n original thermo scan numbers\n Time: [floats]\n list of retention times\n TIC: [floats]\n total ion chromatogram\n Apexes: [int] \n original thermo apex scan number after peak picking \n )\n
\n", "signature": "(\tself,\ttic_data: dict,\tms_type='MS !d',\tpeak_detection=True,\tsmooth=True,\tplot=False,\tax=None,\tlegend=False) -> Tuple[Dict[float, corems.mass_spectra.factory.LC_Temp.EIC_Data], matplotlib.axes._axes.Axes]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.process_ms1", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.process_ms1", "kind": "function", "doc": "\n", "signature": "(self, dict_tarrget_mzs):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Temp", "modulename": "corems.mass_spectra.factory.LC_Temp", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data", "kind": "class", "doc": "Scans: [int]\n original thermo scan numbers\nTime: [floats]\n list of retention times\nTIC: [floats]\n total ion chromatogram\nApexes: [int]
\n original thermo apex scan number after peak picking
\n"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data.__init__", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data.__init__", "kind": "function", "doc": "\n", "signature": "(\tscans: List[int] = <factory>,\ttime: List[float] = <factory>,\ttic: List[float] = <factory>,\tapexes: List[int] = <factory>)"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data.scans", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data.scans", "kind": "variable", "doc": "\n", "annotation": ": List[int]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data.time", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data.time", "kind": "variable", "doc": "\n", "annotation": ": List[float]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data.tic", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data.tic", "kind": "variable", "doc": "\n", "annotation": ": List[float]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data.apexes", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data.apexes", "kind": "variable", "doc": "\n", "annotation": ": List[int]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data", "kind": "class", "doc": "Scans: [int]\n original thermo scan numbers\nTime: [floats]\n list of retention times\nEIC: [floats]\n extracted ion chromatogram\nApexes: [int]
\n original thermo apex scan number after peak picking
\n"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data.__init__", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data.__init__", "kind": "function", "doc": "\n", "signature": "(\tscans: List[int] = <factory>,\ttime: List[float] = <factory>,\teic: List[float] = <factory>,\tapexes: List[int] = <factory>)"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data.scans", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data.scans", "kind": "variable", "doc": "\n", "annotation": ": List[int]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data.time", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data.time", "kind": "variable", "doc": "\n", "annotation": ": List[float]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data.eic", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data.eic", "kind": "variable", "doc": "\n", "annotation": ": List[float]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data.apexes", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data.apexes", "kind": "variable", "doc": "\n", "annotation": ": List[int]"}, {"fullname": "corems.mass_spectra.input", "modulename": "corems.mass_spectra.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF", "modulename": "corems.mass_spectra.input.andiNetCDF", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF", "kind": "class", "doc": "A class for reading AndiNetCDF files and extracting mass spectra data.
\n\nParameters
\n\n\n- file_location (str or Path):\nThe location of the AndiNetCDF file.
\n- analyzer (str, optional):\nThe type of analyzer used (default is 'Quadruple').
\n- instrument_label (str, optional):\nThe label of the instrument (default is 'GCMS-Agilent').
\n- auto_process (bool, optional):\nWhether to automatically process the data (default is True).
\n
\n\nAttributes
\n\n\n- file_location (Path):\nThe path to the AndiNetCDF file.
\n- net_cdf_obj (Dataset):\nThe NetCDF dataset object.
\n- ionization_type (str):\nThe ionization type used in the experiment.
\n- experiment_type (str):\nThe type of experiment.
\n- list_scans (range):\nThe range of scan numbers in the dataset.
\n- initial_scan_number (int):\nThe number of the initial scan.
\n- final_scan_number (int):\nThe number of the final scan.
\n- analyzer (str):\nThe type of analyzer used.
\n- instrument_label (str):\nThe label of the instrument.
\n- gcms (GCMSBase):\nThe GCMSBase object for storing mass spectra data.
\n
\n\nMethods
\n\n\n- polarity(). \nGet the polarity of the ionization.
\n- get_mass_spectrum(mz, abun, rp, d_params). \nAdd a mass spectrum to the GCMSBase object.
\n- run(). \nPopulate the GCMSBase object with mass spectra data.
\n- import_mass_spectra(d_params). \nImport mass spectra data from the AndiNetCDF file.
\n- get_gcms_obj(). \nGet the GCMSBase object.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.__init__", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(\tfile_location: str | pathlib.Path,\tanalyzer='Quadruple',\tinstrument_label='GCMS-Agilent',\tauto_process=True)"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.ionization_type", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.ionization_type", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.experiment_type", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.experiment_type", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.list_scans", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.list_scans", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.initial_scan_number", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.initial_scan_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.final_scan_number", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.final_scan_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.analyzer", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.analyzer", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.instrument_label", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.instrument_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.gcms", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.gcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.polarity", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.polarity", "kind": "variable", "doc": "Get the polarity of the ionization.
\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.get_mass_spectrum", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.get_mass_spectrum", "kind": "function", "doc": "Add a mass spectrum to the GCMSBase object.
\n\nParameters
\n\n\n- mz (array-like):\nThe m/z values of the mass spectrum.
\n- abun (array-like):\nThe abundance values of the mass spectrum.
\n- rp (array-like):\nThe resolution values of the mass spectrum.
\n- d_params (dict):\nAdditional parameters for the mass spectrum.
\n
\n", "signature": "(self, mz, abun, rp, d_params):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.run", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.run", "kind": "function", "doc": "Populate the GCMSBase object with mass spectra data.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.import_mass_spectra", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.import_mass_spectra", "kind": "function", "doc": "Import mass spectra data from the AndiNetCDF file.
\n\nParameters
\n\n\n- d_params (dict):\nAdditional parameters for the mass spectra.
\n
\n", "signature": "(self, d_params):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.get_gcms_obj", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.get_gcms_obj", "kind": "function", "doc": "Get the GCMSBase object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5", "modulename": "corems.mass_spectra.input.boosterHDF5", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra", "kind": "class", "doc": "Class for reading HDF5 files containing booster mass spectra.
\n\nParameters
\n\n\n- file_location (Path or S3Path):\nThe full path to the HDF5 file.
\n- analyzer (str, optional):\nThe type of analyzer used for the mass spectra. Defaults to \"ICR\".
\n- instrument_label (str, optional):\nThe label of the instrument. Defaults to \"21T\".
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectra. Defaults to True.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.__init__", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.__init__", "kind": "function", "doc": "Initialize the ReadHDF_BoosterMassSpectra class.
\n\nParameters
\n\n\n- file_location (Path or S3Path):\nThe full path to the HDF5 file.
\n- analyzer (str, optional):\nThe type of analyzer used for the mass spectra. Defaults to \"ICR\".
\n- instrument_label (str, optional):\nThe label of the instrument. Defaults to \"21T\".
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectra. Defaults to True.
\n
\n", "signature": "(\tfile_location: pathlib.Path | s3path.S3Path,\tanalyzer='ICR',\tinstrument_label='21T',\tauto_process=True)"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.lcms", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.lcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.hdf_obj", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.hdf_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.list_scans", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.list_scans", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.initial_scan_number", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.initial_scan_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.final_scan_number", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.final_scan_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.file_location", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.auto_process", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.auto_process", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.analyzer", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.analyzer", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.instrument_label", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.instrument_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.get_polarity", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.get_polarity", "kind": "function", "doc": "Get the polarity of a scan.
\n\nParameters
\n\n\n- file_location (Path or S3Path):\nThe full path to the HDF5 file.
\n- scan (int):\nThe scan number.
\n
\n", "signature": "(self, file_location: pathlib.Path | s3path.S3Path, scan: int):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.get_attr_data", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.get_attr_data", "kind": "function", "doc": "Get the attribute data of a scan.
\n\nParameters
\n\n\n- scan (int):\nThe scan number.
\n- attr_srt (str):\nThe attribute name.
\n
\n", "signature": "(self, scan, attr_srt):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.import_mass_spectra", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.import_mass_spectra", "kind": "function", "doc": "Import the mass spectra from the HDF5 file.
\n\nParameters
\n\n\n- d_params (dict):\nThe parameters for importing the mass spectra.
\n
\n", "signature": "(self, d_params: dict):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.get_mass_spectrum", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.get_mass_spectrum", "kind": "function", "doc": "Get the mass spectrum for a scan.
\n\nParameters
\n\n\n- scan (int):\nThe scan number.
\n- d_params (dict):\nThe parameters for creating the mass spectrum.
\n
\n", "signature": "(self, scan: int, d_params: dict):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.run", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.run", "kind": "function", "doc": "Run the thread to create the LCMS object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.get_lcms_obj", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.get_lcms_obj", "kind": "function", "doc": "Get the LCMS object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.brukerSolarix", "modulename": "corems.mass_spectra.input.brukerSolarix", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra", "kind": "class", "doc": "Class for reading Bruker Solarix Transient Mass Spectra.
\n\nParameters
\n\n\n- d_directory_location (str, pathlib.Path, or s3path.S3Path):\nPath object from pathlib containing the file location.
\n- analyzer (str, optional):\nType of analyzer used in the mass spectrometer. Defaults to \"ICR\".
\n- instrument_label (str, optional):\nLabel for the instrument. Defaults to \"15T\".
\n- auto_process (bool, optional):\nFlag indicating whether to automatically process the mass spectra. Defaults to True.
\n- keep_profile (bool, optional):\nFlag indicating whether to keep the profile data in the mass spectra. Defaults to False.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.__init__", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(\td_directory_location: str | pathlib.Path | s3path.S3Path,\tanalyzer='ICR',\tinstrument_label='15T',\tauto_process=True,\tkeep_profile=False)"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.scan_attr", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.scan_attr", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.lcms", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.lcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.auto_process", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.auto_process", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.keep_profile", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.keep_profile", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.get_scan_attr", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.get_scan_attr", "kind": "function", "doc": "Get the scan attributes from the scan.xml file.
\n\nReturns
\n\n\n- dict: Dictionary containing the scan number as key and a tuple of retention time and TIC as value.
\n
\n", "signature": "(self) -> dict:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.import_mass_spectra", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.import_mass_spectra", "kind": "function", "doc": "Import the mass spectra from the scan.xml file.
\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.get_mass_spectrum", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.get_mass_spectrum", "kind": "function", "doc": "Get the mass spectrum for a given scan number.
\n\nParameters
\n\n\n- scan_number (int):\nScan number.
\n
\n", "signature": "(self, scan_number: int):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.run", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.run", "kind": "function", "doc": "Run the import_mass_spectra method.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.get_lcms_obj", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.get_lcms_obj", "kind": "function", "doc": "Get the LCMSBase object.
\n\nRaises
\n\n\n- Exception: If the LCMSBase object is empty.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.coremsHDF5", "modulename": "corems.mass_spectra.input.coremsHDF5", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra", "kind": "class", "doc": "Class for reading CoreMS HDF5 mass spectra.
\n\nParameters
\n\n\n- file_location (str):\nThe file location of the CoreMS HDF5 file.
\n
\n\nAttributes
\n\n\n- lcms (LCMSBase):\nThe LCMSBase object for storing mass spectra.
\n- list_scans (list):\nThe list of scan numbers in the HDF5 file.
\n
\n\nMethods
\n\n\n- import_mass_spectra()\nImports the mass spectra from the HDF5 file.
\n- run()\nCreates the LCMS object by importing the mass spectra.
\n- get_lcms_obj()\nReturns the LCMS object.
\n
\n\nRaises
\n\n\n- Exception: If the LCMS object is empty.
\n
\n", "bases": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum, threading.Thread"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.__init__", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(file_location: str)"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.lcms", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.lcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.list_scans", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.list_scans", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.import_mass_spectra", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.import_mass_spectra", "kind": "function", "doc": "Imports the mass spectra from the HDF5 file.
\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.run", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.run", "kind": "function", "doc": "Creates the LCMS object by importing the mass spectra.
\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.get_lcms_obj", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.get_lcms_obj", "kind": "function", "doc": "Returns the LCMS object.
\n\nReturns
\n\n\n- LCMSBase: The LCMS object.
\n
\n\nRaises
\n\n\n- Exception: If the LCMS object is empty.
\n
\n", "signature": "(self) -> corems.mass_spectra.factory.LC_Class.LCMSBase:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.massList", "modulename": "corems.mass_spectra.input.massList", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText", "kind": "class", "doc": "Class for reading CoreMS mass spectra from a text file.
\n\nParameters
\n\n\n- file_location (str, pathlib.Path, or s3path.S3Path):\nPath object from pathlib containing the file location
\n- analyzer (str, optional):\nName of the analyzer, by default 'Unknown'
\n- instrument_label (str, optional):\nLabel of the instrument, by default 'Unknown'
\n
\n\nAttributes
\n\n\n- lcms (LCMSBase):\nLCMSBase object for storing the mass spectra data.
\n
\n\nMethods
\n\n\n- get_scans_filename(). Get the filenames of all the scan files associated with the CoreMS file.
\n- set_filepath_datatype_and_delimiter(file_path_obj). Set the file path, data type, and delimiter based on the file path object.
\n- import_mass_spectra(). Import the mass spectra from the scan files and add them to the LCMSBase object.
\n- run(). Run the import_mass_spectra method to create the LCMSBase object.
\n- get_lcms_obj(). Get the LCMSBase object.
\n
\n", "bases": "corems.mass_spectrum.input.massList.ReadCoremsMasslist, threading.Thread"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.__init__", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(file_location, analyzer='Unknown', instrument_label='Unknown')"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.lcms", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.lcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.get_scans_filename", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.get_scans_filename", "kind": "function", "doc": "\n", "signature": "(self) -> list:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.set_filepath_datatype_and_delimiter", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.set_filepath_datatype_and_delimiter", "kind": "function", "doc": "\n", "signature": "(self, file_path_obj) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.import_mass_spectra", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.import_mass_spectra", "kind": "function", "doc": "\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.run", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.run", "kind": "function", "doc": "Creates the LCMS object and imports mass spectra.
\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.get_lcms_obj", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.get_lcms_obj", "kind": "function", "doc": "Returns the LCMSBase object associated with the massList.
\n\nIf the LCMSBase object is already initialized, it is returned.\nOtherwise, an exception is raised.
\n\nRaises:\n Exception: If the LCMSBase object is not initialized.
\n", "signature": "(self) -> corems.mass_spectra.factory.LC_Class.LCMSBase:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader", "modulename": "corems.mass_spectra.input.rawFileReader", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass", "kind": "class", "doc": "Class for reading Thermo Raw files and extracting information from them.
\n\nParameters:
\n\nfile_location : str or pathlib.Path or s3path.S3Path\n Thermo Raw file path or S3 path.
\n\nAttributes:
\n\nfile_path : str or pathlib.Path or s3path.S3Path\n The file path of the Thermo Raw file.\nparameters : LCMSParameters\n The LCMS parameters for the Thermo Raw file.\nchromatogram_settings : LiquidChromatographSetting\n The chromatogram settings for the Thermo Raw file.\nscans : list or tuple\n The selected scans for the Thermo Raw file.\nstart_scan : int\n The starting scan number for the Thermo Raw file.\nend_scan : int\n The ending scan number for the Thermo Raw file.
\n\nMethods:
\n\n\n- set_msordertype(scanFilter, mstype: str = 'ms1') -> scanFilter\nConvert the user-passed MS Type string to a Thermo MSOrderType object.
\n- get_creation_time() -> datetime.datetime\nExtract the creation date stamp from the .RAW file and return it as a formatted datetime object.
\n- remove_temp_file()\nRemove the temporary file if the path is from S3Path.
\n- get_polarity_mode(scan_number: int) -> int\nGet the polarity mode for the given scan number.
\n- get_filter_for_scan_num(scan_number: int) -> List[str]\nGet the filter for the given scan number.
\n- check_full_scan(scan_number: int) -> bool\nCheck if the given scan number is a full scan.
\n- get_all_filters() -> Tuple[Dict[int, str], List[str]]\nGet all scan filters for the Thermo Raw file.
\n- get_scan_header(scan: int) -> Dict[str, Any]\nGet the full dictionary of scan header metadata for the given scan number.
\n- get_rt_time_from_trace(trace) -> Tuple[List[float], List[float], List[int]]\nGet the retention time, intensity, and scan number from the given trace.
\n- get_eics(target_mzs: List[float], tic_data: Dict[str, Any], ms_type: str = 'MS !d',\n peak_detection: bool = True, smooth: bool = True, plot: bool = False,\n ax: Optional[matplotlib.axes.Axes] = None, legend: bool = False) -> Tuple[Dict[float, EIC_Data], matplotlib.axes.Axes]\nGet the extracted ion chromatograms (EICs) for the target m/z values.
\n
\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.__init__", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.__init__", "kind": "function", "doc": "file_location: srt pathlib.Path or s3path.S3Path\nThermo Raw file path
\n", "signature": "(file_location)"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.iRawDataPlus", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.iRawDataPlus", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.res", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.res", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.file_path", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.file_path", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.iFileHeader", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.iFileHeader", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.parameters", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.parameters", "kind": "variable", "doc": "Get or set the LCMSParameters object.
\n", "annotation": ": corems.encapsulation.factory.parameters.LCMSParameters"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.chromatogram_settings", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.chromatogram_settings", "kind": "variable", "doc": "Get or set the LiquidChromatographSetting object.
\n", "annotation": ": corems.encapsulation.factory.processingSetting.LiquidChromatographSetting"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.scans", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.scans", "kind": "variable", "doc": "scans : list or tuple\nIf list uses Thermo AverageScansInScanRange for selected scans, ortherwise uses Thermo AverageScans for a scan range
\n", "annotation": ": list | tuple"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.start_scan", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.start_scan", "kind": "variable", "doc": "Get the starting scan number for the Thermo Raw file.
\n", "annotation": ": int"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.end_scan", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.end_scan", "kind": "variable", "doc": "Get the ending scan number for the Thermo Raw file.
\n", "annotation": ": int"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.set_msordertype", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.set_msordertype", "kind": "function", "doc": "Function to convert user passed string MS Type to Thermo MSOrderType object\nLimited to MS1 through MS10.
\n\nParameters:
\n\nscanFilter : Thermo.ScanFilter\n The scan filter object.\nmstype : str, optional\n The MS Type string, by default 'ms1'
\n", "signature": "(self, scanFilter, mstype: str = 'ms1'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_creation_time", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_creation_time", "kind": "function", "doc": "Extract the creation date stamp from the .RAW file\nReturn formatted creation date stamp.
\n", "signature": "(self) -> datetime.datetime:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.remove_temp_file", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.remove_temp_file", "kind": "function", "doc": "if the path is from S3Path data cannot be serialized to io.ByteStream and\na temporary copy is stored at the temp dir\nuse this function only at the end of your execution scrip\nsome LCMS class methods depend on this file
\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_polarity_mode", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_polarity_mode", "kind": "function", "doc": "Get the polarity mode for the given scan number.
\n\nParameters:
\n\nscan_number : int\n The scan number.
\n\nRaises:
\n\nException\n If the polarity mode is unknown.
\n", "signature": "(self, scan_number: int) -> int:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_filter_for_scan_num", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_filter_for_scan_num", "kind": "function", "doc": "Returns the closest matching run time that corresponds to scan_number for the current\ncontroller. This function is only supported for MS device controllers.\ne.g. ['FTMS', '-', 'p', 'NSI', 'Full', 'ms', '[200.00-1000.00]']
\n\nParameters:
\n\nscan_number : int\n The scan number.
\n", "signature": "(self, scan_number: int) -> System.Collections.Generic.List[String]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.check_full_scan", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.check_full_scan", "kind": "function", "doc": "\n", "signature": "(self, scan_number: int) -> bool:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_all_filters", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_all_filters", "kind": "function", "doc": "Get all scan filters.\nThis function is only supported for MS device controllers.\ne.g. ['FTMS', '-', 'p', 'NSI', 'Full', 'ms', '[200.00-1000.00]']
\n", "signature": "(self) -> Tuple[Dict[int, str], System.Collections.Generic.List[String]]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_scan_header", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_scan_header", "kind": "function", "doc": "Get full dictionary of scan header meta data, i.e. AGC status, ion injection time, etc.
\n\nParameters:
\n\nscan : int\n The scan number.
\n", "signature": "(self, scan: int) -> Dict[str, Any]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_rt_time_from_trace", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_rt_time_from_trace", "kind": "function", "doc": "trace: ThermoFisher.CommonCore.Data.Business.ChromatogramSignal
\n", "signature": "(\ttrace) -> Tuple[System.Collections.Generic.List[Double], System.Collections.Generic.List[Double], System.Collections.Generic.List[Int32]]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_eics", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_eics", "kind": "function", "doc": "ms_type: str ('MS', MS2')\nstart_scan: int default -1 will select the lowest available\nend_scan: int default -1 will select the highest available
\n\nreturns:
\n\nchroma: dict{target_mz: EIC_Data(\n Scans: [int]\n original thermo scan numbers\n Time: [floats]\n list of retention times\n TIC: [floats]\n total ion chromatogram\n Apexes: [int]\n original thermo apex scan number after peak picking\n )\n
\n", "signature": "(\tself,\ttarget_mzs: System.Collections.Generic.List[Double],\ttic_data: Dict[str, Any],\tms_type='MS !d',\tpeak_detection=True,\tsmooth=True,\tplot=False,\tax: Optional[matplotlib.axes._axes.Axes] = None,\tlegend=False) -> Tuple[Dict[float, corems.mass_spectra.factory.LC_Temp.EIC_Data], matplotlib.axes._axes.Axes]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_tic", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_tic", "kind": "function", "doc": "ms_type: str ('MS', MS2')
\n\nreturns:\n chroma: dict\n {\n Scan: [int]\n original thermo scan numberMS\n Time: [floats]\n list of retention times\n TIC: [floats]\n total ion chromatogram\n Apexes: [int]\n original thermo apex scan number after peak picking\n }
\n", "signature": "(\tself,\tms_type='MS !d',\tpeak_detection=True,\tsmooth=True,\tplot=False,\tax=None) -> Tuple[corems.mass_spectra.factory.LC_Temp.TIC_Data, matplotlib.axes._axes.Axes]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_average_mass_spectrum", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_average_mass_spectrum", "kind": "function", "doc": "Averages mass spectra over a scan range using Thermo's AverageScansInScanRange method\nor a scan list using Thermo's AverageScans method\nspectrum_mode: str\n centroid or profile mass spectrum\nauto_process: bool\n If true performs peak picking, and noise threshold calculation after creation of mass spectrum object\nms_type: str\n String of form 'ms1' or 'ms2' or 'MS3' etc. Valid up to MS10.\n Internal function converts to Thermo MSOrderType class.
\n", "signature": "(\tself,\tspectrum_mode: str = 'profile',\tauto_process: bool = True,\tppm_tolerance: float = 5.0,\tms_type: str = 'MS1') -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile | corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.set_metadata", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.set_metadata", "kind": "function", "doc": "Collect metadata to be ingested in the mass spectrum object
\n\nscans_list: list[int] or false\nlastScanNumber: int\nfirstScanNumber: int
\n", "signature": "(\tself,\tfirstScanNumber=0,\tlastScanNumber=0,\tscans_list=False,\tlabel='Thermo_Profile'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_centroid_msms_data", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_centroid_msms_data", "kind": "function", "doc": "Deprecated since version 2.0:\nThis function will be removed in CoreMS 2.0. Please use get_average_mass_spectrum() instead for similar functionality.
\n", "signature": "(self, scan):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_average_mass_spectrum_by_scanlist", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_average_mass_spectrum_by_scanlist", "kind": "function", "doc": "Averages selected scans mass spectra using Thermo's AverageScans method\nscans_list: list[int]\nauto_process: bool\n If true performs peak picking, and noise threshold calculation after creation of mass spectrum object\nReturns:\n MassSpecProfile
\n\nDeprecated since version 2.0.
\n\nThis function will be removed in CoreMS 2.0. Please use get_average_mass_spectrum() instead for similar functionality.
\n", "signature": "(\tself,\tscans_list: System.Collections.Generic.List[Int32],\tauto_process: bool = True,\tppm_tolerance: float = 5.0) -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader", "kind": "class", "doc": "Collection of methdos to import LC data dependent acquisition from Thermo's raw file\nIntended do create the LCMS object --> ChromaPeaks --> MSobj FullScan --> Dependent MS/MS Obj
\n", "bases": "ThermoBaseClass, corems.mass_spectra.calc.LC_Calc.LC_Calculations"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader.__init__", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader.__init__", "kind": "function", "doc": "target_mzs: list[float] monoisotopic target m/z or None\n Details: None will defalt to depends scans selected m/\nfile_location: str, Path, or S3Path
\n", "signature": "(\tfile_location: str,\tselected_mzs: System.Collections.Generic.List[Double] = None)"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader.lcms", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader.lcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader.selected_mzs", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader.selected_mzs", "kind": "variable", "doc": "\n", "annotation": ": System.Collections.Generic.List[Double]"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader.get_lcms_obj", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader.get_lcms_obj", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader.get_precursors_list", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader.get_precursors_list", "kind": "function", "doc": "returns a set of unique precursors m/z\nprecision_decimals: int\n change this parameters does not seem to affect the number of dependent scans selected\n needs more investigation
\n", "signature": "(self, precision_decimals=5):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportMassSpectraThermoMSFileReader", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportMassSpectraThermoMSFileReader", "kind": "class", "doc": "Collection of methdos to import Summed/Averaged mass spectrum from Thermo's raw file\nCurrently only for profile mode data\nReturns MassSpecProfile object
\n", "bases": "ThermoBaseClass, corems.mass_spectra.calc.LC_Calc.LC_Calculations"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportMassSpectraThermoMSFileReader.get_icr_transient_times", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportMassSpectraThermoMSFileReader.get_icr_transient_times", "kind": "function", "doc": "Return a list for transient time targets for all scans, or selected scans range\nResolving Power and Transient time targets based on 7T FT-ICR MS system
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportMassSpectraThermoMSFileReader.RawFileReader", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportMassSpectraThermoMSFileReader.RawFileReader", "kind": "class", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportMassSpectraThermoMSFileReader.RawFileReader.get_data", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportMassSpectraThermoMSFileReader.RawFileReader.get_data", "kind": "function", "doc": "Retrieve mass spectrometry data for a given scan.
\n\nParameters
\n\n\n- scan (int):\nThe scan number.
\n- d_parameter (dict):\nA dictionary to store additional parameters.
\n- scan_type (str):\nThe type of scan (\"Centroid\" or \"Profile\").
\n
\n", "signature": "(self, scan: int, d_parameter: dict, scan_type: str):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportMassSpectraThermoMSFileReader.get_best_scans_idx", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportMassSpectraThermoMSFileReader.get_best_scans_idx", "kind": "function", "doc": "Method to determine the best scan indexes for selective co-addition.
\n\nParameters
\n\n\n- stdevs (int, optional):\nThe number of standard deviations to use as the cutoff for filtering out datapoints. Default is 2.
\n- method (str, optional):\nThe method to calculate the mean or median of the TIC values. Default is \"mean\".
\n- plot (bool, optional):\nWhether to plot the TIC with horizontal lines for the standard deviation cutoffs. Default is False.
\n
\n\nNotes
\n\nThis method calculates the mean (default) or median of the TIC values and sets an upper and lower limit\nbased on a specified number of standard deviations. The scans with TIC values outside of this range are\nconsidered the best scans for selective co-addition.
\n\nEmpirically, using 1-2 standard deviations is enough to filter out the worst datapoints.
\n\nIf plot is True, a matplotlib figure is returned along with the list of scan indexes.
\n\nExamples
\n\n\n
>>> reader = RawFileReader()\n>>> scans = reader.get_best_scans_idx(stdevs=2, method="mean", plot=True)\n
\n
A class to export low resolution GC-MS data.
\n\nThis class provides methods to export low resolution GC-MS data to various formats such as Excel, CSV, HDF5, and Pandas DataFrame.
\n\nParameters:
\n\nout_file_path : str\n The output file path.\ngcms : object\n The low resolution GCMS object.
\n\nAttributes:
\n\noutput_file : Path\n The output file path as a Path object.\ngcms : object\n The low resolution GCMS object.
\n\nMethods:
\n\n\n- get_pandas_df(id_label=\"corems:\"). Get the exported data as a Pandas DataFrame.
\n- get_json(nan=False, id_label=\"corems:\"). Get the exported data as a JSON string.
\n- to_pandas(write_metadata=True, id_label=\"corems:\"). Export the data to a Pandas DataFrame and save it as a pickle file.
\n- to_excel(write_mode='a', write_metadata=True, id_label=\"corems:\"),\nExport the data to an Excel file.
\n- to_csv(separate_output=False, write_mode=\"w\", write_metadata=True, id_label=\"corems:\").\nExport the data to a CSV file.
\n- to_hdf(id_label=\"corems:\").\nExport the data to an HDF5 file.
\n- get_data_stats(gcms).\nGet statistics about the GCMS data.
\n
\n"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.__init__", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.__init__", "kind": "function", "doc": "\n", "signature": "(out_file_path, gcms)"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.output_file", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.output_file", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.gcms", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.gcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_pandas_df", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_pandas_df", "kind": "function", "doc": "Get the exported data as a Pandas DataFrame.
\n\nParameters:
\n\nid_label : str, optional\n The ID label for the data. Default is \"corems:\".
\n\nReturns:
\n\nDataFrame\n The exported data as a Pandas DataFrame.
\n", "signature": "(self, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_json", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_json", "kind": "function", "doc": "Get the exported data as a JSON string.
\n\nParameters:
\n\nnan : bool, optional\n Whether to include NaN values in the JSON string. Default is False.\nid_label : str, optional\n The ID label for the data. Default is \"corems:\".
\n", "signature": "(self, nan=False, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.to_pandas", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.to_pandas", "kind": "function", "doc": "Export the data to a Pandas DataFrame and save it as a pickle file.
\n\nParameters:
\n\nwrite_metadata : bool, optional\n Whether to write metadata to the output file.\nid_label : str, optional\n The ID label for the data.
\n", "signature": "(self, write_metadata=True, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.to_excel", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.to_excel", "kind": "function", "doc": "Export the data to an Excel file.
\n\nParameters:
\n\nwrite_mode : str, optional\n The write mode for the Excel file. Default is 'a' (append).\nwrite_metadata : bool, optional\n Whether to write metadata to the output file. Default is True.\nid_label : str, optional\n The ID label for the data. Default is \"corems:\".
\n", "signature": "(self, write_mode='a', write_metadata=True, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.to_csv", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.to_csv", "kind": "function", "doc": "Export the data to a CSV file.
\n\nParameters:
\n\nseparate_output : bool, optional\n Whether to separate the output into multiple files. Default is False.\nwrite_mode : str, optional\n The write mode for the CSV file. Default is 'w' (write).\nwrite_metadata : bool, optional\n Whether to write metadata to the output file. Default is True.\nid_label : str, optional\n The ID label for the data. Default is \"corems:\".
\n", "signature": "(\tself,\tseparate_output=False,\twrite_mode='w',\twrite_metadata=True,\tid_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.to_hdf", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.to_hdf", "kind": "function", "doc": "Export the data to an HDF5 file.
\n\nParameters:
\n\nid_label : str, optional\n The ID label for the data. Default is \"corems:\".
\n", "signature": "(self, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_data_stats", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_data_stats", "kind": "function", "doc": "Get statistics about the GCMS data.
\n\nParameters:
\n\ngcms : object\n The low resolution GCMS object.
\n\nReturns:
\n\ndict\n A dictionary containing the data statistics.
\n", "signature": "(self, gcms):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_calibration_stats", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_calibration_stats", "kind": "function", "doc": "Get statistics about the GC-MS calibration.
\n\nParameters:
\n", "signature": "(self, gcms, id_label):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_blank_stats", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_blank_stats", "kind": "function", "doc": "Get statistics about the GC-MS blank.
\n", "signature": "(self, gcms):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_instrument_metadata", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_instrument_metadata", "kind": "function", "doc": "Get metadata about the GC-MS instrument.
\n", "signature": "(self, gcms):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_data_metadata", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_data_metadata", "kind": "function", "doc": "Get metadata about the GC-MS data.
\n\nParameters:
\n\ngcms : object\n The low resolution GCMS object.\nid_label : str \n The ID label for the data.\noutput_path : str\n The output file path.
\n\nReturns:
\n\ndict\n A dictionary containing the data metadata.
\n", "signature": "(self, gcms, id_label, output_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_parameters_json", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_parameters_json", "kind": "function", "doc": "Get the parameters as a JSON string.
\n\nParameters:
\n\ngcms : GCMS object\n The low resolution GCMS object.\nid_label : str\n The ID label for the data.\noutput_path : str\n The output file path.
\n\nReturns:
\n\nstr\n The parameters as a JSON string.
\n", "signature": "(self, gcms, id_label, output_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.write_settings", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.write_settings", "kind": "function", "doc": "Write the settings to a JSON file.
\n\nParameters:
\n\noutput_path : str\n The output file path.\ngcms : GCMS object\n The low resolution GCMS object.\nid_label : str\n The ID label for the data. Default is \"emsl:\".
\n", "signature": "(self, output_path, gcms, id_label='emsl:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_list_dict_data", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_list_dict_data", "kind": "function", "doc": "Get the exported data as a list of dictionaries.
\n\nParameters:
\n\ngcms : object\n The low resolution GCMS object.\ninclude_no_match : bool, optional\n Whether to include no match data. Default is True.\nno_match_inline : bool, optional\n Whether to include no match data inline. Default is False.
\n\nReturns:
\n\nlist\n The exported data as a list of dictionaries.
\n", "signature": "(self, gcms, include_no_match=True, no_match_inline=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport", "kind": "class", "doc": "A class to export high resolution mass spectra data.
\n\nThis class provides methods to export high resolution mass spectra data to various formats such as Excel, CSV, HDF5, and Pandas DataFrame.
\n\nParameters:
\n\nout_file_path : str | Path\n The output file path.\nmass_spectra : object\n The high resolution mass spectra object.\noutput_type : str, optional\n The output type. Default is 'excel'.
\n", "bases": "corems.mass_spectrum.output.export.HighResMassSpecExport"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.__init__", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(out_file_path, mass_spectra, output_type='excel')"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.output_file", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.output_file", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.dir_loc", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.dir_loc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.mass_spectra", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.mass_spectra", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.get_pandas_df", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.get_pandas_df", "kind": "function", "doc": "Get the exported data as a Pandas DataFrame.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.to_pandas", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.to_pandas", "kind": "function", "doc": "Export the data to a Pandas DataFrame and save it as a pickle file.
\n\nParameters:
\n\nwrite_metadata : bool, optional\n Whether to write metadata to the output file. Default is True.
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.to_excel", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.to_excel", "kind": "function", "doc": "Export the data to an Excel file.
\n\nParameters:
\n\nwrite_metadata : bool, optional\n Whether to write metadata to the output file. Default is True.
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.to_csv", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.to_csv", "kind": "function", "doc": "Export the data to a CSV file.
\n\nParameters:
\n\nwrite_metadata : bool, optional\n Whether to write metadata to the output file. Default is True.
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.get_mass_spectra_attrs", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.get_mass_spectra_attrs", "kind": "function", "doc": "Get the mass spectra attributes as a JSON string.
\n\nParameters:
\n\nmass_spectra : object\n The high resolution mass spectra object.
\n\nReturns:
\n\nstr\n The mass spectra attributes as a JSON string.
\n", "signature": "(self, mass_spectra):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.to_hdf", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.to_hdf", "kind": "function", "doc": "Export the data to an HDF5 file.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum", "modulename": "corems.mass_spectrum", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc", "modulename": "corems.mass_spectrum.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "kind": "module", "doc": "Created on March 23 2023
\n\n@author: Will Kew
\n\nModules for automatic mass internal recalibration
\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration", "kind": "class", "doc": "This class is designed for high resolution (FTICR, Orbitrap) data of complex mixture, e.g. Organic matter
\n\nThe tool first does a broad mass range search for the most commonly expected ion type (i.e. CHO, deprotonated - for negative ESI)\nAnd then the assigned data mass error distribution is searched, with a gaussian fit to the most prominent range. \nThis tool works when the data are of sufficient quality, and not outwith the typical expected range of the mass analyzer\nIt presumes the mean error is out by 0-several ppm, but that the spread of error values is modest (<2ppm)
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nCoreMS mass spectrum object
\n- plot (bool, optional):\nWhether to plot the error distribution. The default is False.
\n- docker (bool, optional):\nWhether to use the docker database. The default is True. If not, it uses a dynamically generated sqlite database.
\n- ppmFWHMprior (float, optional):\nThe FWHM of the prior distribution (ppm). The default is 3.
\n- ppmRangeprior (float, optional):\nThe range of the prior distribution (ppm). The default is 15.
\n
\n\nMethods
\n\n\n- determine_error_boundaries(). Determine the error boundaries for recalibration space.
\n
\n\nNotes
\n\nThis initialisation function creates a copy of the MassSpectrum object to avoid over-writing assignments. \nPossible future task is to make the base class copyable.
\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.__init__", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.__init__", "kind": "function", "doc": "\n", "signature": "(\tmass_spectrum,\tplot: bool = False,\tdocker: bool = True,\tppmFWHMprior: float = 3,\tppmRangeprior: float = 15)"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.mass_spectrum", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.plot", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.plot", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.docker", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.docker", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.ppmFWHMprior", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.ppmFWHMprior", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.ppmRangeprior", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.ppmRangeprior", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.set_uncal_settings", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.set_uncal_settings", "kind": "function", "doc": "Set uncalibrated formula search settings
\n\nThis function serves the uncalibrated data (hence broad error tolerance)\nIt only allows CHO formula in deprotonated ion type- as most common for SRFA ESI negative mode
\n\nThis will not work for positive mode data, or for other ion types, or other expected elemental searches.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.positive_search_settings", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.positive_search_settings", "kind": "function", "doc": "Set the positive mode elemental search settings
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.get_error_range", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.get_error_range", "kind": "function", "doc": "Get the error range from the error distribution
\n\nUsing lmfit and seaborn kdeplot to extract the error range from the error distribution of assigned species.
\n\nParameters
\n\n\n- errors (list):\nlist of the errors of the assigned species (ppm)
\n
\n", "signature": "(self, errors: list):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.determine_error_boundaries", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.determine_error_boundaries", "kind": "function", "doc": "Determine the error boundaries for recalibration space
\n\nThis is the main function in this class\nSets the Molecular Formulas search settings, performs the initial formula search\nConverts the data to a dataframe, and gets the error range\nReturns the error thresholds.
\n\nReturns
\n\n\n- mean_error (float):\nmean mass error of the Gaussian distribution (ppm)
\n- fwhm_error (float):\nfull width half max of the gaussian error distribution (ppm)
\n- ppm_thresh (list):\nrecommended thresholds for the recalibration parameters (ppm)\nConsists of [mean_error-fwhm_error,mean_error+fwhm_error]
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration", "modulename": "corems.mass_spectrum.calc.Calibration", "kind": "module", "doc": "Created on Wed May 13 02:16:09 2020
\n\n@author: Will Kew
\n"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration", "kind": "class", "doc": "MzDomainCalibration class for recalibrating mass spectra
\n\nParameters
\n\n\n- mass_spectrum (CoreMS MassSpectrum Object):\nThe mass spectrum to be calibrated.
\n- ref_masslist (str):\nThe path to a reference mass list.
\n- mzsegment (tuple of floats, optional):\nThe mz range to recalibrate, or None. Used for calibration of specific parts of the mz domain at a time.\nFuture work - allow multiple mzsegments to be passed.
\n
\n\nAttributes
\n\n\n- mass_spectrum (CoreMS MassSpectrum Object):\nThe mass spectrum to be calibrated.
\n- mzsegment (tuple of floats or None):\nThe mz range to recalibrate, or None.
\n- ref_mass_list_path (str or Path):\nThe path to the reference mass list.
\n
\n\nMethods
\n\n\n- run(). \nMain function to run this class.
\n- load_ref_mass_list(). \nLoad reference mass list (Bruker format).
\n- gen_ref_mass_list_from_assigned(min_conf=0.7). \nGenerate reference mass list from assigned masses.
\n- find_calibration_points(df_ref, calib_ppm_error_threshold=(-1, 1), calib_snr_threshold=5). \nFind calibration points in the mass spectrum based on the reference mass list.
\n- robust_calib(param, cal_peaks_mz, cal_refs_mz, order=1). \nRecalibration function.
\n- recalibrate_mass_spectrum(cal_peaks_mz, cal_refs_mz, order=1, diagnostic=False). \nMain recalibration function which uses a robust linear regression.
\n
\n"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.__init__", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.__init__", "kind": "function", "doc": "\n", "signature": "(mass_spectrum, ref_masslist, mzsegment=None)"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.mass_spectrum", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.mzsegment", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.mzsegment", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.ref_mass_list_path", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.ref_mass_list_path", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.load_ref_mass_list", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.load_ref_mass_list", "kind": "function", "doc": "Load reference mass list (Bruker format)
\n\nLoads in a reference mass list from a .ref file\nNote that some versions of Bruker's software produce .ref files with a different format. \nAs such, users may need to manually edit the .ref file in a text editor to ensure it is in the correct format. \nCoreMS includes an example .ref file with the correct format for reference.
\n\nReturns
\n\n\n- df_ref (Pandas DataFrame):\nreference mass list object.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.gen_ref_mass_list_from_assigned", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.gen_ref_mass_list_from_assigned", "kind": "function", "doc": "Generate reference mass list from assigned masses
\n\nThis function will generate a ref mass dataframe object from an assigned corems mass spec obj\nusing assigned masses above a certain minimum confidence threshold.
\n\nThis function needs to be retested and check it is covered in the unit tests.
\n\nParameters
\n\n\n- min_conf (float, optional):\nminimum confidence score. The default is 0.7.
\n
\n\nReturns
\n\n\n- df_ref (Pandas DataFrame):\nreference mass list - based on calculated masses.
\n
\n", "signature": "(self, min_conf: float = 0.7):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.find_calibration_points", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.find_calibration_points", "kind": "function", "doc": "Function to find calibration points in the mass spectrum
\n\nBased on the reference mass list.
\n\nParameters
\n\n\n- df_ref (Pandas DataFrame):\nreference mass list for recalibration.
\n- calib_ppm_error_threshold (tuple of floats, optional):\nppm error for finding calibration masses in the spectrum. The default is -1,1.\nNote: This is based on the calculation of ppm = ((mz_measure - mz_theoretical)/mz_theoretical)*1e6. \n Some software does this the other way around and value signs must be inverted for that to work.
\n- calib_snr_threshold (float, optional):\nsnr threshold for finding calibration masses in the spectrum. The default is 5.
\n
\n\nReturns
\n\n\n- cal_peaks_mz (list of floats):\nmasses of measured ions to use in calibration routine
\n- cal_refs_mz (list of floats):\nreference mz values of found calibration points.
\n
\n", "signature": "(\tself,\tdf_ref,\tcalib_ppm_error_threshold: tuple[float, float] = (-1, 1),\tcalib_snr_threshold: float = 5):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.robust_calib", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.robust_calib", "kind": "function", "doc": "Recalibration function
\n\nComputes the rms of m/z errors to minimize when calibrating.\nThis is adapted from from spike.
\n\nParameters
\n\n\n- param (list of floats):\ngenerated by minimize function from scipy optimize.
\n- cal_peaks_mz (list of floats):\nmasses of measured peaks to use in mass calibration.
\n- cal_peaks_mz (list of floats):\nreference mz values of found calibration points.
\n- order (int, optional):\norder of the recalibration function. 1 = linear, 2 = quadratic. The default is 1.
\n
\n\nReturns
\n\n\n- rmserror (float):\nroot mean square mass error for calibration points.
\n
\n", "signature": "(\tself,\tparam: list[float],\tcal_peaks_mz: list[float],\tcal_refs_mz: list[float],\torder: int = 1):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.recalibrate_mass_spectrum", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.recalibrate_mass_spectrum", "kind": "function", "doc": "Main recalibration function which uses a robust linear regression
\n\nThis function performs the recalibration of the mass spectrum object. \nIt iteratively applies
\n\nParameters
\n\n\n- cal_peaks_mz (list of float):\nmasses of measured peaks to use in mass calibration.
\n- cal_refs_mz (list of float):\nreference mz values of found calibration points.
\n- order (int, optional):\norder of the recalibration function. 1 = linear, 2 = quadratic. The default is 1.
\n
\n\nReturns
\n\n\n- mass_spectrum (CoreMS mass spectrum object):\nCalibrated mass spectrum object
\n
\n\nNotes
\n\nThis function is adapted, in part, from the SPIKE project [1,2] and is based on the robust linear regression method.
\n\nReferences
\n\n\n- Chiron L., Coutouly M-A., Starck J-P., Rolando C., Delsuc M-A. \nSPIKE a Processing Software dedicated to Fourier Spectroscopies \nhttps://arxiv.org/abs/1608.06777 (2016)
\n- SPIKE - https://github.com/spike-project/spike
\n
\n", "signature": "(\tself,\tcal_peaks_mz: list[float],\tcal_refs_mz: list[float],\torder: int = 1,\tdiagnostic: bool = False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.run", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.run", "kind": "function", "doc": "Run the calibration routine
\n\nThis function runs the calibration routine.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration", "kind": "class", "doc": "Frequency Domain Calibration class for mass spectrum.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- selected_mass_peaks (list):\nList of selected mass peaks.
\n- include_isotopologue (bool, optional):\nFlag to include isotopologues, by default False.
\n
\n\nAttributes
\n\n\n- mz_exp (ndarray):\nArray of experimental m/z values.
\n- mz_calc (ndarray):\nArray of calculated m/z values.
\n- freq_exp (ndarray):\nArray of experimental frequencies.
\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- freq_exp_ms (ndarray):\nArray of experimental frequencies for mass spectrum.
\n
\n\nMethods
\n\n\n- recal_mass_spec(mz_domain, Aterm, Bterm, Cterm). \nRecalibrate the mass spectrum with the given parameters.
\n- linear(). \nPerform linear calibration.
\n- quadratic(iteration=False). \nPerform quadratic calibration.
\n- ledford_calibration(iteration=False). \nPerform Ledford calibration.
\n- step_fit(steps=4).
\nPerform step fit calibration. \n
\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.__init__", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.__init__", "kind": "function", "doc": "\n", "signature": "(mass_spectrum, selected_mass_peaks, include_isotopologue=False)"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.selected_mspeaks", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.selected_mspeaks", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.mz_exp", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.mz_exp", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.mz_calc", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.mz_calc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.freq_exp", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.freq_exp", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.mass_spectrum", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.freq_exp_ms", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.freq_exp_ms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.recal_mass_spec", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.recal_mass_spec", "kind": "function", "doc": "Recalibrate the mass spectrum with the given parameters.
\n\nParameters
\n\n\n- mz_domain (ndarray):\nArray of m/z values for recalibration.
\n- Aterm (float):\nAterm parameter for recalibration.
\n- Bterm (float):\nBterm parameter for recalibration.
\n- Cterm (float):\nCterm parameter for recalibration.
\n
\n", "signature": "(self, mz_domain, Aterm, Bterm, Cterm):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.linear", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.linear", "kind": "function", "doc": "Perform linear calibration.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.quadratic", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.quadratic", "kind": "function", "doc": "Perform quadratic calibration.
\n\nParameters
\n\n\n- iteration (bool, optional):\nFlag to perform iterative calibration, by default False.
\n
\n", "signature": "(self, iteration: bool = False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.ledford_calibration", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.ledford_calibration", "kind": "function", "doc": "Perform Ledford calibration.
\n\nParameters
\n\n\n- iteration (bool, optional):\nFlag to perform iterative calibration, by default False.
\n
\n", "signature": "(self, iteration: bool = False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.step_fit", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.step_fit", "kind": "function", "doc": "Perform step fit calibration.
\n\nParameters
\n\n\n- steps (int, optional):\nNumber of steps for step fit calibration, by default 4.
\n
\n", "signature": "(self, steps: int = 4):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping", "kind": "class", "doc": "Class for Kendrick grouping of mass spectra.
\n\nMethods
\n\n\n- mz_odd_even_index_lists(). \nGet odd and even indexes lists.
\n- calc_error(current, test). \nCalculate the error between two values.
\n- populate_kendrick_index_dict_error(list_indexes, sort=True). \nPopulate the Kendrick index dictionary based on error.
\n- populate_kendrick_index_dict_rounding(list_indexes, sort=True). \nPopulate the Kendrick index dictionary based on rounding.
\n- sort_abundance_kendrick_dict(even_kendrick_group_index, odd_kendrick_group_index). \nSort the Kendrick index dictionary based on abundance.
\n- kendrick_groups_indexes(sort=True). \nGet the Kendrick groups indexes dictionary.
\n
\n"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.mz_odd_even_index_lists", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.mz_odd_even_index_lists", "kind": "function", "doc": "Get odd and even indexes lists.
\n\nReturns
\n\n\n- tuple: A tuple containing the lists of even and odd indexes.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.calc_error", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.calc_error", "kind": "function", "doc": "Calculate the error between two values.
\n\nParameters
\n\n\n- current (float):\nThe current value.
\n- test (float):\nThe test value.
\n
\n\nReturns
\n\n\n- float: The calculated error.
\n
\n", "signature": "(self, current: float, test: float):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.populate_kendrick_index_dict_error", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.populate_kendrick_index_dict_error", "kind": "function", "doc": "Populate the Kendrick index dictionary based on error.
\n\nParameters
\n\n\n- list_indexes (list):\nThe list of indexes.
\n- sort (bool, optional):\nWhether to sort the dictionary by abundance (default is True).
\n
\n\nReturns
\n\n\n- dict: The Kendrick index dictionary.
\n
\n", "signature": "(self, list_indexes: list, sort: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.populate_kendrick_index_dict_rounding", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.populate_kendrick_index_dict_rounding", "kind": "function", "doc": "Populate the Kendrick index dictionary based on rounding.
\n\nParameters
\n\n\n- list_indexes (list):\nThe list of indexes.
\n- sort (bool, optional):\nWhether to sort the dictionary by abundance (default is True).
\n
\n\nReturns
\n\n\n- dict: The Kendrick index dictionary.
\n
\n", "signature": "(self, list_indexes: list, sort: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.sort_abundance_kendrick_dict", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.sort_abundance_kendrick_dict", "kind": "function", "doc": "Sort the Kendrick index dictionary based on abundance.
\n\nParameters
\n\n\n- even_kendrick_group_index (dict):\nThe Kendrick index dictionary for even indexes.
\n- odd_kendrick_group_index (dict):\nThe Kendrick index dictionary for odd indexes.
\n
\n\nReturns
\n\n\n- dict: The sorted Kendrick index dictionary.
\n
\n", "signature": "(\tself,\teven_kendrick_group_index: dict,\todd_kendrick_group_index: dict):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.kendrick_groups_indexes", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.kendrick_groups_indexes", "kind": "function", "doc": "Get the Kendrick groups indexes dictionary.
\n\nParameters
\n\n\n- sort (bool, optional):\nWhether to sort the dictionary by abundance (default is True).
\n
\n\nReturns
\n\n\n- dict: The Kendrick groups indexes dictionary.
\n
\n", "signature": "(self, sort: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction", "kind": "class", "doc": "Class for mass error prediction.
\n\nParameters
\n\n\n- mass_spectrum (list):\nList of mass spectrum objects.
\n- mz_overlay (int, optional):\nThe mz overlay value for peak simulation. Default is 10.
\n- rp_increments (int, optional):\nThe resolving power increments for peak simulation. Default is 10000.
\n- base_line_target (float, optional):\nThe target value for the baseline resolution. Default is 0.01.
\n- max_interation (int, optional):\nThe maximum number of iterations for peak simulation. Default is 1000.
\n- interpolation (str, optional):\nThe interpolation method for missing data. Default is 'linear'.
\n
\n\nAttributes
\n\n\n- mass_spectrum_obj (list):\nList of mass spectrum objects.
\n- mz_overlay (int):\nThe mz overlay value for peak simulation.
\n- rp_increments (int):\nThe resolving power increments for peak simulation.
\n- base_line_target (float):\nThe target value for the baseline resolution.
\n- max_interation (int):\nThe maximum number of iterations for peak simulation.
\n- df (DataFrame or None):\nThe calculated error distribution dataframe.
\n- interpolation (str):\nThe interpolation method for missing data.
\n
\n\nMethods
\n\n\n- run().\nRuns the mass error prediction calculation.
\n- get_results().\nReturns the calculated error distribution dataframe.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.__init__", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(\tmass_spectrum,\tmz_overlay=10,\trp_increments=10000,\tbase_line_target: float = 0.01,\tmax_interation=1000,\tinterpolation='linear')"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.mass_spectrum_obj", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.mass_spectrum_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.mz_overlay", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.mz_overlay", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.rp_increments", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.rp_increments", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.base_line_target", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.base_line_target", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.max_interation", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.max_interation", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.df", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.df", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.interpolation", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.interpolation", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.run", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.run", "kind": "function", "doc": "Runs the mass error prediction calculation.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.get_results", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.get_results", "kind": "function", "doc": "Returns the calculated error distribution dataframe.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.calc_error_dist", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.calc_error_dist", "kind": "function", "doc": "Calculate the error distribution.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.sum_data", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.sum_data", "kind": "function", "doc": "Sum the abundances of the simulated peaks.
\n\nParameters
\n\n\n- tuple_mz_abun_list (tuple):\nA tuple containing the mz and abundance lists.
\n
\n\nReturns
\n\n\n- tuple: A tuple containing the summed mz and abundance lists.
\n
\n", "signature": "(self, tuple_mz_abun_list: tuple):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.calc_error", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.calc_error", "kind": "function", "doc": "Calculate the error between two values.
\n\nParameters
\n\n\n- mass_ref (float):\nThe reference value.
\n- mass_sim (float):\nThe simulated value.
\n- factor (float):\nThe factor to multiply the error by.
\n
\n\nReturns
\n\n\n- float: The calculated error.
\n
\n", "signature": "(self, mass_ref, mass_sim, factor):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.find_peak_apex", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.find_peak_apex", "kind": "function", "doc": "Find the peak apex.
\n\nParameters
\n\n\n- mz (array):\nThe mz array.
\n- abund (array):\nThe abundance array.
\n
\n\nReturns
\n\n\n- tuple: A tuple containing the peak apex mass and abundance.
\n
\n", "signature": "(self, mz, abund):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.find_peak_valley", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.find_peak_valley", "kind": "function", "doc": "Find the peak valley.
\n\nParameters
\n\n\n- mz (array):\nThe mz array.
\n- abund (array):\nThe abundance array.
\n
\n\nReturns
\n\n\n- tuple: A tuple containing the peak valley mz and abundance.
\n
\n", "signature": "(self, mz, abund):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "qualname": "MassSpecCalc", "kind": "class", "doc": "Class for Mass Spectrum Calculations
\n\nClass including numerical calculations related to mass spectrum class\nInherited PeakPicking and NoiseThresholdCalc ensuring its methods are \navailable to the instantiated mass spectrum class object
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nCoreMS mass spectrum object
\n
\n\nAttributes
\n\n\n- All Attributes are derivative from the MassSpecBase Class
\n
\n\nMethods
\n\n\n- check_mspeaks(). \nCheck if the mspeaks attribute is populated
\n- sort_by_abundance(). \nSort the mspeaks by abundance
\n- percentile_assigned(report_error=False,verbose=True). \nCalculate the percentage of assigned peaks
\n- resolving_power_calc(B, T). \nCalculate the resolving power
\n- number_average_molecular_weight(profile=False). \nCalculate the number average molecular weight
\n- weight_average_molecular_weight(profile=False). \nCalculate the weight average molecular weight
\n
\n", "bases": "corems.mass_spectrum.calc.PeakPicking.PeakPicking, corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc.percentile_assigned", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "qualname": "MassSpecCalc.percentile_assigned", "kind": "function", "doc": "Percentage of peaks which are assigned
\n\nParameters
\n\n\n- report_error (bool, optional):\nReport the error of the assigned peaks. Default is False.
\n- verbose (bool, optional):\nPrint the results. Default is True.
\n
\n", "signature": "(self, report_error: bool = False, verbose: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc.resolving_power_calc", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "qualname": "MassSpecCalc.resolving_power_calc", "kind": "function", "doc": "Calculate the theoretical resolving power
\n\nCalls on the MSPeak object function to calculate the resolving power of a peak, this calcs for all peaks in a spectrum.
\n\nParameters
\n\n\n- T (float):\ntransient time
\n- B (float):\nMagnetic Filed Strength (Tesla)
\n
\n\nReferences
\n\n\n- Marshall et al. (Mass Spectrom Rev. 1998 Jan-Feb;17(1):1-35.)\nDOI: 10.1002/(SICI)1098-2787(1998)17:1<1::AID-MAS1>3.0.CO;2-K
\n
\n", "signature": "(self, B: float, T: float):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc.number_average_molecular_weight", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "qualname": "MassSpecCalc.number_average_molecular_weight", "kind": "function", "doc": "Average molecular weight calculation
\n\nParameters
\n\n\n- profile (bool, optional):\nis data profile or centroid mode. The default is False (e.g. Centroid data)
\n
\n\nReturns
\n\n\n- float: The average molecular weight.
\n
\n", "signature": "(self, profile: bool = False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc.weight_average_molecular_weight", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "qualname": "MassSpecCalc.weight_average_molecular_weight", "kind": "function", "doc": "Weighted Average molecular weight calculation
\n\nReturns
\n\n\n- float: The weight average molecular weight.
\n
\n", "signature": "(self, profile: bool = False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "kind": "module", "doc": "Created on June 2nd 2023
\n\n@author: Will Kew
\n\nModule for mean resolving power filtration\nBased upon the work in:
\n\nKanawati, B, Bader, TM, Wanczek, K-P, Li, Y, Schmitt-Kopplin, P. \nFourier transform (FT)-artifacts and power-function resolution filter in Fourier transform mass spectrometry. \nRapid Commun Mass Spectrom. 2017; 31: 1607- 1615. https://doi.org/10.1002/rcm.7940
\n\nCalculates a m/z normalised resolving power, fits a gaussian distribution to this, and then filters out peaks which are outside of the user defined number of standard deviations
\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter", "kind": "class", "doc": "Class for for mean resolving power filtration.
\n\nThis module implements a mean resolving power filter based on the work described [1]
\n\nThe MeanResolvingPowerFilter class provides methods to calculate the m/z normalized resolving power, fit a Gaussian distribution to it, and filter out peaks that are outside of the user-defined number of standard deviations.
\n\nAttributes
\n\n\nmass_spectrum (object) (The mass spectrum object.):
ndeviations (int) (The number of standard deviations used for filtering.):
plot (bool) (Flag indicating whether to plot the results.):
guess_pars (bool) (Flag indicating whether to guess the parameters for the Gaussian model.):
\n\nMethods
\n\n\n- extract_peaks(): Extracts the peaks from the mass spectrum.
\n- normalise_rps(tmpdf_ms): Normalizes the resolving powers to be independent of m/z.
\n- calculate_distribution(tmpdf_ms): Calculates the distribution of the resolving powers.
\n- create_index_list_to_remove(tmpdf_ms, rps_thresh): Creates an index list of peaks to remove based on the calculated thresholds.
\n- main(): Executes the main filtering process and returns the index list of peaks to remove.
\n
\n\nReferences
\n\n\n- Kanawati, B, Bader, TM, Wanczek, K-P, Li, Y, Schmitt-Kopplin, P. \nFourier transform (FT)-artifacts and power-function resolution filter in Fourier transform mass spectrometry. \nRapid Commun Mass Spectrom. 2017; 31: 1607- 1615. https://doi.org/10.1002/rcm.7940
\n
\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.__init__", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.__init__", "kind": "function", "doc": "\n", "signature": "(\tmass_spectrum,\tndeviations: float = 3,\tplot: bool = False,\tguess_pars: bool = False)"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.mass_spectrum", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.plot", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.plot", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.ndeviations", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.ndeviations", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.guess_pars", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.guess_pars", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.extract_peaks", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.extract_peaks", "kind": "function", "doc": "Extracts the peaks from the mass spectrum.
\n\nReturns
\n\n\n- tmpdf_ms (Pandas DataFrame):\nA DataFrame containing the extracted peaks.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.normalise_rps", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.normalise_rps", "kind": "function", "doc": "Normalizes the resolving powers to be independent of m/z.
\n\nParameters
\n\n\n- tmpdf_ms (Pandas DataFrame):\nA DataFrame containing the extracted peaks.
\n
\n\nReturns
\n\n\n- tmpdf_ms (Pandas DataFrame):\nA DataFrame with the resolving powers normalized.
\n
\n", "signature": "(self, tmpdf_ms):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.calculate_distribution", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.calculate_distribution", "kind": "function", "doc": "Calculates the distribution of the resolving powers.
\n\nParameters
\n\n\n- tmpdf_ms (Pandas DataFrame):\nA DataFrame containing the extracted peaks with normalized resolving powers.
\n
\n\nReturns
\n\n\n- rps_thresh (list):\nA list of the calculated thresholds for filtering.
\n
\n", "signature": "(self, tmpdf_ms):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.create_index_list_to_remove", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.create_index_list_to_remove", "kind": "function", "doc": "Creates an index list of peaks to remove based on the calculated thresholds.
\n\nParameters
\n\n\n- tmpdf_ms (Pandas DataFrame):\nA DataFrame containing the extracted peaks with normalized resolving powers.
\n- rps_thresh (list):\nA list of the calculated thresholds for filtering.
\n
\n\nReturns
\n\n\n- index_to_keep (list):\nA list of indices of peaks to keep.
\n
\n", "signature": "(self, tmpdf_ms, rps_thresh: list):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.main", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.main", "kind": "function", "doc": "Executes the main filtering process and returns the index list of peaks to remove.
\n\nReturns
\n\n\n- index_to_remove (list):\nA list of indices of peaks to remove.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc", "kind": "class", "doc": "Class for noise threshold calculation.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- settings (MSParameters):\nThe mass spectrum parameters object.
\n- is_centroid (bool):\nFlag indicating whether the mass spectrum is centroid or profile.
\n- baseline_noise (float):\nThe baseline noise.
\n- baseline_noise_std (float):\nThe baseline noise standard deviation.
\n- max_signal_to_noise (float):\nThe maximum signal to noise.
\n- max_abundance (float):\nThe maximum abundance.
\n- abundance (np.array):\nThe abundance array.
\n- abundance_profile (np.array):\nThe abundance profile array.
\n- mz_exp (np.array):\nThe experimental m/z array.
\n- mz_exp_profile (np.array):\nThe experimental m/z profile array.
\n
\n\nAttributes
\n\n\n\nMethods
\n\n\n- get_noise_threshold(). Get the noise threshold.
\n- cut_mz_domain_noise(). Cut the m/z domain to the noise threshold regions.
\n- get_noise_average(ymincentroid). \nGet the average noise and standard deviation.
\n- get_abundance_minima_centroid(abun_cut)\nGet the abundance minima for centroid data.
\n- run_log_noise_threshold_calc(). \nRun the log noise threshold calculation.
\n- run_noise_threshold_calc(). \nRun the noise threshold calculation.
\n
\n"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.get_noise_threshold", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.get_noise_threshold", "kind": "function", "doc": "Get the noise threshold.
\n\nReturns
\n\n\n- Tuple[Tuple[float, float], Tuple[float, float]]: A tuple containing the m/z and abundance noise thresholds.\n(min_mz, max_mz), (noise_threshold, noise_threshold)
\n
\n", "signature": "(self) -> Tuple[Tuple[float, float], Tuple[float, float]]:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.cut_mz_domain_noise", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.cut_mz_domain_noise", "kind": "function", "doc": "Cut the m/z domain to the noise threshold regions.
\n\nReturns
\n\n\n- Tuple[np.array, np.array]: A tuple containing the m/z and abundance arrays of the truncated spectrum region.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.get_noise_average", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.get_noise_average", "kind": "function", "doc": "Get the average noise and standard deviation.
\n\nParameters
\n\n\n- ymincentroid (np.array):\nThe ymincentroid array.
\n
\n\nReturns
\n\n\n- Tuple[float, float]: A tuple containing the average noise and standard deviation.
\n
\n", "signature": "(self, ymincentroid):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.get_abundance_minima_centroid", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.get_abundance_minima_centroid", "kind": "function", "doc": "Get the abundance minima for centroid data.
\n\nParameters
\n\n\n- abun_cut (np.array):\nThe abundance cut array.
\n
\n\nReturns
\n\n\n- np.array: The abundance minima array.
\n
\n", "signature": "(self, abun_cut):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.run_log_noise_threshold_calc", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.run_log_noise_threshold_calc", "kind": "function", "doc": "Run the log noise threshold calculation.
\n\nReturns
\n\n\n- Tuple[float, float]: A tuple containing the average noise and standard deviation.
\n
\n\nNotes
\n\nMethod for estimating the noise based on decimal log of all the data point
\n\nIdea is that you calculate a histogram of of the log10(abundance) values. \nThe maximum of the histogram == the standard deviation of the noise.
\n\nFor aFT data it is a gaussian distribution of noise - not implemented here!\nFor mFT data it is a Rayleigh distribution, and the value is actually 10^(abu_max)*0.463.
\n\nSee the publication cited above for the derivation of this.
\n\nReferences
\n\n\n- dx.doi.org/10.1021/ac403278t | Anal. Chem. 2014, 86, 3308\u22123316
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.run_noise_threshold_calc", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.run_noise_threshold_calc", "kind": "function", "doc": "Runs noise threshold calculation (not log based method)
\n\nReturns
\n\n\n- Tuple[float, float]: A tuple containing the average noise and standard deviation.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "modulename": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "kind": "module", "doc": "This code is for Bayesian estimation of the noise levels. \nIt is it not implemented or used in the current code base. \nThe packages it uses are not part of the requirements. \nIf you want to use it, you will need to install them manually.
\n"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc_Bayes.BayesNoiseCalc", "modulename": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "qualname": "BayesNoiseCalc", "kind": "class", "doc": "Class for noise threshold calculation.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- settings (MSParameters):\nThe mass spectrum parameters object.
\n- is_centroid (bool):\nFlag indicating whether the mass spectrum is centroid or profile.
\n- baseline_noise (float):\nThe baseline noise.
\n- baseline_noise_std (float):\nThe baseline noise standard deviation.
\n- max_signal_to_noise (float):\nThe maximum signal to noise.
\n- max_abundance (float):\nThe maximum abundance.
\n- abundance (np.array):\nThe abundance array.
\n- abundance_profile (np.array):\nThe abundance profile array.
\n- mz_exp (np.array):\nThe experimental m/z array.
\n- mz_exp_profile (np.array):\nThe experimental m/z profile array.
\n
\n\nAttributes
\n\n\n\nMethods
\n\n\n- get_noise_threshold(). Get the noise threshold.
\n- cut_mz_domain_noise(). Cut the m/z domain to the noise threshold regions.
\n- get_noise_average(ymincentroid). \nGet the average noise and standard deviation.
\n- get_abundance_minima_centroid(abun_cut)\nGet the abundance minima for centroid data.
\n- run_log_noise_threshold_calc(). \nRun the log noise threshold calculation.
\n- run_noise_threshold_calc(). \nRun the noise threshold calculation.
\n
\n", "bases": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc_Bayes.BayesNoiseCalc.from_posterior", "modulename": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "qualname": "BayesNoiseCalc.from_posterior", "kind": "function", "doc": "Legacy code for Bayesian efforts - not used.
\n\npymc3 is not installed by default, \n if have plans to use it manual installation of pymc3 \n package before using this method is needed
\n", "signature": "(self, param, samples):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc_Bayes.BayesNoiseCalc.error_model_from_trace", "modulename": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "qualname": "BayesNoiseCalc.error_model_from_trace", "kind": "function", "doc": "Legacy code for Bayesian efforts - not used.
\n\npymc3 is not installed by default, \n if have plans to use it manual installation of pymc3 \n package before using this method is needed
\n", "signature": "(self, trace, ymincentroid):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc_Bayes.BayesNoiseCalc.simple_model_error_dist", "modulename": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "qualname": "BayesNoiseCalc.simple_model_error_dist", "kind": "function", "doc": "Legacy code for Bayesian efforts - not used.
\n\npymc3 is not installed by default, \n if have plans to use it manual installation of pymc3 \n package before using this method is needed
\n", "signature": "(self, ymincentroid):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking", "modulename": "corems.mass_spectrum.calc.PeakPicking", "kind": "module", "doc": "@author: Yuri E. Corilo\n@date: Jun 27, 2019
\n"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking", "kind": "class", "doc": "Class for peak picking.
\n\nParameters
\n\n\n\nAttributes
\n\n\n\nMethods
\n\n\n- cut_mz_domain_peak_picking().\nCut the m/z domain for peak picking.
\n- extrapolate_axes_for_pp().\nExtrapolate the m/z axis and fill the abundance axis with 0s.
\n- do_peak_picking().\nPerform peak picking.
\n- find_minima(apex_index, abundance, len_abundance, right=True).\nFind the minima of a peak.
\n- calculate_resolving_power(intes, massa, current_index).\nCalculate the resolving power of a peak.
\n- cal_minima(mass, abun).\nCalculate the minima of a peak.
\n- calc_centroid(mass, abund, freq).\nCalculate the centroid of a peak.
\n
\n"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.cut_mz_domain_peak_picking", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.cut_mz_domain_peak_picking", "kind": "function", "doc": "Cut the m/z domain for peak picking.
\n\nReturns
\n\n\n- mz_domain_X_low_cutoff (ndarray):\nThe m/z values within the specified range.
\n- mz_domain_low_Y_cutoff (ndarray):\nThe abundance values within the specified range.
\n- freq_domain_low_Y_cutoff (ndarray or None):\nThe frequency values within the specified range, if available.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.extrapolate_axes_for_pp", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.extrapolate_axes_for_pp", "kind": "function", "doc": "Extrapolate the m/z axis and fill the abundance axis with 0s.
\n\nReturns
\n\n\n- mz (ndarray):\nThe extrapolated m/z axis.
\n- abund (ndarray):\nThe abundance axis with 0s filled.
\n- freq (ndarray or None):\nThe extrapolated frequency axis, if available.
\n
\n\nNotes
\n\nThis function will extrapolate the mz axis by N datapoints, and fill the abundance axis with 0s. \nThis should prevent peak picking issues at the spectrum edge.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.do_peak_picking", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.do_peak_picking", "kind": "function", "doc": "Perform peak picking.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.find_minima", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.find_minima", "kind": "function", "doc": "Find the minima of a peak.
\n\nParameters
\n\n\n- apex_index (int):\nThe index of the peak apex.
\n- abundance (ndarray):\nThe abundance values.
\n- len_abundance (int):\nThe length of the abundance array.
\n- right (bool, optional):\nFlag indicating whether to search for minima to the right of the apex (default is True).
\n
\n\nReturns
\n\n\n- int: The index of the minima.
\n
\n", "signature": "(self, apex_index, abundance, len_abundance, right=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.calculate_resolving_power", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.calculate_resolving_power", "kind": "function", "doc": "Calculate the resolving power of a peak.
\n\nParameters
\n\n\n- intes (ndarray):\nThe intensity values.
\n- massa (ndarray):\nThe mass values.
\n- current_index (int):\nThe index of the current peak.
\n
\n\nReturns
\n\n\n- float: The resolving power of the peak.
\n
\n\nNotes
\n\nThis is a conservative calculation of resolving power,\nthe peak need to be resolved at least at the half-maximum magnitude,\notherwise, the combined full width at half maximum is used to calculate resolving power.
\n", "signature": "(self, intes, massa, current_index):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.cal_minima", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.cal_minima", "kind": "function", "doc": "Calculate the minima of a peak.
\n\nParameters
\n\n\n- mass (ndarray):\nThe mass values.
\n- abun (ndarray):\nThe abundance values.
\n
\n\nReturns
\n\n\n- ndarray or None: The mass values at the minima, if found.
\n
\n", "signature": "(self, mass, abun):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.calc_centroid", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.calc_centroid", "kind": "function", "doc": "Calculate the centroid of a peak.
\n\nParameters
\n\n\n- mass (ndarray):\nThe mass values.
\n- abund (ndarray):\nThe abundance values.
\n- freq (ndarray or None):\nThe frequency values, if available.
\n
\n\nReturns
\n\n\n", "signature": "(self, mass, abund, freq):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.get_threshold", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.get_threshold", "kind": "function", "doc": "Get the intensity threshold for peak picking.
\n\nParameters
\n\n\n- intes (ndarray):\nThe intensity values.
\n
\n\nReturns
\n\n\n- float: The intensity threshold.
\n- float: The factor to multiply the intensity threshold by.
\n
\n", "signature": "(self, intes):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.find_apex_fit_quadratic", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.find_apex_fit_quadratic", "kind": "function", "doc": "Find the apex of a peak.
\n\nParameters
\n\n\n- mass (ndarray):\nThe mass values.
\n- abund (ndarray):\nThe abundance values.
\n- freq (ndarray or None):\nThe frequency values, if available.
\n- current_index (int):\nThe index of the current peak.
\n
\n\nReturns
\n\n\n- float: The m/z value of the peak apex.
\n- float: The frequency value of the peak apex, if available.
\n- float: The abundance value of the peak apex.
\n
\n", "signature": "(self, mass, abund, freq, current_index):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.check_prominence", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.check_prominence", "kind": "function", "doc": "Check the prominence of a peak.
\n\nParameters
\n\n\n- abun (ndarray):\nThe abundance values.
\n- current_index (int):\nThe index of the current peak.
\n- len_abundance (int):\nThe length of the abundance array.
\n- peak_height_diff (function):\nThe function to calculate the peak height difference.
\n
\n\nReturns
\n\n\n- tuple or False: A tuple containing the indexes of the peak, if the prominence is above the threshold.\nOtherwise, False.
\n
\n", "signature": "(self, abun, current_index, len_abundance, peak_height_diff) -> tuple:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.use_the_max", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.use_the_max", "kind": "function", "doc": "Use the max peak height as the centroid
\n\nParameters
\n\n\n- mass (ndarray):\nThe mass values.
\n- abund (ndarray):\nThe abundance values.
\n- current_index (int):\nThe index of the current peak.
\n- len_abundance (int):\nThe length of the abundance array.
\n- peak_height_diff (function):\nThe function to calculate the peak height difference.
\n
\n\nReturns
\n\n\n- float: The m/z value of the peak apex.
\n- float: The abundance value of the peak apex.
\n- tuple or None: A tuple containing the indexes of the peak, if the prominence is above the threshold.\nOtherwise, None.
\n
\n", "signature": "(self, mass, abund, current_index, len_abundance, peak_height_diff):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.calc_centroid_legacy", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.calc_centroid_legacy", "kind": "function", "doc": "Legacy centroid calculation\nDeprecated - for deletion.
\n", "signature": "(self, mass, abund, freq):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory", "modulename": "corems.mass_spectrum.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.overrides", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "overrides", "kind": "function", "doc": "Checks if the method overrides a method from an interface class.
\n", "signature": "(interface_class):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase", "kind": "class", "doc": "A mass spectrum base class, stores the profile data and instrument settings.
\n\nIteration over a list of MSPeaks classes stored at the _mspeaks attributes.\n_mspeaks is populated under the hood by calling process_mass_spec method.\nIteration is null if _mspeaks is empty.
\n\nParameters
\n\n\n- mz_exp (array_like):\nThe m/z values of the mass spectrum.
\n- abundance (array_like):\nThe abundance values of the mass spectrum.
\n- d_params (dict):\nA dictionary of parameters for the mass spectrum.
\n- **kwargs: Additional keyword arguments.
\n
\n\nAttributes
\n\n\n- mspeaks (list):\nA list of mass peaks.
\n- is_calibrated (bool):\nWhether the mass spectrum is calibrated.
\n- is_centroid (bool):\nWhether the mass spectrum is centroided.
\n- has_frequency (bool):\nWhether the mass spectrum has a frequency domain.
\n- calibration_order (None or int):\nThe order of the mass spectrum's calibration.
\n- calibration_points (None or ndarray):\nThe calibration points of the mass spectrum.
\n- calibration_RMS (None or float):\nThe root mean square of the mass spectrum's calibration.
\n- calibration_segment (None or CalibrationSegment):\nThe calibration segment of the mass spectrum.
\n- _abundance (ndarray):\nThe abundance values of the mass spectrum.
\n- _mz_exp (ndarray):\nThe m/z values of the mass spectrum.
\n- _mspeaks (list):\nA list of mass peaks.
\n- _dict_nominal_masses_indexes (dict):\nA dictionary of nominal masses and their indexes.
\n- _baseline_noise (float):\nThe baseline noise of the mass spectrum.
\n- _baseline_noise_std (float):\nThe standard deviation of the baseline noise of the mass spectrum.
\n- _dynamic_range (float or None):\nThe dynamic range of the mass spectrum.
\n- _transient_settings (None or TransientSettings):\nThe transient settings of the mass spectrum.
\n- _frequency_domain (None or FrequencyDomain):\nThe frequency domain of the mass spectrum.
\n- _mz_cal_profile (None or MzCalibrationProfile):\nThe m/z calibration profile of the mass spectrum.
\n
\n\nMethods
\n\n\n- process_mass_spec(). Main function to process the mass spectrum, \nincluding calculating the noise threshold, peak picking, and resetting the MSpeak indexes.
\n
\n\nSee also: MassSpecCentroid(), MassSpecfromFreq(), MassSpecProfile()
\n", "bases": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc, corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.__init__", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.__init__", "kind": "function", "doc": "\n", "signature": "(mz_exp, abundance, d_params, **kwargs)"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mspeaks", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mspeaks", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.is_calibrated", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.is_calibrated", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.is_centroid", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.is_centroid", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.has_frequency", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.has_frequency", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.calibration_order", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.calibration_order", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.calibration_points", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.calibration_points", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.calibration_RMS", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.calibration_RMS", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.calibration_segment", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.calibration_segment", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.set_indexes", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.set_indexes", "kind": "function", "doc": "Set the mass spectrum to iterate over only the selected MSpeaks indexes.
\n\nParameters
\n\n\n- list_indexes (list of int):\nA list of integers representing the indexes of the MSpeaks to iterate over.
\n
\n", "signature": "(self, list_indexes):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.reset_indexes", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.reset_indexes", "kind": "function", "doc": "Reset the mass spectrum to iterate over all MSpeaks objects.
\n\nThis method resets the mass spectrum to its original state, allowing iteration over all MSpeaks objects.\nIt also sets the index of each MSpeak object to its corresponding position in the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.add_mspeak", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.add_mspeak", "kind": "function", "doc": "Add a new MSPeak object to the MassSpectrum object.
\n\nParameters
\n\n\n- ion_charge (int):\nThe ion charge of the MSPeak.
\n- mz_exp (float):\nThe experimental m/z value of the MSPeak.
\n- abundance (float):\nThe abundance of the MSPeak.
\n- resolving_power (float):\nThe resolving power of the MSPeak.
\n- signal_to_noise (float):\nThe signal-to-noise ratio of the MSPeak.
\n- massspec_indexes (list):\nA list of indexes of the MSPeak in the MassSpectrum object.
\n- exp_freq (float, optional):\nThe experimental frequency of the MSPeak. Defaults to None.
\n- ms_parent (MSParent, optional):\nThe MSParent object associated with the MSPeak. Defaults to None.
\n
\n", "signature": "(\tself,\tion_charge,\tmz_exp,\tabundance,\tresolving_power,\tsignal_to_noise,\tmassspec_indexes,\texp_freq=None,\tms_parent=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.reset_cal_therms", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.reset_cal_therms", "kind": "function", "doc": "Reset calibration terms and recalculate the mass-to-charge ratio and abundance.
\n\nParameters
\n\n\n- Aterm (float):\nThe A-term calibration coefficient.
\n- Bterm (float):\nThe B-term calibration coefficient.
\n- C (float):\nThe C-term calibration coefficient.
\n- fas (float, optional):\nThe frequency amplitude scaling factor. Default is 0.
\n
\n", "signature": "(self, Aterm, Bterm, C, fas=0):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.clear_molecular_formulas", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.clear_molecular_formulas", "kind": "function", "doc": "Clear the molecular formulas for all mspeaks in the MassSpectrum.
\n\nReturns
\n\n\n- numpy.ndarray: An array of the cleared molecular formulas for each mspeak in the MassSpectrum.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.process_mass_spec", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.process_mass_spec", "kind": "function", "doc": "Process the mass spectrum.
\n\nParameters
\n\n\n- keep_profile (bool, optional):\nWhether to keep the profile data after processing. Defaults to True.
\n
\n\nNotes
\n\nThis method does the following:
\n\n\n- calculates the noise threshold
\n- does peak picking (creates mspeak_objs)
\n- resets the mspeak_obj indexes
\n
\n", "signature": "(self, keep_profile=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.cal_noise_threshold", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.cal_noise_threshold", "kind": "function", "doc": "Calculate the noise threshold of the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.parameters", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.parameters", "kind": "variable", "doc": "Return the parameters of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.set_parameter_from_json", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.set_parameter_from_json", "kind": "function", "doc": "Set the parameters of the mass spectrum from a JSON file.
\n\nParameters
\n\n\n- parameters_path (str):\nThe path to the JSON file containing the parameters.
\n
\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.set_parameter_from_toml", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.set_parameter_from_toml", "kind": "function", "doc": "\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mspeaks_settings", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mspeaks_settings", "kind": "variable", "doc": "Return the MS peak settings of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.settings", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.settings", "kind": "variable", "doc": "Return the settings of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.molecular_search_settings", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.molecular_search_settings", "kind": "variable", "doc": "Return the molecular search settings of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mz_cal_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mz_cal_profile", "kind": "variable", "doc": "Return the calibrated m/z profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mz_cal", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mz_cal", "kind": "variable", "doc": "Return the calibrated m/z values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mz_exp", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mz_exp", "kind": "variable", "doc": "Return the experimental m/z values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.freq_exp_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.freq_exp_profile", "kind": "variable", "doc": "Return the experimental frequency profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mz_exp_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mz_exp_profile", "kind": "variable", "doc": "Return the experimental m/z profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.abundance_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.abundance_profile", "kind": "variable", "doc": "Return the abundance profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.abundance", "kind": "variable", "doc": "Return the abundance values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.freq_exp", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.freq_exp", "kind": "function", "doc": "Return the experimental frequency values of the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.resolving_power", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.resolving_power", "kind": "variable", "doc": "Return the resolving power values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.signal_to_noise", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.signal_to_noise", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.nominal_mz", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.nominal_mz", "kind": "variable", "doc": "Return the nominal m/z values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.get_mz_and_abundance_peaks_tuples", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.get_mz_and_abundance_peaks_tuples", "kind": "function", "doc": "Return a list of tuples containing the m/z and abundance values of the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.kmd", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.kmd", "kind": "variable", "doc": "Return the Kendrick mass defect values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.kendrick_mass", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.kendrick_mass", "kind": "variable", "doc": "Return the Kendrick mass values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.max_mz_exp", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.max_mz_exp", "kind": "variable", "doc": "Return the maximum experimental m/z value of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.min_mz_exp", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.min_mz_exp", "kind": "variable", "doc": "Return the minimum experimental m/z value of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.max_abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.max_abundance", "kind": "variable", "doc": "Return the maximum abundance value of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.max_signal_to_noise", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.max_signal_to_noise", "kind": "variable", "doc": "Return the maximum signal-to-noise ratio of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.most_abundant_mspeak", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.most_abundant_mspeak", "kind": "variable", "doc": "Return the most abundant MSpeak object of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.min_abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.min_abundance", "kind": "variable", "doc": "Return the minimum abundance value of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.dynamic_range", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.dynamic_range", "kind": "variable", "doc": "Return the dynamic range of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.baseline_noise", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.baseline_noise", "kind": "variable", "doc": "Return the baseline noise of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.baseline_noise_std", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.baseline_noise_std", "kind": "variable", "doc": "Return the standard deviation of the baseline noise of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.Aterm", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.Aterm", "kind": "variable", "doc": "Return the A-term calibration coefficient of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.Bterm", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.Bterm", "kind": "variable", "doc": "Return the B-term calibration coefficient of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.Cterm", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.Cterm", "kind": "variable", "doc": "Return the C-term calibration coefficient of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filename", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filename", "kind": "variable", "doc": "Return the filename of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.dir_location", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.dir_location", "kind": "variable", "doc": "Return the directory location of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.sort_by_mz", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.sort_by_mz", "kind": "function", "doc": "Sort the mass spectrum by m/z values.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.sort_by_abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.sort_by_abundance", "kind": "function", "doc": "Sort the mass spectrum by abundance values.
\n", "signature": "(self, reverse=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.tic", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.tic", "kind": "variable", "doc": "Return the total ion current of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.check_mspeaks_warning", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.check_mspeaks_warning", "kind": "function", "doc": "Check if the mass spectrum has MSpeaks objects.
\n\nRaises
\n\n\n- Warning: If the mass spectrum has no MSpeaks objects.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.check_mspeaks", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.check_mspeaks", "kind": "function", "doc": "Check if the mass spectrum has MSpeaks objects.
\n\nRaises
\n\n\n- Exception: If the mass spectrum has no MSpeaks objects.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.remove_assignment_by_index", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.remove_assignment_by_index", "kind": "function", "doc": "Remove the molecular formula assignment of the MSpeaks objects at the specified indexes.
\n\nParameters
\n\n\n- indexes (list of int):\nA list of indexes of the MSpeaks objects to remove the molecular formula assignment from.
\n
\n", "signature": "(self, indexes):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_index", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_index", "kind": "function", "doc": "Filter the mass spectrum by the specified indexes.
\n\nParameters
\n\n\n- list_indexes (list of int):\nA list of indexes of the MSpeaks objects to keep.
\n
\n", "signature": "(self, list_indexes):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_mz", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_mz", "kind": "function", "doc": "Filter the mass spectrum by the specified m/z range.
\n\nParameters
\n\n\n- min_mz (float):\nThe minimum m/z value to keep.
\n- max_mz (float):\nThe maximum m/z value to keep.
\n
\n", "signature": "(self, min_mz, max_mz):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_s2n", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_s2n", "kind": "function", "doc": "Filter the mass spectrum by the specified signal-to-noise ratio range.
\n\nParameters
\n\n\n- min_s2n (float):\nThe minimum signal-to-noise ratio to keep.
\n- max_s2n (float, optional):\nThe maximum signal-to-noise ratio to keep. Defaults to False (no maximum).
\n
\n", "signature": "(self, min_s2n, max_s2n=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_abundance", "kind": "function", "doc": "Filter the mass spectrum by the specified abundance range.
\n\nParameters
\n\n\n- min_abund (float):\nThe minimum abundance to keep.
\n- max_abund (float, optional):\nThe maximum abundance to keep. Defaults to False (no maximum).
\n
\n", "signature": "(self, min_abund, max_abund=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_max_resolving_power", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_max_resolving_power", "kind": "function", "doc": "Filter the mass spectrum by the specified maximum resolving power.
\n\nParameters
\n\n\nB (float):
T (float):
\n", "signature": "(self, B, T):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_mean_resolving_power", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_mean_resolving_power", "kind": "function", "doc": "Filter the mass spectrum by the specified mean resolving power.
\n\nParameters
\n\n\n- ndeviations (float, optional):\nThe number of standard deviations to use for filtering. Defaults to 3.
\n- plot (bool, optional):\nWhether to plot the resolving power distribution. Defaults to False.
\n- guess_pars (bool, optional):\nWhether to guess the parameters for the Gaussian model. Defaults to False.
\n
\n", "signature": "(self, ndeviations=3, plot=False, guess_pars=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_min_resolving_power", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_min_resolving_power", "kind": "function", "doc": "Filter the mass spectrum by the specified minimum resolving power.
\n\nParameters
\n\n\nB (float):
T (float):
\n", "signature": "(self, B, T):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_noise_threshold", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_noise_threshold", "kind": "function", "doc": "Filter the mass spectrum by the noise threshold.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.find_peaks", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.find_peaks", "kind": "function", "doc": "Find the peaks of the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.change_kendrick_base_all_mspeaks", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.change_kendrick_base_all_mspeaks", "kind": "function", "doc": "Change the Kendrick base of all MSpeaks objects.
\n\nParameters
\n\n\n- kendrick_dict_base (dict):\nA dictionary of the Kendrick base to change to.
\n
\n\nNotes
\n\nExample of kendrick_dict_base parameter: kendrick_dict_base = {\"C\": 1, \"H\": 2} or {\"C\": 1, \"H\": 1, \"O\":1} etc
\n", "signature": "(self, kendrick_dict_base):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.get_nominal_mz_first_last_indexes", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.get_nominal_mz_first_last_indexes", "kind": "function", "doc": "Return the first and last indexes of the MSpeaks objects with the specified nominal mass.
\n\nParameters
\n\n\n- nominal_mass (int):\nThe nominal mass to get the indexes for.
\n
\n\nReturns
\n\n\n- tuple: A tuple containing the first and last indexes of the MSpeaks objects with the specified nominal mass.
\n
\n", "signature": "(self, nominal_mass):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.get_masses_count_by_nominal_mass", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.get_masses_count_by_nominal_mass", "kind": "function", "doc": "Return a dictionary of the nominal masses and their counts.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.datapoints_count_by_nominal_mz", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.datapoints_count_by_nominal_mz", "kind": "function", "doc": "Return a dictionary of the nominal masses and their counts.
\n\nParameters
\n\n\n- mz_overlay (float, optional):\nThe m/z overlay to use for counting. Defaults to 0.1.
\n
\n\nReturns
\n\n\n- dict: A dictionary of the nominal masses and their counts.
\n
\n", "signature": "(self, mz_overlay=0.1):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.get_nominal_mass_indexes", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.get_nominal_mass_indexes", "kind": "function", "doc": "Return the indexes of the MSpeaks objects with the specified nominal mass.
\n\nParameters
\n\n\n- nominal_mass (int):\nThe nominal mass to get the indexes for.
\n- overlay (float, optional):\nThe m/z overlay to use for counting. Defaults to 0.1.
\n
\n\nReturns
\n\n\n- generator: A generator of the indexes of the MSpeaks objects with the specified nominal mass.
\n
\n", "signature": "(self, nominal_mass, overlay=0.1):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.plot_centroid", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.plot_centroid", "kind": "function", "doc": "Plot the centroid data of the mass spectrum.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nThe matplotlib axes to plot on. Defaults to None.
\n- c (str, optional):\nThe color to use for the plot. Defaults to 'g' (green).
\n
\n\nReturns
\n\n\n- matplotlib.axes.Axes: The matplotlib axes containing the plot.
\n
\n\nRaises
\n\n\n- Exception: If no centroid data is found.
\n
\n", "signature": "(self, ax=None, c='g'):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.plot_profile_and_noise_threshold", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.plot_profile_and_noise_threshold", "kind": "function", "doc": "Plot the profile data and noise threshold of the mass spectrum.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nThe matplotlib axes to plot on. Defaults to None.
\n- legend (bool, optional):\nWhether to show the legend. Defaults to False.
\n
\n\nReturns
\n\n\n- matplotlib.axes.Axes: The matplotlib axes containing the plot.
\n
\n\nRaises
\n\n\n- Exception: If no noise threshold is found.
\n
\n", "signature": "(self, ax=None, legend=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.plot_mz_domain_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.plot_mz_domain_profile", "kind": "function", "doc": "Plot the m/z domain profile of the mass spectrum.
\n\nParameters
\n\n\n- color (str, optional):\nThe color to use for the plot. Defaults to 'green'.
\n- ax (matplotlib.axes.Axes, optional):\nThe matplotlib axes to plot on. Defaults to None.
\n
\n\nReturns
\n\n\n- matplotlib.axes.Axes: The matplotlib axes containing the plot.
\n
\n", "signature": "(self, color='green', ax=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_excel", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_excel", "kind": "function", "doc": "Export the mass spectrum to an Excel file.
\n\nParameters
\n\n\n- out_file_path (str):\nThe path to the Excel file to export to.
\n- write_metadata (bool, optional):\nWhether to write the metadata to the Excel file. Defaults to True.
\n
\n\nReturns
\n\n\n", "signature": "(self, out_file_path, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_hdf", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_hdf", "kind": "function", "doc": "Export the mass spectrum to an HDF file.
\n\nParameters
\n\n\n- out_file_path (str):\nThe path to the HDF file to export to.
\n
\n\nReturns
\n\n\n", "signature": "(self, out_file_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_csv", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_csv", "kind": "function", "doc": "Export the mass spectrum to a CSV file.
\n\nParameters
\n\n\n- out_file_path (str):\nThe path to the CSV file to export to.
\n- write_metadata (bool, optional):\nWhether to write the metadata to the CSV file. Defaults to True.
\n
\n", "signature": "(self, out_file_path, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_pandas", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_pandas", "kind": "function", "doc": "Export the mass spectrum to a Pandas dataframe with pkl extension.
\n\nParameters
\n\n\n- out_file_path (str):\nThe path to the CSV file to export to.
\n- write_metadata (bool, optional):\nWhether to write the metadata to the CSV file. Defaults to True.
\n
\n", "signature": "(self, out_file_path, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_dataframe", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_dataframe", "kind": "function", "doc": "Return the mass spectrum as a Pandas dataframe.
\n\nReturns
\n\n\n- pandas.DataFrame: The mass spectrum as a Pandas dataframe.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_json", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_json", "kind": "function", "doc": "Return the mass spectrum as a JSON file.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.parameters_json", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.parameters_json", "kind": "function", "doc": "Return the parameters of the mass spectrum as a JSON string.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.parameters_toml", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.parameters_toml", "kind": "function", "doc": "Return the parameters of the mass spectrum as a TOML string.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecProfile", "kind": "class", "doc": "A mass spectrum class when the entry point is on profile format
\n\nNotes
\n\nStores the profile data and instrument settings. \nIteration over a list of MSPeaks classes stored at the _mspeaks attributes.\n_mspeaks is populated under the hood by calling process_mass_spec method.\nIteration is null if _mspeaks is empty. Many more attributes and methods inherited from MassSpecBase().
\n\nParameters
\n\n\n- data_dict (dict):\nA dictionary containing the profile data.
\n- d_params : dict{'str' (float, int or str}):\ncontains the instrument settings and processing settings
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectrum. Defaults to True.
\n
\n\nAttributes
\n\n_abundance : ndarray\n The abundance values of the mass spectrum.\n_mz_exp : ndarray\n The m/z values of the mass spectrum.\n_mspeaks : list\n A list of mass peaks.
\n\nMethods
\n\n\n- process_mass_spec(). Process the mass spectrum.
\n
\n\nsee also: MassSpecBase(), MassSpecfromFreq(), MassSpecCentroid()
\n", "bases": "MassSpecBase"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile.__init__", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecProfile.__init__", "kind": "function", "doc": "\n", "signature": "(data_dict, d_params, auto_process=True)"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq", "kind": "class", "doc": "A mass spectrum class when data entry is on frequency domain
\n\nNotes
\n\n\n- Transform to m/z based on the settings stored at d_params
\n- Stores the profile data and instrument settings
\n- Iteration over a list of MSPeaks classes stored at the _mspeaks attributes
\n- _mspeaks is populated under the hood by calling process_mass_spec method
\n- iteration is null if _mspeaks is empty
\n
\n\nParameters
\n\n\n- frequency_domain (list(float)):\nall datapoints in frequency domain in Hz
\n- magnitude : frequency_domain (list(float)):\nall datapoints in for magnitude of each frequency datapoint
\n- d_params : dict{'str' (float, int or str}):\ncontains the instrument settings and processing settings
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectrum. Defaults to True.
\n- keep_profile (bool, optional):\nWhether to keep the profile data. Defaults to True.
\n
\n\nAttributes
\n\n\n- has_frequency (bool):\nWhether the mass spectrum has frequency data.
\n- _frequency_domain (list(float)):\nFrequency domain in Hz
\n- label (str):\nstore label (Bruker, Midas Transient, see Labels class ). It across distinct processing points
\n- _abundance (ndarray):\nThe abundance values of the mass spectrum.
\n- _mz_exp (ndarray):\nThe m/z values of the mass spectrum.
\n- _mspeaks (list):\nA list of mass peaks.
\n- See Also (all the attributes of MassSpecBase class):
\n
\n\nMethods
\n\n\n- _set_mz_domain().\ncalculates the m_z based on the setting of d_params
\n- process_mass_spec(). Process the mass spectrum.
\n
\n\nsee also: MassSpecBase(), MassSpecProfile(), MassSpecCentroid()
\n", "bases": "MassSpecBase"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.__init__", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.__init__", "kind": "function", "doc": "\n", "signature": "(\tfrequency_domain,\tmagnitude,\td_params,\tauto_process=True,\tkeep_profile=True)"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.has_frequency", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.has_frequency", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.magnetron_frequency", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.magnetron_frequency", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.magnetron_frequency_sigma", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.magnetron_frequency_sigma", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.transient_settings", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.transient_settings", "kind": "variable", "doc": "Return the transient settings of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.calc_magnetron_freq", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.calc_magnetron_freq", "kind": "function", "doc": "Calculates the magnetron frequency of the mass spectrum.
\n\nParameters
\n\n\n- max_magnetron_freq (float, optional):\nThe maximum magnetron frequency. Defaults to 50.
\n- magnetron_freq_bins (int, optional):\nThe number of bins to use for the histogram. Defaults to 300.
\n
\n\nReturns
\n\n\n\nNotes
\n\nCalculates the magnetron frequency by examining all the picked peaks and the distances between them in the frequency domain.\nA histogram of those values below the threshold 'max_magnetron_freq' with the 'magnetron_freq_bins' number of bins is calculated.\nA gaussian model is fit to this histogram - the center value of this (statistically probably) the magnetron frequency.\nThis appears to work well or nOmega datasets, but may not work well for 1x datasets or those with very low magnetron peaks.
\n", "signature": "(self, max_magnetron_freq=50, magnetron_freq_bins=300):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid", "kind": "class", "doc": "A mass spectrum class when the entry point is on centroid format
\n\nNotes
\n\n\n- Stores the centroid data and instrument settings
\n- Simulate profile data based on Gaussian or Lorentzian peak shape
\n- Iteration over a list of MSPeaks classes stored at the _mspeaks attributes
\n- _mspeaks is populated under the hood by calling process_mass_spec method
\n- iteration is null if _mspeaks is empty
\n
\n\nParameters
\n\n\n- data_dict : dict {string (numpy array float64 )):\ncontains keys [m/z, Abundance, Resolving Power, S/N]
\n- d_params : dict{'str' (float, int or str}):\ncontains the instrument settings and processing settings
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectrum. Defaults to True.
\n
\n\nAttributes
\n\n\n- label (str):\nstore label (Bruker, Midas Transient, see Labels class)
\n- _baseline_noise (float):\nstore baseline noise
\n- _baseline_noise_std (float):\nstore baseline noise std
\n- _abundance (ndarray):\nThe abundance values of the mass spectrum.
\n- _mz_exp (ndarray):\nThe m/z values of the mass spectrum.
\n- _mspeaks (list):\nA list of mass peaks.
\n
\n\nMethods
\n\n\n- process_mass_spec().\nProcess the mass spectrum. Overriden from MassSpecBase. Populates the _mspeaks list with MSpeaks class using the centroid data.
\n- __simulate_profile__data__().\nSimulate profile data based on Gaussian or Lorentzian peak shape. Needs theoretical resolving power calculation and define peak shape, intended for plotting and inspection purposes only.
\n
\n\nsee also: MassSpecBase(), MassSpecfromFreq(), MassSpecProfile()
\n", "bases": "MassSpecBase"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.__init__", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.__init__", "kind": "function", "doc": "\n", "signature": "(data_dict, d_params, auto_process=True)"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.is_centroid", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.is_centroid", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.data_dict", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.data_dict", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.mz_exp_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.mz_exp_profile", "kind": "variable", "doc": "Return the m/z profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.abundance_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.abundance_profile", "kind": "variable", "doc": "Return the abundance profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.tic", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.tic", "kind": "variable", "doc": "Return the total ion current of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.process_mass_spec", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.process_mass_spec", "kind": "function", "doc": "Process the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes", "kind": "class", "doc": "A mass spectrum class when the entry point is on low resolution centroid format
\n\nNotes
\n\nDoes not store MSPeak Objs, will iterate over mz, abundance pairs instead
\n\nParameters
\n\n\n- data_dict : dict {string (numpy array float64 )):\ncontains keys [m/z, Abundance, Resolving Power, S/N]
\n- d_params : dict{'str' (float, int or str}):\ncontains the instrument settings and processing settings
\n
\n\nAttributes
\n\n\n- _processed_tic (float):\nstore processed total ion current
\n- _abundance (ndarray):\nThe abundance values of the mass spectrum.
\n- _mz_exp (ndarray):\nThe m/z values of the mass spectrum.
\n
\n", "bases": "MassSpecCentroid"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.__init__", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.__init__", "kind": "function", "doc": "\n", "signature": "(data_dict, d_params)"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.mz_exp", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.mz_exp", "kind": "variable", "doc": "Return the m/z values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.abundance", "kind": "variable", "doc": "Return the abundance values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.processed_tic", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.processed_tic", "kind": "variable", "doc": "Return the processed total ion current of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.tic", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.tic", "kind": "variable", "doc": "Return the total ion current of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.mz_abun_tuples", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.mz_abun_tuples", "kind": "variable", "doc": "Return the m/z and abundance values of the mass spectrum as a list of tuples.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.mz_abun_dict", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.mz_abun_dict", "kind": "variable", "doc": "Return the m/z and abundance values of the mass spectrum as a dictionary.
\n"}, {"fullname": "corems.mass_spectrum.input", "modulename": "corems.mass_spectrum.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass", "modulename": "corems.mass_spectrum.input.baseClass", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass", "kind": "class", "doc": "The MassListBaseClass object reads mass list data types and returns the mass spectrum obj
\n\nParameters
\n\n\n- file_location (Path or S3Path):\nFull data path.
\n- isCentroid (bool, optional):\nDetermines the mass spectrum data structure. If set to True, it assumes centroid mode. If set to False, it assumes profile mode and attempts to peak pick. Default is True.
\n- analyzer (str, optional):\nThe analyzer used for the mass spectrum. Default is 'Unknown'.
\n- instrument_label (str, optional):\nThe label of the instrument used for the mass spectrum. Default is 'Unknown'.
\n- sample_name (str, optional):\nThe name of the sample. Default is None.
\n- header_lines (int, optional):\nThe number of lines to skip in the file, including the column labels line. Default is 0.
\n- isThermoProfile (bool, optional):\nDetermines the number of expected columns in the file. If set to True, only m/z and intensity columns are expected. Signal-to-noise ratio (S/N) and resolving power (RP) will be calculated based on the data. Default is False.
\n- headerless (bool, optional):\nIf True, assumes that there are no headers present in the file (e.g., a .xy file from Bruker) and assumes two columns: m/z and intensity. Default is False.
\n
\n\nAttributes
\n\n\n- parameters (DataInputSetting):\nThe data input settings for the mass spectrum.
\n- data_type (str):\nThe type of data in the file.
\n- delimiter (str):\nThe delimiter used to read text-based files.
\n
\n\nMethods
\n\n\n- set_parameter_from_toml(parameters_path). Sets the data input settings from a TOML file.
\n- set_parameter_from_json(parameters_path). Sets the data input settings from a JSON file.
\n- get_dataframe(). Reads the file and returns the data as a pandas DataFrame.
\n- load_settings(mass_spec_obj, output_parameters). Loads the settings for the mass spectrum.
\n- get_output_parameters(polarity, scan_index=0). Returns the output parameters for the mass spectrum.
\n- clean_data_frame(dataframe). Cleans the data frame by removing columns that are not in the expected columns set.
\n
\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.__init__", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.__init__", "kind": "function", "doc": "\n", "signature": "(\tfile_location: pathlib.Path | s3path.S3Path,\tisCentroid: bool = True,\tanalyzer: str = 'Unknown',\tinstrument_label: str = 'Unknown',\tsample_name: str = None,\theader_lines: int = 0,\tisThermoProfile: bool = False,\theaderless: bool = False)"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.file_location", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.header_lines", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.header_lines", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.isCentroid", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.isCentroid", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.isThermoProfile", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.isThermoProfile", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.headerless", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.headerless", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.analyzer", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.analyzer", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.instrument_label", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.instrument_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.sample_name", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.sample_name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.parameters", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.parameters", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.set_parameter_from_toml", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.set_parameter_from_toml", "kind": "function", "doc": "\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.set_parameter_from_json", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.set_parameter_from_json", "kind": "function", "doc": "\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.data_type", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.data_type", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.delimiter", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.delimiter", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.encoding_detector", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.encoding_detector", "kind": "function", "doc": "Detects the encoding of a file.
\n\nParameters
\n\n\n- file_location (str):\nThe location of the file to be analyzed.
\n
\n\nReturns
\n\n\n- str: The detected encoding of the file.
\n
\n", "signature": "(self, file_location) -> str:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.set_data_type", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.set_data_type", "kind": "function", "doc": "Set the data type and delimiter based on the file extension.
\n\nRaises
\n\n\n- TypeError: If the data type could not be automatically recognized.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.get_dataframe", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.get_dataframe", "kind": "function", "doc": "Get the data as a pandas DataFrame.
\n\nReturns
\n\n\n- pandas.DataFrame: The data as a pandas DataFrame.
\n
\n\nRaises
\n\n\n- TypeError: If the data type is not supported.
\n
\n", "signature": "(self) -> pandas.core.frame.DataFrame:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.load_settings", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.load_settings", "kind": "function", "doc": "TODO loading output parameters from json file is not functional
\n\nLoad settings from a JSON file and apply them to the given mass_spec_obj.
\n\nParameters
\n\n\n- mass_spec_obj (MassSpec):\nThe mass spectrum object to apply the settings to.
\n
\n", "signature": "(self, mass_spec_obj, output_parameters):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.get_output_parameters", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.get_output_parameters", "kind": "function", "doc": "Get the output parameters for the mass spectrum.
\n\nParameters
\n\n\n- polarity (int):\nThe polarity of the mass spectrum +1 or -1.
\n- scan_index (int, optional):\nThe index of the scan. Default is 0.
\n
\n\nReturns
\n\n\n- dict: A dictionary containing the output parameters.
\n
\n", "signature": "(self, polarity: int, scan_index: int = 0) -> dict:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.clean_data_frame", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.clean_data_frame", "kind": "function", "doc": "Clean the input dataframe by removing columns that are not expected.
\n\nParameters
\n\n\n- pandas.DataFrame: The input dataframe to be cleaned.
\n
\n", "signature": "(self, dataframe):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.check_columns", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.check_columns", "kind": "function", "doc": "Check if the given header labels match the expected columns.
\n\nParameters
\n\n\n- header_labels (list):\nThe header labels to be checked.
\n
\n\nRaises
\n\n\n- Exception: If any expected column is not found in the header labels.
\n
\n", "signature": "(self, header_labels: list[str]):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.read_xml_peaks", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.read_xml_peaks", "kind": "function", "doc": "Read peaks from a Bruker .xml file and return a pandas DataFrame.
\n\nParameters
\n\n\n- data (str):\nThe path to the .xml file.
\n
\n\nReturns
\n\n\n- pandas.DataFrame: A DataFrame containing the peak data with columns: 'm/z', 'I', 'Resolving Power', 'Area', 'S/N', 'fwhm'.
\n
\n", "signature": "(self, data: str) -> pandas.core.frame.DataFrame:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.get_xml_polarity", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.get_xml_polarity", "kind": "function", "doc": "Get the polarity from an XML peaklist.
\n\nReturns
\n\n\n- int: The polarity of the XML peaklist. Returns -1 for negative polarity, +1 for positive polarity.
\n
\n\nRaises
\n\n\n- Exception: If the data type is not XML peaklist in Bruker format or if the polarity is unhandled.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5", "modulename": "corems.mass_spectrum.input.boosterHDF5", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum", "kind": "class", "doc": "The ReadHDF_BoosterMassSpectrum class parses the mass spectrum data from an HDF file and generate a mass spectrum object.
\n\nParameters
\n\n\n- file_location (str):\nThe path to the HDF file.
\n- isCentroid (bool, optional):\nSpecifies whether the mass spectrum is centroided or not. Default is False.
\n
\n\nAttributes
\n\n\n- polarity (int):\nThe polarity of the mass spectrum.
\n- h5pydata (h5py.File):\nThe HDF file object.
\n- scans (list):\nThe list of scan names in the HDF file.
\n
\n\nMethods
\n\n\n- get_data_profile(mz, abundance, auto_process). Returns a MassSpecProfile object from the given m/z and abundance arrays.
\n- get_attr_data(scan, attr_srt). Returns the attribute value for the given scan and attribute name.
\n- get_polarity(file_location). Returns the polarity of the mass spectrum.
\n- get_mass_spectrum(auto_process). Returns the mass spectrum as a MassSpecProfile object.
\n- get_output_parameters(). Returns the default output parameters for the mass spectrum.
\n
\n", "bases": "corems.mass_spectrum.input.baseClass.MassListBaseClass"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.__init__", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.__init__", "kind": "function", "doc": "\n", "signature": "(file_location, isCentroid=False)"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.polarity", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.polarity", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.get_data_profile", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.get_data_profile", "kind": "function", "doc": "Returns a MassSpecProfile object from the given m/z and abundance arrays.
\n\nParameters
\n\n\n- mz (array_like):\nThe m/z values.
\n- abundance (array_like):\nThe abundance values.
\n- auto_process (bool):\nSpecifies whether to automatically process the mass spectrum.
\n
\n\nReturns
\n\n\n- MassSpecProfile: The MassSpecProfile object.
\n
\n", "signature": "(\tself,\tmz,\tabundance,\tauto_process) -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.get_attr_data", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.get_attr_data", "kind": "function", "doc": "Returns the attribute value for the given scan and attribute name.
\n\nParameters
\n\n\n- scan (int):\nThe scan index.
\n- attr_srt (str):\nThe attribute name.
\n
\n\nReturns
\n\n\n- object: The attribute value.
\n
\n", "signature": "(self, scan, attr_srt):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.get_polarity", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.get_polarity", "kind": "function", "doc": "Returns the polarity of the mass spectrum.
\n\nParameters
\n\n\n- file_location (str):\nThe path to the HDF file.
\n
\n\nReturns
\n\n\n- int: The polarity of the mass spectrum.
\n
\n", "signature": "(self, file_location: str | s3path.S3Path) -> int:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.get_mass_spectrum", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.get_mass_spectrum", "kind": "function", "doc": "Returns the mass spectrum as a MassSpecProfile object.
\n\nParameters
\n\n\n- auto_process (bool, optional):\nSpecifies whether to automatically process the mass spectrum. Default is True.
\n
\n\nReturns
\n\n\n- MassSpecProfile: The MassSpecProfile object.
\n
\n", "signature": "(\tself,\tauto_process=True) -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.get_output_parameters", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.get_output_parameters", "kind": "function", "doc": "Returns the default output parameters for the mass spectrum.
\n\nReturns
\n\n\n- dict: The default output parameters.
\n
\n", "signature": "(self) -> dict:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5", "modulename": "corems.mass_spectrum.input.coremsHDF5", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum", "kind": "class", "doc": "Class for reading mass spectrum data from a CoreMS HDF5 file.
\n\nAttributes
\n\n\n- h5pydata (h5py.File):\nThe HDF5 file object.
\n- scans (list):\nList of scan labels in the HDF5 file.
\n
\n\nParameters
\n\n\n- file_location (str or S3Path):\nThe path to the CoreMS HDF5 file.
\n
\n\nMethods
\n\n\n- load_raw_data(mass_spectrum, scan_index=0) Load raw data into the mass spectrum object.
\n- get_mass_spectrum(scan_number=0, time_index=-1, auto_process=True, load_settings=True, load_raw=True).Get a mass spectrum object.
\n- load_settings(mass_spectrum, scan_index=0, time_index=-1). Load settings into the mass spectrum object.
\n- get_dataframe(scan_index=0, time_index=-1). Get a pandas DataFrame representing the mass spectrum.
\n- get_time_index_to_pull(scan_label, time_index). Get the time index to pull from the HDF5 file.
\n- get_high_level_attr_data(attr_str). Get high-level attribute data from the HDF5 file.
\n- get_scan_group_attr_data(scan_index, time_index, attr_group, attr_srt=None). Get scan group attribute data from the HDF5 file.
\n- get_raw_data_attr_data(scan_index, attr_group, attr_str). Get raw data attribute data from the HDF5 file.
\n- get_output_parameters(polarity, scan_index=0). Get the output parameters for the mass spectrum.
\n
\n", "bases": "corems.mass_spectrum.input.massList.ReadCoremsMasslist"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.__init__", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.__init__", "kind": "function", "doc": "\n", "signature": "(file_location)"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.h5pydata", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.h5pydata", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.scans", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.scans", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.load_raw_data", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.load_raw_data", "kind": "function", "doc": "Load raw data into the mass spectrum object.
\n\nParameters
\n\n\n- mass_spectrum (MassSpecCentroid):\nThe mass spectrum object to load the raw data into.
\n- scan_index (int, optional):\nThe index of the scan to load the raw data from. Default is 0.
\n
\n", "signature": "(self, mass_spectrum, scan_index=0):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_mass_spectrum", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_mass_spectrum", "kind": "function", "doc": "Get a mass spectrum object.
\n\nParameters
\n\n\n- scan_number (int, optional):\nThe index of the scan to retrieve the mass spectrum from. Default is 0.
\n- time_index (int, optional):\nThe index of the time point to retrieve the mass spectrum from. Default is -1.
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectrum. Default is True.
\n- load_settings (bool, optional):\nWhether to load the settings into the mass spectrum object. Default is True.
\n- load_raw (bool, optional):\nWhether to load the raw data into the mass spectrum object. Default is True.
\n
\n\nReturns
\n\n\n- MassSpecCentroid: The mass spectrum object.
\n
\n", "signature": "(\tself,\tscan_number=0,\ttime_index=-1,\tauto_process=True,\tload_settings=True,\tload_raw=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.load_settings", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.load_settings", "kind": "function", "doc": "Load settings into the mass spectrum object.
\n\nParameters
\n\n\n- mass_spectrum (MassSpecCentroid):\nThe mass spectrum object to load the settings into.
\n- scan_index (int, optional):\nThe index of the scan to load the settings from. Default is 0.
\n- time_index (int, optional):\nThe index of the time point to load the settings from. Default is -1.
\n
\n", "signature": "(self, mass_spectrum, scan_index=0, time_index=-1):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_dataframe", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_dataframe", "kind": "function", "doc": "Get a pandas DataFrame representing the mass spectrum.
\n\nParameters
\n\n\n- scan_index (int, optional):\nThe index of the scan to retrieve the DataFrame from. Default is 0.
\n- time_index (int, optional):\nThe index of the time point to retrieve the DataFrame from. Default is -1.
\n
\n\nReturns
\n\n\n- DataFrame: The pandas DataFrame representing the mass spectrum.
\n
\n", "signature": "(self, scan_index=0, time_index=-1):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_time_index_to_pull", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_time_index_to_pull", "kind": "function", "doc": "Get the time index to pull from the HDF5 file.
\n\nParameters
\n\n\n- scan_label (str):\nThe label of the scan.
\n- time_index (int):\nThe index of the time point.
\n
\n\nReturns
\n\n\n- str: The time index to pull.
\n
\n", "signature": "(self, scan_label, time_index):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_high_level_attr_data", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_high_level_attr_data", "kind": "function", "doc": "Get high-level attribute data from the HDF5 file.
\n\nParameters
\n\n\n- attr_str (str):\nThe attribute string.
\n
\n\nReturns
\n\n\n- dict: The attribute data.
\n
\n\nRaises
\n\n\n- KeyError: If the attribute string is not found in the HDF5 file.
\n
\n", "signature": "(self, attr_str):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_scan_group_attr_data", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_scan_group_attr_data", "kind": "function", "doc": "Get scan group attribute data from the HDF5 file.
\n\nParameters
\n\n\n- scan_index (int):\nThe index of the scan.
\n- time_index (int):\nThe index of the time point.
\n- attr_group (str):\nThe attribute group.
\n- attr_srt (str, optional):\nThe attribute string. Default is None.
\n
\n\nReturns
\n\n\n- dict: The attribute data.
\n
\n\nNotes
\n\nThis method retrieves attribute data from the HDF5 file for a specific scan and time point.\nThe attribute data is stored in the specified attribute group.\nIf an attribute string is provided, only the corresponding attribute value is returned.\nIf no attribute string is provided, all attribute data in the group is returned as a dictionary.
\n", "signature": "(self, scan_index, time_index, attr_group, attr_srt=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_raw_data_attr_data", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_raw_data_attr_data", "kind": "function", "doc": "Get raw data attribute data from the HDF5 file.
\n\nParameters
\n\n\n- scan_index (int):\nThe index of the scan.
\n- attr_group (str):\nThe attribute group.
\n- attr_str (str):\nThe attribute string.
\n
\n\nReturns
\n\n\n- dict: The attribute data.
\n
\n\nRaises
\n\n\n- KeyError: If the attribute string is not found in the attribute group.
\n
\n\nNotes
\n\nThis method retrieves the attribute data associated with a specific scan, attribute group, and attribute string\nfrom the HDF5 file. It returns the attribute data as a dictionary.
\n\nExample usage:
\n\n\n
>>> data = get_raw_data_attr_data(0, "group1", "attribute1")\n>>> print(data)\n{'key1': 'value1', 'key2': 'value2'}\n
\n
Get the output parameters for the mass spectrum.
\n\nParameters
\n\n\n- polarity (str):\nThe polarity of the mass spectrum.
\n- scan_index (int, optional):\nThe index of the scan. Default is 0.
\n
\n\nReturns
\n\n\n- dict: The output parameters.
\n
\n", "signature": "(self, polarity, scan_index=0):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.massList", "modulename": "corems.mass_spectrum.input.massList", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.massList.ReadCoremsMasslist", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadCoremsMasslist", "kind": "class", "doc": "The ReadCoremsMasslist object reads processed mass list data types\nand returns the mass spectrum obj with the molecular formula obj
\n\nOnly available for centroid mass spectrum type: it will ignore the parameter isCentroid \nPlease see MassListBaseClass for more details
\n", "bases": "corems.mass_spectrum.input.baseClass.MassListBaseClass"}, {"fullname": "corems.mass_spectrum.input.massList.ReadCoremsMasslist.get_mass_spectrum", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadCoremsMasslist.get_mass_spectrum", "kind": "function", "doc": "Get the mass spectrum object from the processed mass list data.
\n\nParameters
\n\n\n- loadSettings (bool, optional):\nWhether to load the settings for the mass spectrum. Default is True.
\n
\n\nReturns
\n\n\n- MassSpecCentroid: The mass spectrum object.
\n
\n\nRaises
\n\n\n- ValueError: If the input file is not a valid CoreMS file.
\n
\n", "signature": "(\tself,\tloadSettings: bool = True) -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.massList.ReadCoremsMasslist.add_molecular_formula", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadCoremsMasslist.add_molecular_formula", "kind": "function", "doc": "Add molecular formula information to the mass spectrum object.
\n\nParameters
\n\n\n- mass_spec_obj (MassSpecCentroid):\nThe mass spectrum object to add the molecular formula to.
\n- dataframe (pandas.DataFrame):\nThe processed mass list data.
\n
\n", "signature": "(self, mass_spec_obj, dataframe):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.massList.ReadMassList", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadMassList", "kind": "class", "doc": "The ReadMassList object reads unprocessed mass list data types\nand returns the mass spectrum object.
\n\nParameters
\n\n\n- MassListBaseClass (class):\nThe base class for reading mass list data types.
\n
\n\nMethods
\n\n\n- get_mass_spectrum(polarity, scan=0, auto_process=True, loadSettings=True). Reads mass list data types and returns the mass spectrum object.
\n
\n", "bases": "corems.mass_spectrum.input.baseClass.MassListBaseClass"}, {"fullname": "corems.mass_spectrum.input.massList.ReadMassList.get_mass_spectrum", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadMassList.get_mass_spectrum", "kind": "function", "doc": "Reads mass list data types and returns the mass spectrum object.
\n\nParameters
\n\n\n- polarity (int):\nThe polarity of the mass spectrum (+1 or -1).
\n- scan (int, optional):\nThe scan number of the mass spectrum (default is 0).
\n- auto_process (bool, optional):\nFlag indicating whether to automatically process the mass spectrum (default is True).
\n- loadSettings (bool, optional):\nFlag indicating whether to load settings for the mass spectrum (default is True).
\n
\n\nReturns
\n\n\n- mass_spec (MassSpecCentroid or MassSpecProfile):\nThe mass spectrum object.
\n
\n", "signature": "(\tself,\tpolarity: int,\tscan: int = 0,\tauto_process: bool = True,\tloadSettings: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.massList.ReadBrukerXMLList", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadBrukerXMLList", "kind": "class", "doc": "The ReadBrukerXMLList object reads Bruker XML objects\nand returns the mass spectrum object.\nSee MassListBaseClass for details
\n\nParameters
\n\n\n- MassListBaseClass (class):\nThe base class for reading mass list data types and returning the mass spectrum object.
\n
\n\nMethods
\n\n\n- get_mass_spectrum(polarity: bool = None, scan: int = 0, auto_process: bool = True, loadSettings: bool = True). Reads mass list data types and returns the mass spectrum object.
\n
\n", "bases": "corems.mass_spectrum.input.baseClass.MassListBaseClass"}, {"fullname": "corems.mass_spectrum.input.massList.ReadBrukerXMLList.get_mass_spectrum", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadBrukerXMLList.get_mass_spectrum", "kind": "function", "doc": "Reads mass list data types and returns the mass spectrum object.
\n\nParameters
\n\n\n- polarity (bool, optional):\nThe polarity of the mass spectrum. Can be +1 or -1. If not provided, it will be determined from the XML file.
\n- scan (int, optional):\nThe scan number of the mass spectrum. Default is 0.
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectrum. Default is True.
\n- loadSettings (bool, optional):\nWhether to load the settings for the mass spectrum. Default is True.
\n
\n\nReturns
\n\n\n- mass_spec (MassSpecCentroid):\nThe mass spectrum object representing the centroided mass spectrum.
\n
\n", "signature": "(\tself,\tpolarity: bool = None,\tscan: int = 0,\tauto_process: bool = True,\tloadSettings: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.numpyArray", "modulename": "corems.mass_spectrum.input.numpyArray", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.numpyArray.ms_from_array_profile", "modulename": "corems.mass_spectrum.input.numpyArray", "qualname": "ms_from_array_profile", "kind": "function", "doc": "Create a MassSpecProfile object from an array of m/z values and abundance values.
\n\nParameters:\n mz (numpy.ndarray): Array of m/z values.\n abundance (numpy.ndarray): Array of abundance values.\n dataname (str): Name of the data.\n polarity (int, optional): Polarity of the data. Defaults to -1.\n auto_process (bool, optional): Flag to automatically process the data. Defaults to True.\n data_type (str, optional): Type of the data. Defaults to Labels.simulated_profile.
\n\nReturns:\n MassSpecProfile: The created MassSpecProfile object.
\n", "signature": "(\tmz,\tabundance,\tdataname: str,\tpolarity: int = -1,\tauto_process: bool = True,\tdata_type: str = 'Simulated Profile'):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.numpyArray.ms_from_array_centroid", "modulename": "corems.mass_spectrum.input.numpyArray", "qualname": "ms_from_array_centroid", "kind": "function", "doc": "Create a MassSpecCentroid object from an array of m/z values, abundance values, resolution power, and signal-to-noise ratio.
\n\nParameters:\n mz (numpy.ndarray): Array of m/z values.\n abundance (numpy.ndarray): Array of abundance values.\n rp list(float): Resolution power.\n s2n list(float): Signal-to-noise ratio.\n dataname (str): Name of the data.\n polarity (int, optional): Polarity of the data. Defaults to -1.\n auto_process (bool, optional): Flag to automatically process the data. Defaults to True.
\n\nReturns:\n MassSpecCentroid: The created MassSpecCentroid object.
\n", "signature": "(\tmz,\tabundance,\trp: list[float],\ts2n: list[float],\tdataname: str,\tpolarity: int = -1,\tauto_process: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.numpyArray.get_output_parameters", "modulename": "corems.mass_spectrum.input.numpyArray", "qualname": "get_output_parameters", "kind": "function", "doc": "Get the output parameters for creating a MassSpecProfile or MassSpecCentroid object.
\n\nParameters:\n polarity (int): Polarity of the data.\n file_location (str): File location.
\n\nReturns:\n dict: Output parameters.
\n", "signature": "(polarity: int, file_location: str):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.win_only", "modulename": "corems.mass_spectrum.input.win_only", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output", "modulename": "corems.mass_spectrum.output", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output.export", "modulename": "corems.mass_spectrum.output.export", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport", "kind": "class", "doc": "A class for exporting high-resolution mass spectra.
\n\nParameters
\n\n\n- out_file_path (str):\nThe output file path.
\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n- output_type (str, optional):\nThe type of output file. Defaults to 'excel'. Can be 'excel', 'csv', 'pandas' or 'hdf5'.
\n
\n\nAttributes
\n\n\n- output_file (Path):\nThe output file path.
\n- output_type (str):\nThe type of output file.
\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n- atoms_order_list (list):\nThe list of assigned atoms in the order specified by Atoms.atoms_order list.
\n- columns_label (list):\nThe column labels in order.
\n
\n\nMethods
\n\n\n- save().\nSave the mass spectrum data to the output file.
\n- run().\nRun the export process.
\n- get_pandas_df().\nReturns the mass spectrum data as a pandas DataFrame.
\n- write_settings(output_path, mass_spectrum).\nWrites the settings of the mass spectrum to a JSON file.
\n- to_pandas(write_metadata=True).\nExports the mass spectrum data to a pandas DataFrame and saves it as a pickle file.
\n- to_excel(write_metadata=True).\nExports the mass spectrum data to an Excel file.
\n- to_csv(write_metadata=True).\nExports the mass spectrum data to a CSV file.
\n- to_json().\nExports the mass spectrum data to a JSON string.
\n- to_hdf().\nExports the mass spectrum data to an HDF5 file.
\n- parameters_to_toml().\nConverts the mass spectrum parameters to a TOML string.
\n- parameters_to_json().\nConverts the mass spectrum parameters to a JSON string.
\n- get_mass_spec_attrs(mass_spectrum).\nReturns the mass spectrum attributes as a dictionary.
\n- get_all_used_atoms_in_order(mass_spectrum).\nReturns the list of assigned atoms in the order specified by Atoms.atoms_order list.
\n- list_dict_to_list(mass_spectrum, is_hdf5=False).\nReturns the mass spectrum data as a list of dictionaries.
\n- get_list_dict_data(mass_spectrum, include_no_match=True, include_isotopologues=True, isotopologue_inline=True, no_match_inline=False, is_hdf5=False).\nReturns the mass spectrum data as a list of dictionaries.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.__init__", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(out_file_path, mass_spectrum, output_type='excel')"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.output_file", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.output_file", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.output_type", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.output_type", "kind": "variable", "doc": "Returns the output type of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.mass_spectrum", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.atoms_order_list", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.atoms_order_list", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.save", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.save", "kind": "function", "doc": "Save the mass spectrum data to the output file.
\n\nRaises
\n\n\n- ValueError: If the output type is not supported.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.run", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.run", "kind": "function", "doc": "Run the export process.
\n\nThis method is called when the thread starts.\nIt calls the save method to perform the export.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.get_pandas_df", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.get_pandas_df", "kind": "function", "doc": "Returns the mass spectrum data as a pandas DataFrame.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.write_settings", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.write_settings", "kind": "function", "doc": "Writes the settings of the mass spectrum to a JSON file.
\n\nParameters
\n\n\n- output_path (str):\nThe output file path.
\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n
\n", "signature": "(self, output_path, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.to_pandas", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.to_pandas", "kind": "function", "doc": "Exports the mass spectrum data to a pandas DataFrame and saves it as a pickle file.
\n\nParameters
\n\n\n- write_metadata (bool, optional):\nWhether to write the metadata to a JSON file. Defaults to True.
\n
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.to_excel", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.to_excel", "kind": "function", "doc": "Exports the mass spectrum data to an Excel file.
\n\nParameters
\n\n\n- write_metadata (bool, optional):\nWhether to write the metadata to a JSON file. Defaults to True.
\n
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.to_csv", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.to_csv", "kind": "function", "doc": "Exports the mass spectrum data to a CSV file.
\n\nParameters
\n\n\n- write_metadata (bool, optional):\nWhether to write the metadata to a JSON file. Defaults to True.
\n
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.to_json", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.to_json", "kind": "function", "doc": "Exports the mass spectrum data to a JSON string.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.to_hdf", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.to_hdf", "kind": "function", "doc": "Exports the mass spectrum data to an HDF5 file.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.parameters_to_toml", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.parameters_to_toml", "kind": "function", "doc": "Converts the mass spectrum parameters to a TOML string.
\n\nReturns
\n\n\n- str: The TOML string of the mass spectrum parameters.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.parameters_to_json", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.parameters_to_json", "kind": "function", "doc": "Converts the mass spectrum parameters to a JSON string.
\n\nReturns
\n\n\n- str: The JSON string of the mass spectrum parameters.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.get_mass_spec_attrs", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.get_mass_spec_attrs", "kind": "function", "doc": "Returns the mass spectrum attributes as a dictionary.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n
\n\nReturns
\n\n\n- dict: The mass spectrum attributes.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.get_all_used_atoms_in_order", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.get_all_used_atoms_in_order", "kind": "function", "doc": "Returns the list of assigned atoms in the order specified by Atoms.atoms_order list.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n
\n\nReturns
\n\n\n- list: The list of assigned atoms in the order specified by Atoms.atoms_order list.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.list_dict_to_list", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.list_dict_to_list", "kind": "function", "doc": "Returns the mass spectrum data as a list of dictionaries.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n- is_hdf5 (bool, optional):\nWhether the mass spectrum is being exported to an HDF5 file. Defaults to False.
\n
\n\nReturns
\n\n\n- list: The mass spectrum data as a list of dictionaries.
\n
\n", "signature": "(self, mass_spectrum, is_hdf5=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.get_list_dict_data", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.get_list_dict_data", "kind": "function", "doc": "Returns the mass spectrum data as a list of dictionaries.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n- include_no_match (bool, optional):\nWhether to include unassigned (no match) data. Defaults to True.
\n- include_isotopologues (bool, optional):\nWhether to include isotopologues. Defaults to True.
\n- isotopologue_inline (bool, optional):\nWhether to include isotopologues inline. Defaults to True.
\n- no_match_inline (bool, optional):\nWhether to include unassigned (no match) data inline. Defaults to False.
\n- is_hdf5 (bool, optional):\nWhether the mass spectrum is being exported to an HDF5 file. Defaults to False.
\n
\n\nReturns
\n\n\n- list: The mass spectrum data as a list of dictionaries.
\n
\n", "signature": "(\tself,\tmass_spectrum,\tinclude_no_match=True,\tinclude_isotopologues=True,\tisotopologue_inline=True,\tno_match_inline=False,\tis_hdf5=False):", "funcdef": "def"}, {"fullname": "corems.molecular_formula", "modulename": "corems.molecular_formula", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.calc", "modulename": "corems.molecular_formula.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.calc.MolecularFormulaCalc", "modulename": "corems.molecular_formula.calc.MolecularFormulaCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.calc.MolecularFormulaCalc.MolecularFormulaCalc", "modulename": "corems.molecular_formula.calc.MolecularFormulaCalc", "qualname": "MolecularFormulaCalc", "kind": "class", "doc": "Class of calculations related to molecular formula
\n\nThis class is not intended to be used directly, but rather to be inherited by other classes in the molecular_formula/factory module like MolecularFormula, MolecularFormulaIsotopologue, and LCMSLibRefMolecularFormula
\n\nAttributes
\n\n\n- mz_calc (float):\nThe m/z value of the molecular formula.
\n- neutral_mass (float):\nThe neutral mass of the molecular formula.
\n- ion_charge (int):\nThe ion charge of the molecular formula.
\n- _external_mz (float):\nThe externally provided m/z value of the molecular formula.
\n- _d_molecular_formula (dict):\nThe dictionary representation of the molecular formula.
\n- _mspeak_parent (object):\nThe parent MS peak object associated with the molecular formula.
\n- _assignment_mass_error (float):\nThe mass error of the molecular formula.
\n
\n\nMethods
\n\n\n- _calc_resolving_power_low_pressure(B, T) \nCalculate the resolving power at low pressure.
\n- _calc_resolving_power_high_pressure(B, T)\nCalculate the resolving power at high pressure.
\n- _adduct_mz(adduct_atom, ion_charge)\nGet the m/z value of an adducted ion version of the molecular formula.
\n- _protonated_mz(ion_charge)\nGet the m/z value of a protonated or deprotonated ion version of the molecular formula.
\n- _radical_mz(ion_charge)\nGet the m/z value of a radical ion version of the molecular formula.
\n- _neutral_mass()\nGet the neutral mass of the molecular formula.
\n- _calc_mz()\nGet the m/z value of the molecular formula.
\n- _calc_assignment_mass_error(method='ppm')\nCalculate the mass error of the molecular formula.
\n- _calc_mz_confidence(mean=0)\nCalculate the m/z confidence of the molecular formula.
\n- _calc_isotopologue_confidence()\nCalculate the isotopologue confidence of the molecular formula.
\n- normalize_distance(dist, dist_range)\nNormalize the distance value.
\n- subtract_formula(formula_obj, formated=True)\nSubtract a formula from the current formula object.
\n- _calc_average_mz_score()\nCalculate the average m/z error score of the molecular formula identification, including the isotopologues.
\n
\n"}, {"fullname": "corems.molecular_formula.calc.MolecularFormulaCalc.MolecularFormulaCalc.normalize_distance", "modulename": "corems.molecular_formula.calc.MolecularFormulaCalc", "qualname": "MolecularFormulaCalc.normalize_distance", "kind": "function", "doc": "Normalize the distance value.
\n\nParameters
\n\n\n- dist (float):\nThe distance value to be normalized.
\n- dist_range (list):\nThe range of the distance value.
\n
\n", "signature": "(self, dist, dist_range):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.calc.MolecularFormulaCalc.MolecularFormulaCalc.subtract_formula", "modulename": "corems.molecular_formula.calc.MolecularFormulaCalc", "qualname": "MolecularFormulaCalc.subtract_formula", "kind": "function", "doc": "Subtract a formula from the current formula object
\n\nParameters
\n\n\n- formula_obj (MolecularFormula):\nMolecularFormula object to be subtracted from the current formula object
\n- formated (bool, optional):\nIf True, returns the formula in string format, by default True
\n
\n", "signature": "(self, formula_obj, formated=True):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.calc.MolecularFormulaCalc.MolecularFormulaCalc.dbe_ai", "modulename": "corems.molecular_formula.calc.MolecularFormulaCalc", "qualname": "MolecularFormulaCalc.dbe_ai", "kind": "variable", "doc": "Calculate the double bond equivalent (DBE) of the molecular formula, based on the number of carbons, hydrogens, and oxygens.
\n"}, {"fullname": "corems.molecular_formula.factory", "modulename": "corems.molecular_formula.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase", "kind": "class", "doc": "Base class for representing a molecular formula.
\n\nParameters
\n\n\n- molecular_formula (dict, list, str):\nThe molecular formula.
\n- ion_charge (int):\nThe ion charge.
\n- ion_type (str, optional):\nThe ion type. Defaults to None.
\n- adduct_atom (str, optional):\nThe adduct atom. Defaults to None.
\n- mspeak_parent (_MSPeak, optional):\nThe parent mass spectrum peak object instance. Defaults to None.
\n- external_mz (float, optional):\nThe external m/z value. Defaults to None.
\n
\n\nRaises
\n\n\n- TypeError: If the ion type is not 'DE_OR_PROTONATED', 'RADICAL' or 'ADDUCT'.
\n
\n\nAttributes
\n\n\n- isotopologue_count_percentile (float):\nThe isotopologue count percentile.
\n- O_C (float):\nThe O/C ratio.
\n- H_C (float):\nThe H/C ratio.
\n- dbe (float):\nThe double bond equivalent.
\n- mz_nominal_calc (int):\nThe nominal m/z value.
\n- mz_error (float):\nThe m/z error.
\n- mz_calc (float):\nThe m/z value.
\n- protonated_mz (float):\nThe protonated or deprotonated m/z value.
\n- radical_mz (float):\nThe radical m/z value.
\n- neutral_mass (float):\nThe neutral mass.
\n- ion_type (str):\nThe ion type.
\n- ion_charge (int):\nThe ion charge.
\n- atoms (list):\nThe atoms in the molecular formula.
\n- confidence_score (float):\nThe confidence score of the molecular formula identification.
\n- isotopologue_similarity (float):\nThe isotopologue similarity score of the molecular formula identification.
\n- average_mz_error_score (float):\nThe average m/z error score of the molecular formula identification, including the isotopologues.
\n- mz_error_score (float):\nThe m/z error score of the molecular formula identification.
\n- kmd (float):\nThe Kendrick mass defect (KMD).
\n- kendrick_mass (float):\nThe Kendrick mass.
\n- knm (float):\nThe nominal Kendrick mass.
\n- string (str):\nThe molecular formula string.
\n- string_formated (str):\nThe molecular formula string formated with subscripts and superscripts.
\n- class_label (str):\nThe class label.
\n- class_dict (dict):\nThe class dictionary.
\n
\n\nMethods
\n\n\n- change_kendrick_base(kendrick_dict_base).\nChange the Kendrick base.
\n- isotopologues(min_abundance, current_mono_abundance, dynamic_range).\nCalculate the isotopologues.
\n- atoms_qnt(atom).\nGet the atom quantity.
\n- atoms_symbol(atom).\nGet the atom symbol without the mass number.
\n- to_dict().\nGet the molecular formula as a dictionary.
\n- to_list().\nGet the molecular formula as a list.
\n
\n", "bases": "corems.molecular_formula.calc.MolecularFormulaCalc.MolecularFormulaCalc"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.__init__", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.__init__", "kind": "function", "doc": "\n", "signature": "(\tmolecular_formula,\tion_charge,\tion_type=None,\tadduct_atom=None,\tmspeak_parent=None,\texternal_mz=None)"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.is_isotopologue", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.is_isotopologue", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.expected_isotopologues", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.expected_isotopologues", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.mspeak_mf_isotopologues_indexes", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.mspeak_mf_isotopologues_indexes", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.get", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.get", "kind": "function", "doc": "Get the atom quantity of a specific atom.
\n\nParameters
\n\n\n- atom (str):\nThe atom symbol.
\n
\n\nReturns
\n\n\n- int: The atom quantity.
\n
\n", "signature": "(self, atom):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.split", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.split", "kind": "function", "doc": "Splits the molecular formula string.
\n\nParameters
\n\n\n- delimiters (list):\nThe list of delimiters.
\n- string (str):\nThe molecular formula string.
\n- maxsplit (int, optional):\nThe maximum number of splits. Defaults to 0.
\n
\n\nReturns
\n\n\n- list: The molecular formula list.
\n
\n\nNotes
\n\nDoes not work when formula has atoms with same characters in a row that below to different atoms, i.e. C10H21NNa.
\n", "signature": "(self, delimiters, string, maxsplit=0):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.isotopologue_count_percentile", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.isotopologue_count_percentile", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.O_C", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.O_C", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.H_C", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.H_C", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.dbe", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.dbe", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.mz_nominal_calc", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.mz_nominal_calc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.mz_error", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.mz_error", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.mz_calc", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.mz_calc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.protonated_mz", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.protonated_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.radical_mz", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.radical_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.neutral_mass", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.neutral_mass", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.adduct_mz", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.adduct_mz", "kind": "function", "doc": "Get m/z of an adducted ion version of the molecular formula.
\n\nParameters
\n\n\n- adduct_atom (str):\nThe adduct atom.
\n
\n\nReturns
\n\n\n- float: The m/z value of the adducted ion version of the molecular formula.
\n
\n", "signature": "(self, adduct_atom):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.ion_type", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.ion_type", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.ion_charge", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.ion_charge", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.atoms", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.atoms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.confidence_score", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.confidence_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.isotopologue_similarity", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.isotopologue_similarity", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.average_mz_error_score", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.average_mz_error_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.mz_error_score", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.mz_error_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.kmd", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.kmd", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.kendrick_mass", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.kendrick_mass", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.knm", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.knm", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.change_kendrick_base", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.change_kendrick_base", "kind": "function", "doc": "Change the Kendrick base.
\n\nParameters
\n\n\n- kendrick_dict_base (dict):\nThe Kendrick base dictionary. Ex: {\"C\": 1, \"H\": 2}
\n
\n", "signature": "(self, kendrick_dict_base):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.isotopologues", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.isotopologues", "kind": "function", "doc": "Calculate the isotopologues for a given molecular formula.
\n\nParameters
\n\n\n- min_abundance (float):\nThe minimum abundance.
\n- current_mono_abundance (float):\nThe current monoisotopic abundance.
\n- dynamic_range (float):\nThe dynamic range.
\n
\n\nYields
\n\n\n- MolecularFormulaIsotopologue: The molecular formula isotopologue.
\n
\n\nNotes
\n\nThis calculation ignores the hydrogen isotopes.
\n", "signature": "(self, min_abundance, current_mono_abundance, dynamic_range):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.atoms_qnt", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.atoms_qnt", "kind": "function", "doc": "Get the atom quantity of a specific atom in the molecular formula.
\n", "signature": "(self, atom):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.atoms_symbol", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.atoms_symbol", "kind": "function", "doc": "Get the atom symbol without the mass number.
\n", "signature": "(self, atom):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.string", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.string", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.string_formated", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.string_formated", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.to_dict", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.to_dict", "kind": "function", "doc": "Returns the molecular formula as a dictionary.
\n\nReturns
\n\n\n- dict: The molecular formula as a dictionary.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.to_list", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.to_list", "kind": "function", "doc": "Returns the molecular formula as a list.
\n\nReturns
\n\n\n- list: The molecular formula as a list.
\n
\n\nRaises
\n\n\n- Exception: If the molecular formula identification was not performed yet.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.class_label", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.class_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.class_dict", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.class_dict", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue", "kind": "class", "doc": "Class for representing a molecular formula isotopologue.
\n\nParameters
\n\n\n- _d_molecular_formula (dict):\nThe molecular formula as a dictionary.
\n- prob_ratio (float):\nThe probability ratio.
\n- mono_abundance (float):\nThe monoisotopic abundance.
\n- ion_charge (int):\nThe ion charge.
\n- mspeak_parent (object, optional):\nThe parent mass spectrum peak object instance. Defaults to None.
\n
\n\nAttributes
\n\n\n- prob_ratio (float):\nThe probability ratio.
\n- abundance_calc (float):\nThe calculated abundance.
\n- area_error (float):\nThe area error.
\n- abundance_error (float):\nThe abundance error.
\n- is_isotopologue (bool):\nThe isotopologue flag. Defaults to True.
\n- mspeak_index_mono_isotopic (int):\nThe index of the monoisotopic peak in the mass spectrum peak list. Defaults to None.
\n- mono_isotopic_formula_index (int):\nThe index of the monoisotopic formula in the molecular formula list. Defaults to None.
\n
\n", "bases": "MolecularFormulaBase"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.__init__", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.__init__", "kind": "function", "doc": "\n", "signature": "(\t_d_molecular_formula,\tprob_ratio,\tmono_abundance,\tion_charge,\tmspeak_parent=None)"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.prob_ratio", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.prob_ratio", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.abundance_calc", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.abundance_calc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.is_isotopologue", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.is_isotopologue", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.mspeak_index_mono_isotopic", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.mspeak_index_mono_isotopic", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.mono_isotopic_formula_index", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.mono_isotopic_formula_index", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.area_error", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.area_error", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.abundance_error", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.abundance_error", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "LCMSLibRefMolecularFormula", "kind": "class", "doc": "Class for representing a molecular formula associated with a molecule in a LCMS library reference.
\n\nParameters
\n\n\n- molecular_formula (dict, list, str):\nThe molecular formula.
\n- ion_charge (int):\nThe ion charge.
\n- ion_type (str, optional):\nThe ion type. Defaults to None.
\n- adduct_atom (str, optional):\nThe adduct atom. Defaults to None.
\n- mspeak_parent (object, optional):\nThe parent mass spectrum peak object instance. Defaults to None.
\n- name (str, optional):\nThe name of the reference molecule. Defaults to None.
\n- kegg_id (str, optional):\nThe KEGG ID of the reference molecule. Defaults to None.
\n- cas (str, optional):\nThe CAS number of the reference molecule. Defaults to None.
\n
\n", "bases": "MolecularFormulaBase"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula.__init__", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "LCMSLibRefMolecularFormula.__init__", "kind": "function", "doc": "\n", "signature": "(\tmolecular_formula,\tion_charge,\tion_type=None,\tadduct_atom=None,\tmspeak_parent=None,\tname=None,\tkegg_id=None,\tcas=None)"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula.name", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "LCMSLibRefMolecularFormula.name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula.kegg_id", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "LCMSLibRefMolecularFormula.kegg_id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula.cas", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "LCMSLibRefMolecularFormula.cas", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormula", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormula", "kind": "class", "doc": "General class for representing a molecular formula.
\n\nParameters
\n\n\n- molecular_formula (dict, list, str):\nThe molecular formula.
\n- ion_charge (int):\nThe ion charge.
\n- ion_type (str, optional):\nThe ion type. Defaults to None.
\n- adduct_atom (str, optional):\nThe adduct atom. Defaults to None.
\n- mspeak_parent (object, optional):\nThe parent mass spectrum peak object instance. Defaults to None.
\n- external_mz (float, optional):\nThe external m/z value. Defaults to False.
\n
\n", "bases": "MolecularFormulaBase"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormula.__init__", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormula.__init__", "kind": "function", "doc": "\n", "signature": "(\tmolecular_formula,\tion_charge,\tion_type=None,\tadduct_atom=None,\tmspeak_parent=None,\texternal_mz=False)"}, {"fullname": "corems.molecular_formula.input", "modulename": "corems.molecular_formula.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref", "modulename": "corems.molecular_formula.input.masslist_ref", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy", "kind": "class", "doc": "Proxy class for MolecularFormulaLink to be used in the molecular formula ref file import
\n\nParameters
\n\n\n- molecular_formula (MolecularFormula | LCMSLibRefMolecularFormula):\ncorems MolecularFormula or LCMSLibRefMolecularFormula object
\n- mz (float):\ntarget m/z
\n
\n\nAttributes
\n\n\n- C (int):\nnumber of carbon atoms
\n- H (int):\nnumber of hydrogen atoms
\n- H_C (float):\nratio of hydrogen to carbon atoms
\n- class_label (str):\nmolecular formula class label
\n- mz_calc (float):\ncalculated m/z
\n- dbe (int):\ndouble bond equivalent
\n- formula_dict (dict):\nmolecular formula dictionary
\n
\n\nMethods
\n\n\n- to_dict(). \nreturn molecular formula dictionary
\n
\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.__init__", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.__init__", "kind": "function", "doc": "\n", "signature": "(molecular_formula, mz)"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.C", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.C", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.H", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.H", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.H_C", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.H_C", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.class_label", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.class_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.mz_calc", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.mz_calc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.dbe", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.dbe", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.formula_dict", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.formula_dict", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.to_dict", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.to_dict", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef", "kind": "class", "doc": "Import Mass List from Reference File
\n\nParameters
\n\n\n- ref_file_location (str):\npath to the reference file
\n
\n\nAttributes
\n\n\n- ref_file_location (str):\npath to the reference file
\n
\n\nMethods
\n\n\n- molecular_formula_ref(mz, molecular_formula). \nReturn MolecularFormulaLinkProxy object
\n- from_lcms_lib_file(ion_charge, ion_types).\nReturn Dict[standard_name, Dict[m/z, List[MolecularFormula]]] from LCMS library reference file
\n- from_bruker_ref_file().\nReturn List[MolecularFormula] from Bruker reference file
\n- from_corems_ref_file(delimiter).\nReturn List[MolecularFormula] from CoreMS reference file
\n- split(delimiters, string, maxsplit).\nSplits a string using a list of delimiters.
\n- mformula_s_to_dict(s_mformulatring, iontype).\nConverts a molecular formula string to a dict
\n
\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.__init__", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.__init__", "kind": "function", "doc": "\n", "signature": "(ref_file_location)"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.ref_file_location", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.ref_file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.molecular_formula_ref", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.molecular_formula_ref", "kind": "function", "doc": "Instantiate a MolecularFormulaLinkProxy object
\n\nParameters
\n\n\n- mz (float):\ntarget m/z
\n- molecular_formula (MolecularFormula | LCMSLibRefMolecularFormula):\ncorems MolecularFormula or LCMSLibRefMolecularFormula object
\n
\n\nReturns
\n\n\n- MolecularFormulaLinkProxy: MolecularFormulaLinkProxy object
\n
\n", "signature": "(self, mz, molecular_formula):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.from_lcms_lib_file", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.from_lcms_lib_file", "kind": "function", "doc": "Create a dictionary of LCMSLibRefMolecularFormula objects from LCMS library reference file
\n\nParameters
\n\n\n- ion_charge (float):\nion charge
\n- ion_types (List[str]):\nlist of ion types
\n
\n\nReturns
\n\n\n- Dict: Dict[standard_name, Dict[m/z, List[MolecularFormula]]] from LCMS library reference file. m/z is the target m/z; standard_name is the name of the molecular standard mix; MolecularFormula is the corems molecular formula class
\n
\n", "signature": "(\tself,\tion_charge: float,\tion_types: List[str]) -> Dict[str, Dict[float, List[corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula]]]:", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.from_bruker_ref_file", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.from_bruker_ref_file", "kind": "function", "doc": "Create a list of MolecularFormula objects from Bruker reference file
\n\nReturns
\n\n\n- List[MolecularFormula]: List of MolecularFormula objects from Bruker reference file
\n
\n", "signature": "(\tself) -> List[corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormula]:", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.from_corems_ref_file", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.from_corems_ref_file", "kind": "function", "doc": "Create a list of MolecularFormula objects from CoreMS reference file
\n\nNot being used
\n\nParameters
\n\n\n- delimiter (str):\ndelimiter used in the reference file
\n
\n\nReturns
\n\n\n- List[MolecularFormula]: List of MolecularFormula objects from CoreMS reference file
\n
\n", "signature": "(self, delimiter='\\t'):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.split", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.split", "kind": "function", "doc": "Splits a string using a list of delimiters.
\n\nDoes not work when formula has atoms with same characters, i.e - C10H21NNa
\n\nParameters
\n\n\n- delimiters (list):\nlist of delimiters
\n- string (str):\nstring to be split
\n- maxsplit (int, optional):\nmaximum number of splits. Default is 0
\n
\n\nReturns
\n\n\n- list: list of strings obtained after splitting the string
\n- list: list of counts obtained after splitting the string
\n
\n", "signature": "(self, delimiters, string, maxsplit=0):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.mformula_s_to_dict", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.mformula_s_to_dict", "kind": "function", "doc": "Converts a molecular formula string to a dict
\n\nParameters
\n\n\n- s_mformulatring (str):\nmolecular formula string, i.e. 'C10H21NNa'
\n- iontype (str, optional):\nion type. Default is 'unknown'
\n
\n\nReturns
\n\n\n- dict: molecular formula dictionary
\n
\n\nNotes
\n\nDoes not work if the atomic mass number is passed i.e. 37Cl, 81Br, convention follow the light isotope labeling 35Cl is Cl, 12C is C, etc.\nIf you need to use heavy isotopes please use another reference file format that separate the formula string by a blank space and parse it using the function corems_ref_file
\n\nRaises
\n\n\n- TypeError: Atom does not exist in Atoms.atoms_order list
\n- Exception: Empty molecular formula
\n
\n", "signature": "(self, s_mformulatring, iontype='unknown'):", "funcdef": "def"}, {"fullname": "corems.molecular_id", "modulename": "corems.molecular_id", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc", "modulename": "corems.molecular_id.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.ClusterFilter", "modulename": "corems.molecular_id.calc.ClusterFilter", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter", "kind": "class", "doc": "Class for filtering and clustering mass spectra data using various algorithms.
\n\nAttributes
\n\n\n- mass_spectrum (MassSpectrum):\nMass spectrum object.
\n- ms_peaks (list):\nList of mass peaks.
\n- ms_peak_indexes (list):\nList of peak indexes.
\n- min_samples (int):\nMinimum number of samples in a cluster.
\n- eps (float):\nThe maximum distance between two samples for one to be considered as in the neighborhood of the other.
\n- bandwidth (float):\nBandwidth used in MeanShift algorithm.
\n- quantile (float):\nQuantile used in estimate_bandwidth function.
\n- n_samples (int):\nNumber of samples used in estimate_bandwidth function.
\n- bin_seeding (bool):\nIf true, initial kernel locations are not locations of all points, but rather the location of the discretized version of points, where points are binned onto a grid whose coarseness corresponds to the bandwidth. Setting this option to True will speed up the algorithm because fewer seeds will be initialized.
\n- min_peaks_per_class (int):\nMinimum number of peaks per class.
\n
\n\nMethods
\n\n\n- get_mass_error_matrix_data(ms_peaks).\nGet the mass error matrix data from a list of mass peaks.
\n- get_kendrick_matrix_data(mass_spectrum).\nGet the Kendrick matrix data from a mass spectrum.
\n- filter_kendrick(mass_spectrum).\nFilter the mass spectrum data using the Kendrick algorithm.
\n- filter_kendrick_by_index(ms_peak_indexes, mass_spectrum_obj).\nFilter the mass spectrum data using the Kendrick algorithm based on a list of peak indexes.
\n- remove_assignment_by_mass_error(mass_spectrum).\nRemove assignments from the mass spectrum based on mass error.
\n
\n"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter.get_mass_error_matrix_data", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter.get_mass_error_matrix_data", "kind": "function", "doc": "Get the mass error matrix data from a list of mass peaks.
\n\nParameters
\n\n\n- ms_peaks (list):\nList of mass peaks.
\n
\n\nReturns
\n\n\n- matrix_data (ndarray):\nMatrix data containing mass and error values.
\n- list_indexes_mass_spec (list):\nList of indexes of mass peaks in the original mass spectrum.
\n
\n", "signature": "(self, ms_peaks):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter.get_kendrick_matrix_data", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter.get_kendrick_matrix_data", "kind": "function", "doc": "Get the Kendrick matrix data from a mass spectrum.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nMass spectrum object.
\n
\n\nReturns
\n\n\n- matrix_data (ndarray):\nMatrix data containing Kendrick mass and Kendrick mass defect values.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter.filter_kendrick", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter.filter_kendrick", "kind": "function", "doc": "Filter the mass spectrum data using the Kendrick algorithm.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nMass spectrum object.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter.filter_kendrick_by_index", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter.filter_kendrick_by_index", "kind": "function", "doc": "Filter the mass spectrum data using the Kendrick algorithm based on a list of peak indexes.
\n\nParameters
\n\n\n- ms_peak_indexes (list):\nList of peak indexes.
\n- mass_spectrum_obj (MassSpectrum):\nMass spectrum object.
\n
\n\nReturns
\n\n\n- noise_idx (list):\nList of indexes of noise points in the mass spectrum.
\n
\n", "signature": "(self, ms_peak_indexes, mass_spectrum_obj):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter.remove_assignment_by_mass_error", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter.remove_assignment_by_mass_error", "kind": "function", "doc": "Remove assignments from the mass spectrum based on mass error.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nMass spectrum object.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.KendrickGroup", "modulename": "corems.molecular_id.calc.KendrickGroup", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.MolecularFilter", "modulename": "corems.molecular_id.calc.MolecularFilter", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.MolecularFilter.MolecularFormulaSearchFilters", "modulename": "corems.molecular_id.calc.MolecularFilter", "qualname": "MolecularFormulaSearchFilters", "kind": "class", "doc": "Class containing static methods for filtering molecular formulas in a mass spectrum.
\n\nMethods
\n\n\n- filter_kendrick(ms_peak_indexes, mass_spectrum_obj).
\nApply Kendrick filter to the mass spectrum. \n- check_min_peaks(ms_peak_indexes, mass_spectrum_obj).
\nCheck if the number of peaks per class meets the minimum requirement. \n- filter_isotopologue(ms_peak_indexes, mass_spectrum_obj).
\nApply isotopologue filter to the mass spectrum. \n
\n"}, {"fullname": "corems.molecular_id.calc.MolecularFilter.MolecularFormulaSearchFilters.filter_kendrick", "modulename": "corems.molecular_id.calc.MolecularFilter", "qualname": "MolecularFormulaSearchFilters.filter_kendrick", "kind": "function", "doc": "Apply Kendrick filter to the mass spectrum.
\n\nParameters
\n\n\n- ms_peak_indexes (list):\nList of peak indexes and their associated molecular formula objects.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n
\n\nReturns
\n\n\n- filtered_ms_peak_indexes (list):\nList of peak indexes and their associated molecular formula objects after applying the Kendrick filter.
\n
\n", "signature": "(ms_peak_indexes, mass_spectrum_obj):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.MolecularFilter.MolecularFormulaSearchFilters.check_min_peaks", "modulename": "corems.molecular_id.calc.MolecularFilter", "qualname": "MolecularFormulaSearchFilters.check_min_peaks", "kind": "function", "doc": "Check if the number of peaks per class meets the minimum requirement.
\n\nParameters
\n\n\n- ms_peak_indexes (list):\nList of peak indexes and their associated molecular formula objects.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n
\n", "signature": "(ms_peak_indexes, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.MolecularFilter.MolecularFormulaSearchFilters.filter_isotopologue", "modulename": "corems.molecular_id.calc.MolecularFilter", "qualname": "MolecularFormulaSearchFilters.filter_isotopologue", "kind": "function", "doc": "Apply isotopologue filter to the mass spectrum.
\n\nParameters
\n\n\n- ms_peak_indexes (list):\nList of peak indexes and their associated molecular formula objects.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n
\n\nReturns
\n\n\n- filtered_ms_peak_indexes (list):\nList of peak indexes and their associated molecular formula objects after applying the isotopologue filter.
\n
\n", "signature": "(ms_peak_indexes, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.methods_name", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "methods_name", "kind": "variable", "doc": "\n", "default_value": "{'chebyshev_distance': 'Chebyshev Distance', 'squared_euclidean_distance': 'Squared Euclidean Distance', 'fidelity_similarity': 'Fidelity Similarity', 'matusita_distance': 'Matusita Distance', 'squared_chord_distance': 'Squared-chord Distance', 'harmonic_mean_similarity': 'Harmonic mean Distance', 'Pearson_chi_squared_distance': 'Pearson Chi Squared Distance', 'Neyman_chi_squared_distance': 'Neyman Chi Squared Distance', 'probabilistic_symmetric_chi_squared_distance': 'Probabilistic symmetric X2 Distance', 'topsoe_distance': 'Topsoe Distance', 'chernoff_distance': 'Chernoff Distance', 'ruzicka_distance': 'Ruzicka Distance', 'roberts_distance': 'Roberts Distance', 'motyka_distance': 'Motyka Distance', 'canberra_distance': 'Canberra Distance', 'canberra_metric': 'Canberra Metric', 'kulczynski_1_distance': 'Kulczynski 1 Distance', 'lorentzian_distance': 'Lorentzian Distance', 'clark_distance': 'Clark Distance', 'hellinger_distance': 'Hellinger Distance', 'whittaker_index_of_association_distance': 'Whittaker index of association Distance', 'spectral_contrast_angle_distance': 'Spectral Contrast Angle', 'wave_hedges_distance': 'Wave Hedges Distance', 'dice_similarity': 'Dice Similarity', 'inner_product_distance': 'Inner Product Distance', 'divergence_distance': 'Divergence Distance', 'jensen_difference_distance': 'Jensen Differences Distance', 'kumar_johnson_distance': 'Kumar Johnson Distance', 'avg_l_distance': 'Avg (L1, L8) Distance', 'vicis_wave_hadges_distance': 'Vicis Wave Hadges Distance', 'vicis_symmetric_chi_squared_1_distance': 'Vicis-Symmetric X2 1 Distance', 'vicis_symmetric_chi_squared_2_distance': 'Vicis-Symmetric X2 2 Distance', 'vicis_symmetric_chi_squared_3_distance': 'Vicis-Symmetric X2 3 Distance', 'max_symmetric_chi_squared_distance': 'Max Symmetric Chi Squared Distance', 'min_symmetric_chi_squared_distance': 'Min Symmetric Chi Squared Distance', 'additive_sym_chi_sq': 'Additive Symmetric Chi Squared', 'bhattacharya_distance': 'Battacharya Distance', 'generalized_ochiai_index': 'Generalized Ochiai Index', 'gower_distance': 'Gower Distance', 'impr_sqrt_cosine_sim': 'Improved Square Root Cosine Similarity', 'intersection_sim': 'Intersection Similarity', 'j_divergence': 'J Divergence', 'jensen_shannon_index': 'Jensen Shannon Index', 'k_divergence': 'K Divergence', 'VW6': 'VW6', 'VW5': 'VW5', 'VW4': 'VW4', 'VW3': 'VW3', 'VW2': 'VW2', 'VW1': 'VW1', 'taneja_divergence': 'Taneja Divergence', 'symmetric_chi_squared_distance': 'Symmetric Chi Squared Distance', 'squared_chi_squared_distance': 'Squared Chi Squared Distance', 'square_root_cosine_correlation': 'Square Root Cosine Correlation', 'sorensen_distance': 'Sorensen Distance', 'Minokowski_3': 'Minokowski 3 Distance', 'Minokowski_4': 'Minokowski 4 Distance', 'kumarjohnson_divergence': 'Kumar Johnson Divergence', 'kumarhassebrook_similarity': 'Kumar Hassebrook Similarity', 'kullbackleibler_divergence': 'Kullback Leibler Divergence', 'soergel_distance': 'Soergel Distance'}"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.methods_scale", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "methods_scale", "kind": "variable", "doc": "\n", "default_value": "{'entropy': [0, 1.3862943611198906], 'weighted_entropy': [0, 1.3862943611198906], 'absolute_value': [0, 2], 'avg_l': [0, 1.5], 'bhattacharya_1': [0, 2.4674011002723395], 'bhattacharya_2': [0, inf], 'canberra': [0, inf], 'clark': [0, inf], 'divergence': [0, inf], 'euclidean': [0, 1.4142135623730951], 'hellinger': [0, inf], 'improved_similarity': [0, inf], 'lorentzian': [0, inf], 'manhattan': [0, 2], 'matusita': [0, 1.4142135623730951], 'mean_character': [0, 2], 'motyka': [-0.5, 0], 'ms_for_id': [-inf, 0], 'ms_for_id_v1': [0, inf], 'pearson_correlation': [-1, 1], 'penrose_shape': [0, 1.4142135623730951], 'penrose_size': [0, inf], 'probabilistic_symmetric_chi_squared': [0, 1], 'similarity_index': [0, inf], 'squared_chord': [0, 2], 'squared_euclidean': [0, 2], 'symmetric_chi_squared': [0, 0.7071067811865476], 'topsoe': [0, 1.4142135623730951], 'vicis_symmetric_chi_squared_3': [0, 2], 'wave_hedges': [0, inf], 'whittaker_index_of_association': [0, inf]}"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity", "kind": "class", "doc": "Class containing methods for calculating spectral similarity between two mass spectra.
\n\nParameters
\n\n\n- ms_mz_abun_dict (dict):\nDictionary of mass to abundance values for the experimental mass spectrum.
\n- ref_obj (dict):\nDictionary of mass to abundance values for the reference mass spectrum.
\n- norm_func (function):\nFunction to normalize the abundance values.
\n
\n\nAttributes
\n\n\n- normalize_func (function):\nFunction to normalize the abundance values.
\n- ms_mz_abun_dict (dict):\nDictionary of mass to abundance values for the experimental mass spectrum.
\n- ref_obj (dict):\nDictionary of mass to abundance values for the reference mass spectrum.
\n- exp_abun (list):\nList of abundance values for the experimental mass spectrum.
\n- exp_mz (list):\nList of mass values for the experimental mass spectrum.
\n- ref_mz (list):\nList of mass values for the reference mass spectrum.
\n- ref_abun (list):\nList of abundance values for the reference mass spectrum.
\n- ref_mz_abun_dict (dict):\nDictionary of mass to abundance values for the reference mass spectrum.
\n- df (DataFrame):\nDataFrame containing the experimental and reference mass spectrum data.
\n- zero_filled_u_l (tuple):\nTuple containing the experimental and reference mass spectrum data after zero filling and normalization.
\n- common_mz_values (list):\nList of common mass values between the experimental and reference mass spectra.
\n- n_x_y (int):\nNumber of common mass values between the experimental and reference mass spectra.
\n
\n\nMethods
\n\n\n- nan_fill(df, fill_with=0).\nFill missing mass values with a given value.
\n- normalize(x, y, norm_func=sum).\nNormalize the abundance values.
\n- weighted_cosine_correlation(a=0.5, b=1.3, nanfill=1e-10).\nCalculate the weighted cosine correlation between the experimental and reference mass spectra.
\n- cosine_correlation().\nCalculate the cosine correlation between the experimental and reference mass spectra.
\n- stein_scott().\nCalculate the Stein-Scott similarity between the experimental and reference mass spectra.
\n- pearson_correlation().\nCalculate the Pearson correlation between the experimental and reference mass spectra.
\n- spearman_correlation().\nCalculate the Spearman correlation between the experimental and reference mass spectra.
\n
\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.__init__", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.__init__", "kind": "function", "doc": "\n", "signature": "(ms_mz_abun_dict, ref_obj, norm_func=<built-in function sum>)"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.normalize_func", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.normalize_func", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.ms_mz_abun_dict", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.ms_mz_abun_dict", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.ref_obj", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.ref_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.exp_abun", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.exp_abun", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.exp_mz", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.exp_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.ref_mz", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.ref_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.ref_abun", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.ref_abun", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.ref_mz_abun_dict", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.ref_mz_abun_dict", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.df", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.df", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.zero_filled_u_l", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.zero_filled_u_l", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.common_mz_values", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.common_mz_values", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.n_x_y", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.n_x_y", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.nan_fill", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.nan_fill", "kind": "function", "doc": "Fill missing mass values with a given value.
\n\nParameters
\n\n\n- df (DataFrame):\nDataFrame containing the experimental and reference mass spectrum data.
\n- fill_with (float):\nValue to fill missing mass values with.
\n
\n\nReturns
\n\n\n- x (list):\nList of abundance values for the experimental mass spectrum.
\n- y (list):\nList of abundance values for the reference mass spectrum.
\n
\n", "signature": "(self, df, fill_with=0):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.normalize", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.normalize", "kind": "function", "doc": "Normalize the abundance values.
\n\nParameters
\n\n\n- x (list):\nList of abundance values for the experimental mass spectrum.
\n- y (list):\nList of abundance values for the reference mass spectrum.
\n- norm_func (function):\nFunction to normalize the abundance values.\nDefault is sum
\n
\n\nReturns
\n\n\n- u_l (tuple):\nTuple containing the experimental and reference mass spectrum data after zero filling and normalization.
\n
\n", "signature": "(self, x, y, norm_func=<built-in function sum>):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.weighted_cosine_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.weighted_cosine_correlation", "kind": "function", "doc": "Calculate the weighted cosine correlation between the experimental and reference mass spectra.
\n\nParameters
\n\n\n- a (float):\nWeighting factor for the abundance values.\nDefault is 0.5
\n- b (float):\nWeighting factor for the mass values.\nDefault is 1.3
\n- nanfill (float):\nValue to fill missing mass values with.\nDefault is 1e-10
\n
\n\nReturns
\n\n\n- correlation (float):\nWeighted cosine correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self, a=0.5, b=1.3, nanfill=1e-10):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.cosine_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.cosine_correlation", "kind": "function", "doc": "Calculate the cosine correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nCosine correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.stein_scott", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.stein_scott", "kind": "function", "doc": "Calculate the Stein-Scott similarity between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- s_ss_x_y (float):\nStein-Scott similarity between the experimental and reference mass spectra.
\n- s_ss_x_y_nist (float):\nStein-Scott similarity between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.pearson_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.pearson_correlation", "kind": "function", "doc": "Calculate the Pearson correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nPearson correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.spearman_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.spearman_correlation", "kind": "function", "doc": "Calculate the Spearman correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- coorelation (float):\nSpearman correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.kendall_tau", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.kendall_tau", "kind": "function", "doc": "Calculate the Kendall's tau correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nKendall's tau correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.dft_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.dft_correlation", "kind": "function", "doc": "Calculate the DFT correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nDFT correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.dwt_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.dwt_correlation", "kind": "function", "doc": "Calculate the DWT correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nDWT correlation between the experimental and reference mass spectra.
\n
\n\nNotes
\n\nThis function requires the PyWavelets library to be installed. \n This is not a default requirement as this function is not widely used.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.euclidean_distance", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.euclidean_distance", "kind": "function", "doc": "Calculate the Euclidean distance between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nEuclidean distance between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.manhattan_distance", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.manhattan_distance", "kind": "function", "doc": "Calculate the Manhattan distance between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nManhattan distance between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.jaccard_distance", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.jaccard_distance", "kind": "function", "doc": "Calculate the Jaccard distance between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nJaccard distance between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.extra_distances", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.extra_distances", "kind": "function", "doc": "Function to calculate distances using additional metrics defined in math_distance.py
\n\nCurrently, calculates all distances.
\n\nReturns
\n\n\n- dict_res (dict):\nDictionary containing the distances between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance", "modulename": "corems.molecular_id.calc.math_distance", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.math_distance.entropy_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "entropy_distance", "kind": "function", "doc": "Calculate entropy distance between two vectors
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Entropy distance between v and y
\n
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.weighted_entropy_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "weighted_entropy_distance", "kind": "function", "doc": "Calculate weighted entropy distance between two vectors
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Weighted entropy distance between v and y
\n
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.chebyshev_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "chebyshev_distance", "kind": "function", "doc": "Chebyshev distance
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Chebyshev distance between v and y
\n
\n\nNotes
\n\n$$\\underset{i}{\\max}{(|v_{i}\\ -\\ y_{i}|)}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.squared_euclidean_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "squared_euclidean_distance", "kind": "function", "doc": "Squared Euclidean distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Squared Euclidean distance between v and y
\n
\n\nNotes
\n\n$$\\sum(v_{i}-y_{i})^2$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.fidelity_similarity", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "fidelity_similarity", "kind": "function", "doc": "Fidelity similarity:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Fidelity similarity between v and y
\n
\n\nNotes
\n\n$$\\sum\\sqrt{v_{i}y_{i}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.matusita_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "matusita_distance", "kind": "function", "doc": "Matusita distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Matusita distance between v and y
\n
\n\nNotes
\n\n$$\\sqrt{\\sum(\\sqrt{v_{i}}-\\sqrt{y_{i}})^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.squared_chord_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "squared_chord_distance", "kind": "function", "doc": "Squared-chord distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Squared-chord distance between v and y
\n
\n\nNotes
\n\n$$\\sum(\\sqrt{v_{i}}-\\sqrt{y_{i}})^2$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.bhattacharya_1_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "bhattacharya_1_distance", "kind": "function", "doc": "Bhattacharya 1 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Bhattacharya 1 distance between v and y
\n
\n\nNotes
\n\n$$(\\arccos{(\\sum\\sqrt{v_{i}y_{i}})})^2$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.bhattacharya_2_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "bhattacharya_2_distance", "kind": "function", "doc": "Bhattacharya 2 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Bhattacharya 2 distance between v and y
\n
\n\nNotes
\n\n$$-\\ln{(\\sum\\sqrt{v_{i}y_{i}})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.harmonic_mean_similarity", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "harmonic_mean_similarity", "kind": "function", "doc": "Harmonic mean similarity:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Harmonic mean similarity between v and y
\n
\n\nNotes
\n\n$$#1-2\\sum(\\frac{v_{i}y_{i}}{v_{i}+y_{i}})\n2\\sum(\\frac{v_{i}y_{i}}{v_{i}+y_{i}})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.chernoff_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "chernoff_distance", "kind": "function", "doc": "Chernoff distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Chernoff distance between v and y
\n
\n\nNotes
\n\n$$\\max{(-ln\\sum(v_{i}^ty_{i}^{1-t})^{1-t})},\\ t=0.1,\\ 0\\le\\ t<1$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.ruzicka_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "ruzicka_distance", "kind": "function", "doc": "Ruzicka distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Ruzicka distance between v and y
\n
\n\nNotes
\n\n$$\\frac{\\sum{|v_{i}-y_{i}|}}{\\sum{\\max(v_{i},y_{i})}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.roberts_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "roberts_distance", "kind": "function", "doc": "Roberts distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Roberts distance between v and y
\n
\n\nNotes
\n\n$$1-\\sum\\frac{(v_{i}+y_{i})\\frac{\\min{(v_{i},y_{i})}}{\\max{(v_{i},y_{i})}}}{\\sum(v_{i}+y_{i})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.intersection_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "intersection_distance", "kind": "function", "doc": "Intersection distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Intersection distance between v and y
\n
\n\nNotes
\n\n$$1-\\frac{\\sum\\min{(v_{i},y_{i})}}{\\min(\\sum{v_{i},\\sum{y_{i})}}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.motyka_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "motyka_distance", "kind": "function", "doc": "Motyka distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Motyka distance between v and y
\n
\n\nNotes
\n\n$$-\\frac{\\sum\\min{(y_{i},v_{i})}}{\\sum(y_{i}+v_{i})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.canberra_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "canberra_distance", "kind": "function", "doc": "Canberra distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Canberra distance between v and y
\n
\n\nNotes
\n\n$$#\\sum\\frac{|v_{i}-y_{i}|}{|v_{i}|+|y_{i}|}\n\\sum_{i}\\frac{|y_{i} - v_{i}|}{y_{i} + v_{i}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.canberra_metric", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "canberra_metric", "kind": "function", "doc": "Canberra Metric
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Canberra metric between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{\\sum_{i}I(v_{i}\\neq 0)}\\sum_{i}\\frac{|y_{i}-v_{i}|}{(y_{i}+v_{i})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.kulczynski_1_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "kulczynski_1_distance", "kind": "function", "doc": "Kulczynski 1 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Kulczynski 1 distance between v and y
\n
\n\nNotes
\n\n$$\\frac{\\sum{|v_i}-y_i|}{\\sum m\\ i\\ n\\ (v_i,y_i)}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.baroni_urbani_buser_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "baroni_urbani_buser_distance", "kind": "function", "doc": "Baroni-Urbani-Buser distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Baroni-Urbani-Buser distance between v and y
\n
\n\nNotes
\n\n$$1-\\frac{\\sum\\min{(v_i,y_i)}+\\sqrt{\\sum\\min{(v_i,y_i)}\\sum(\\max{(v)}-\\max{(v_i,y_i)})}}{\\sum{\\max{(v_i,y_i)}+\\sqrt{\\sum{\\min{(v_i,y_i)}\\sum(\\max{(v)}-\\max{(v_i,y_i)})}}}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.penrose_size_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "penrose_size_distance", "kind": "function", "doc": "Penrose size distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Penrose size distance between v and y
\n
\n\nNotes
\n\n$$\\sqrt N\\sum{|y_i-v_i|}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.mean_character_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "mean_character_distance", "kind": "function", "doc": "Mean character distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Mean character distance between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{N}\\sum{|y_i-v_i|}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.lorentzian_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "lorentzian_distance", "kind": "function", "doc": "Lorentzian distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Lorentzian distance between v and y
\n
\n\nNotes
\n\n$$\\sum{\\ln(1+|v_i-y_i|)}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.penrose_shape_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "penrose_shape_distance", "kind": "function", "doc": "Penrose shape distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Penrose shape distance between v and y
\n
\n\nNotes
\n\n$$\\sqrt{\\sum((v_i-\\bar{v})-(y_i-\\bar{y}))^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.clark_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "clark_distance", "kind": "function", "doc": "Clark distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Clark distance between v and y
\n
\n\nNotes
\n\n$$#(\\frac{1}{N}\\sum(\\frac{v_i-y_i}{|v_i|+|y_i|})^2)^\\frac{1}{2}\n\\sqrt{\\sum(\\frac{|v_i-y_i|}{v_i+y_i})^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.hellinger_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "hellinger_distance", "kind": "function", "doc": "Hellinger distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Hellinger distance between v and y
\n
\n\nNotes
\n\n$$#\\sqrt{2\\sum(\\sqrt{\\frac{v_i}{\\bar{v}}}-\\sqrt{\\frac{y_i}{\\bar{y}}})^2}\n\\sqrt{2\\sum(\\sqrt{v_i}-\\sqrt{y_i})^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.whittaker_index_of_association_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "whittaker_index_of_association_distance", "kind": "function", "doc": "Whittaker index of association distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Whittaker index of association distance between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{2}\\sum|\\frac{v_i}{\\bar{v}}-\\frac{y_i}{\\bar{y}}|$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.similarity_index_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "similarity_index_distance", "kind": "function", "doc": "Similarity Index Distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Similarity Index Distance between v and y
\n
\n\nNotes
\n\n$$\\sqrt{\\frac{\\sum{\\frac{v_i-y_i}{y_i}}^2}{N}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.improved_similarity_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "improved_similarity_distance", "kind": "function", "doc": "Improved Similarity Index:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Improved Similarity Index between v and y
\n
\n\nNotes
\n\n$$\\sqrt{\\frac{1}{N}\\sum{\\frac{y_i-v_i}{y_i+v_i}}^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.absolute_value_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "absolute_value_distance", "kind": "function", "doc": "Absolute Value Distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Absolute Value Distance between v and y
\n
\n\nNotes
\n\n$$\\frac { \\sum(|y_i-v_i|)}{\\sum v_i}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.spectral_contrast_angle_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "spectral_contrast_angle_distance", "kind": "function", "doc": "Spectral Contrast Angle:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Spectral Contrast Angle between v and y
\n
\n\nNotes
\n\n$$1 - \\frac{\\sum{y_iv_i}}{\\sqrt{\\sum y_i^2\\sum v_i^2}}\n\\arccos(\\frac{\\sum_{P}y_{p}^* v_{p}^}{\\sqrt{\\sum_{P}y_{p}^{2} \\sum_{P}v_{p}^{*2}}})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.wave_hedges_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "wave_hedges_distance", "kind": "function", "doc": "Wave Hedges distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Wave Hedges distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{|v_i-y_i|}{\\max{(v_i,y_i)}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.dice_similarity", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "dice_similarity", "kind": "function", "doc": "Dice similarity:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Dice similarity between v and y
\n
\n\nNotes
\n\n$$\\frac{\\sum(v_i-y_i)^2}{\\sum v_i^2+\\sum y_i^2}\n\\frac{2 * \\sum_{i}v_{i}y_{i}}{\\sum_{i}y_{i}^2 + \\sum_{i}v_{i}^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.inner_product_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "inner_product_distance", "kind": "function", "doc": "Inner Product distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Inner product distance between v and y
\n
\n\nNotes
\n\n$$1-\\sum{v_iy_i}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.divergence_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "divergence_distance", "kind": "function", "doc": "Divergence distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Divergence distance between v and y
\n
\n\nNotes
\n\n$$2\\sum\\frac{(v_i-y_i)^2}{(v_i+y_i)^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.jensen_difference_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "jensen_difference_distance", "kind": "function", "doc": "Jensen difference:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Jensen difference distance between v and y
\n
\n\nNotes
\n\n$$\\sum[\\frac{1}{2}(v_i\\ln{v_i}+y_i\\ln{y_i})-(\\frac{v_i+y_i}{2})\\ln{(\\frac{v_i+y_i}{2})}]$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.kumar_johnson_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "kumar_johnson_distance", "kind": "function", "doc": "Kumar-Johnson distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Kumar Johnson distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{(v_i^2-y_i^2)^2}{2(v_iy_i)^\\frac{3}{2}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.avg_l_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "avg_l_distance", "kind": "function", "doc": "Avg (L1, L\u221e) distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Average L distance between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{2}(\\sum|v_i-y_i|+\\underset{i}{\\max}{|v_i-y_i|})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.vicis_wave_hadges_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "vicis_wave_hadges_distance", "kind": "function", "doc": "Vicis-Wave Hadges distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Vicis Wave Hadges distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{|v_i-y_i|}{\\min{(v_i,\\ y_i)}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.vicis_symmetric_chi_squared_1_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "vicis_symmetric_chi_squared_1_distance", "kind": "function", "doc": "Vicis-Symmetric \u03c72 1 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Vici Symmetric \u03c72 1 distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{(v_i-y_i)^2}{\\min{(v_i,y_i)^2}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.vicis_symmetric_chi_squared_2_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "vicis_symmetric_chi_squared_2_distance", "kind": "function", "doc": "Vicis-Symmetric \u03c72 2 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Vicis Symmetric \u03c72 2 distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{(v_i-y_i)^2}{\\min{(v_i,y_i)}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.vicis_symmetric_chi_squared_3_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "vicis_symmetric_chi_squared_3_distance", "kind": "function", "doc": "Vicis-Symmetric \u03c72 3 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Vici Symmetric \u03c72 3 distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{(v_i-y_i)^2}{\\max{(v_i,y_i)}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.max_symmetric_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "max_symmetric_chi_squared_distance", "kind": "function", "doc": "Max-Symmetric \u03c72 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Max-Symmetric \u03c72 distance between v and y
\n
\n\nNotes
\n\n$$\\max{(\\sum\\frac{(v_i-y_i)^2}{v_i},\\sum\\frac{(v_i-y_i)^2}{y_i})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.min_symmetric_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "min_symmetric_chi_squared_distance", "kind": "function", "doc": "Min-Symmetric \u03c72 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Min-Symmetric \u03c72 distance between v and y
\n
\n\nNotes
\n\n$$\\min{(\\sum\\frac{(v_i-y_i)^2}{v_i},\\sum\\frac{(v_i-y_i)^2}{y_i})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.additive_sym_chi_sq", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "additive_sym_chi_sq", "kind": "function", "doc": "Additive Symmetric \u03c72 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Additive Symmetric \u03c72 distance between v and y
\n
\n\nNotes
\n\n$$\\sum_{i}\\frac{(y_{i} - v_{i})^2(y_{i}+v_{i})}{y_{i}v_{i}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.bhattacharya_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "bhattacharya_distance", "kind": "function", "doc": "Bhattacharya Distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Bhattcharya distance between v and y
\n
\n\nNotes
\n\n$$-ln(\\sum_{i}\\sqrt{y_{i}v_{i}})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.generalized_ochiai_index", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "generalized_ochiai_index", "kind": "function", "doc": "Generalized Ochiai Index
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Generalized Ochiai Index between v and y
\n
\n\nNotes
\n\n$$1 - \\frac{\\sum_{i}min(y_{i}, v_{i})}{\\sqrt{\\sum_{i}y_{i} \\sum_{i}v_{i}}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.gower_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "gower_distance", "kind": "function", "doc": "Gower Distance
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Gower distance between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{N}\\sum_{i}|y_{i} - v_{i}|$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.impr_sqrt_cosine_sim", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "impr_sqrt_cosine_sim", "kind": "function", "doc": "Improved Square Root Cosine Similarity
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Improved Square Root Cosine Similarity between v and y
\n
\n\nNotes
\n\n$$\\frac{\\sum_{i}\\sqrt{y_{i}v_{i}}}{\\sum_{i}\\sqrt{y_{i}}\\sum_{i}\\sqrt{v_{i}}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.intersection_sim", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "intersection_sim", "kind": "function", "doc": "Intersection Similarity
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Intersection Similarity between v and y
\n
\n\nNotes
\n\n$$\\sum_{i}min(y_{i}, v_{i})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.j_divergence", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "j_divergence", "kind": "function", "doc": "J Divergence
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: J Divergence between v and y
\n
\n\nNotes
\n\n$$\\sum_{i}(y_{i} - v_{i}) ln(\\frac{y_{i}}{v_{i}})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.jensen_shannon_index", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "jensen_shannon_index", "kind": "function", "doc": "Jensen-Shannon Index
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Jensen Shannon Index between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{2}[\\sum_{i}y_{i}ln(\\frac{2y_{i}}{y_{i} + v_{i}}) + \\sum_{i}v_{i}ln(\\frac{2v_{i}}{y_{i}+v_{i}})]$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.k_divergence", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "k_divergence", "kind": "function", "doc": "K-Divergence
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: K-Divergence between v and y
\n
\n\nNotes
\n\n$$\\sum_{i}y_{i}ln(\\frac{2y_{i}}{y_{i} + v_{i}})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.topsoe_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "topsoe_distance", "kind": "function", "doc": "Topsoe distance
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Topsoe distance between v and y
\n- Notes
\n- -----
\n
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.probabilistic_symmetric_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "probabilistic_symmetric_chi_squared_distance", "kind": "function", "doc": "Fixed\n\"I commented out the previous one; please review\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW6", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW6", "kind": "function", "doc": "\"appears to be the same as max_symmetric_chi_squared_distance\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW5", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW5", "kind": "function", "doc": "\"appears to be the same as max_symmetric_chi_squared_distance\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW4", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW4", "kind": "function", "doc": "\"Tecnically the Symmetric chi2 eq63\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW3", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW3", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW2", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW2", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW1", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW1", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.taneja_divergence", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "taneja_divergence", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.symmetric_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "symmetric_chi_squared_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.squared_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "squared_chi_squared_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.square_root_cosine_correlation", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "square_root_cosine_correlation", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.sorensen_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "sorensen_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.Pearson_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "Pearson_chi_squared_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.Neyman_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "Neyman_chi_squared_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.Minokowski_3", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "Minokowski_3", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.Minokowski_4", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "Minokowski_4", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.kumarjohnson_divergence", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "kumarjohnson_divergence", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.kumarhassebrook_similarity", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "kumarhassebrook_similarity", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.kullbackleibler_divergence", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "kullbackleibler_divergence", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.soergel_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "soergel_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory", "modulename": "corems.molecular_id.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL", "modulename": "corems.molecular_id.factory.EI_SQL", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Base", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Base", "kind": "class", "doc": "The base class of the class hierarchy.
\n\nWhen called, it accepts no arguments and returns a new featureless\ninstance that has no instance attributes and cannot be given any.
\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Base.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Base.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Base.registry", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Base.registry", "kind": "variable", "doc": "\n", "default_value": "<sqlalchemy.orm.decl_api.registry object>"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Base.metadata", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Base.metadata", "kind": "variable", "doc": "\n", "default_value": "MetaData()"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar", "kind": "class", "doc": "This class is used to store the metadata of the compounds in the database
\n\nAttributes
\n\n\n- id (int):\nThe id of the compound.
\n- cas (str):\nThe CAS number of the compound.
\n- inchikey (str):\nThe InChiKey of the compound.
\n- inchi (str):\nThe InChi of the compound.
\n- chebi (str):\nThe ChEBI ID of the compound.
\n- smiles (str):\nThe SMILES of the compound.
\n- kegg (str):\nThe KEGG ID of the compound.
\n- iupac_name (str):\nThe IUPAC name of the compound.
\n- traditional_name (str):\nThe traditional name of the compound.
\n- common_name (str):\nThe common name of the compound.
\n- data_id (int):\nThe id of the compound in the molecularData table.
\n- data (LowResolutionEICompound):\nThe compound object.
\n
\n", "bases": "sqlalchemy.orm.decl_api.Base"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.cas", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.cas", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.inchikey", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.inchikey", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.inchi", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.inchi", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.chebi", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.chebi", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.smiles", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.smiles", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.kegg", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.kegg", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.iupac_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.iupac_name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.traditional_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.traditional_name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.common_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.common_name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.data_id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.data_id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.data", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.data", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound", "kind": "class", "doc": "This class is used to store the molecular and spectral data of the compounds in the low res EI database
\n\nAttributes
\n\n\n- id (int):\nThe id of the compound.
\n- name (str):\nThe name of the compound.
\n- classify (str):\nThe classification of the compound.
\n- formula (str):\nThe formula of the compound.
\n- ri (float):\nThe retention index of the compound.
\n- retention_time (float):\nThe retention time of the compound.
\n- source (str):\nThe source of the compound.
\n- casno (str):\nThe CAS number of the compound.
\n- comment (str):\nThe comment of the compound.
\n- source_temp_c (float):\nThe source temperature of the spectra.
\n- ev (float):\nThe electron volts of the spectra.
\n- peaks_count (int):\nThe number of peaks in the spectra.
\n- mz (numpy.ndarray):\nThe m/z values of the spectra.
\n- abundance (numpy.ndarray):\nThe abundance values of the spectra.
\n- metadatar (Metadatar):\nThe metadata object.
\n
\n", "bases": "sqlalchemy.orm.decl_api.Base"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.__init__", "kind": "function", "doc": "\n", "signature": "(dict_data)"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.classify", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.classify", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.formula", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.formula", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.ri", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.ri", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.retention_time", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.retention_time", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.derivativenum", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.derivativenum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.derivatization", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.derivatization", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.source", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.source", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.casno", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.casno", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.comment", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.comment", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.source_temp_c", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.source_temp_c", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.ev", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.ev", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.peaks_count", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.peaks_count", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.mz", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.abundance", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.abundance", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.metadatar", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.metadatar", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata", "kind": "class", "doc": "Dataclass for the Metabolite Metadata
\n\nAttributes
\n\n\n- id (int):\nThe id of the compound.
\n- cas (str):\nThe CAS number of the compound.
\n- inchikey (str):\nThe InChiKey of the compound.
\n- inchi (str):\nThe InChi of the compound.
\n- chebi (str):\nThe ChEBI ID of the compound.
\n- smiles (str):\nThe SMILES of the compound.
\n- kegg (str):\nThe KEGG ID of the compound.
\n- iupac_name (str):\nThe IUPAC name of the compound.
\n- traditional_name (str):\nThe traditional name of the compound.
\n- common_name (str):\nThe common name of the compound.
\n- data_id (int):\nThe id of the compound in the molecularData table.
\n
\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.__init__", "kind": "function", "doc": "\n", "signature": "(\tid: int,\tcas: str,\tinchikey: str,\tinchi: str,\tchebi: str,\tsmiles: str,\tkegg: str,\tdata_id: int,\tiupac_name: str,\ttraditional_name: str,\tcommon_name: str)"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.id", "kind": "variable", "doc": "\n", "annotation": ": int"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.cas", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.cas", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.inchikey", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.inchikey", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.inchi", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.inchi", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.chebi", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.chebi", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.smiles", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.smiles", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.kegg", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.kegg", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.data_id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.data_id", "kind": "variable", "doc": "\n", "annotation": ": int"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.iupac_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.iupac_name", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.traditional_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.traditional_name", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.common_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.common_name", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef", "kind": "class", "doc": "Dataclass for the Low Resolution Compound Reference
\n\nThis class is used to store the molecular and spectral data of the compounds in the low res EI database
\n\nParameters
\n\n\n- compounds_dict (dict):\nA dictionary representing the compound.
\n
\n\nAttributes
\n\n\n- id (int):\nThe id of the compound.
\n- name (str):\nThe name of the compound.
\n- ri (str):\nThe retention index of the compound.
\n- retention_time (str):\nThe retention time of the compound.
\n- casno (str):\nThe CAS number of the compound.
\n- comment (str):\nThe comment of the compound.
\n- peaks_count (int):\nThe number of peaks in the spectra.
\n- classify (str):\nThe classification of the compound.
\n- derivativenum (str):\nThe derivative number of the compound.
\n- derivatization (str):\nThe derivatization applied to the compound.
\n- mz (numpy.ndarray):\nThe m/z values of the spectra.
\n- abundance (numpy.ndarray):\nThe abundance values of the spectra.
\n- source_temp_c (float):\nThe source temperature of the spectra.
\n- ev (float):\nThe electron volts of the spectra.
\n- formula (str):\nThe formula of the compound.
\n- source (str):\nThe source of the spectra data.
\n- classify (str):\nThe classification of the compound.
\n- metadata (MetaboliteMetadata):\nThe metadata object.
\n- similarity_score (float):\nThe similarity score of the compound.
\n- ri_score (float):\nThe RI score of the compound.
\n- spectral_similarity_score (float):\nThe spectral similarity score of the compound.
\n- spectral_similarity_scores (dict):\nThe spectral similarity scores of the compound.
\n
\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.__init__", "kind": "function", "doc": "\n", "signature": "(compounds_dict)"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.ri", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.ri", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.retention_time", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.retention_time", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.casno", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.casno", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.comment", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.comment", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.peaks_count", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.peaks_count", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.classify", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.classify", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.derivativenum", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.derivativenum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.derivatization", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.derivatization", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.mz", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.abundance", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.abundance", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.source_temp_c", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.source_temp_c", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.ev", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.ev", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.formula", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.formula", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.source", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.source", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.similarity_score", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.similarity_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.ri_score", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.ri_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.spectral_similarity_score", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.spectral_similarity_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.spectral_similarity_scores", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.spectral_similarity_scores", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite", "kind": "class", "doc": "A class for interacting with a SQLite database for low-resolution EI compounds.
\n\nParameters
\n\n\n- url (str, optional):\nThe URL of the SQLite database. Default is 'sqlite://'.
\n
\n\nAttributes
\n\n\n- engine (sqlalchemy.engine.Engine):\nThe SQLAlchemy engine for connecting to the database.
\n- session (sqlalchemy.orm.Session):\nThe SQLAlchemy session for executing database operations.
\n
\n\nMethods
\n\n\n- __init__(self, url='sqlite://').\nInitializes the EI_LowRes_SQLite object.
\n- __exit__(self, exc_type, exc_val, exc_tb).\nCloses the database connection.
\n- init_engine(self, url).\nInitializes the SQLAlchemy engine.
\n- __enter__(self).\nReturns the EI_LowRes_SQLite object.
\n- add_compound_list(self, data_dict_list).\nAdds a list of compounds to the database.
\n- add_compound(self, data_dict).\nAdds a single compound to the database.
\n- commit(self).\nCommits the changes to the database.
\n- row_to_dict(self, row).\nConverts a database row to a dictionary.
\n- get_all(self).\nRetrieves all compounds from the database.
\n- query_min_max_rt(self, min_max_rt).\nQueries compounds based on retention time range.
\n- query_min_max_ri(self, min_max_ri).\nQueries compounds based on RI range.
\n- query_names_and_rt(self, min_max_rt, compound_names).\nQueries compounds based on compound names and retention time range.
\n- query_min_max_ri_and_rt(self, min_max_ri, min_max_rt).\nQueries compounds based on RI range and retention time range.
\n- delete_compound(self, compound).\nDeletes a compound from the database.
\n- purge(self).\nDeletes all compounds from the database table.
\n- clear_data(self).\nClears all tables in the database.
\n
\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.__init__", "kind": "function", "doc": "\n", "signature": "(url='sqlite://')"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.engine", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.engine", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.session", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.session", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.init_engine", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.init_engine", "kind": "function", "doc": "Initializes the SQLAlchemy engine.
\n\nParameters
\n\n\n- url (str):\nThe URL of the SQLite database.
\n
\n\nReturns
\n\n\n- sqlalchemy.engine.Engine: The SQLAlchemy engine for connecting to the database.
\n
\n", "signature": "(self, url):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.add_compound_list", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.add_compound_list", "kind": "function", "doc": "Adds a list of compounds to the database.
\n\nParameters
\n\n\n- data_dict_list (list of dict):\nA list of dictionaries representing the compounds.
\n
\n", "signature": "(self, data_dict_list):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.add_compound", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.add_compound", "kind": "function", "doc": "Adds a single compound to the database.
\n\nParameters
\n\n\n- data_dict (dict):\nA dictionary representing the compound.
\n
\n", "signature": "(self, data_dict):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.commit", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.commit", "kind": "function", "doc": "Commits the changes to the database.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.row_to_dict", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.row_to_dict", "kind": "function", "doc": "Converts a database row to a dictionary.
\n\nParameters
\n\n\n- row (sqlalchemy.engine.row.Row):\nA row from the database.
\n
\n\nReturns
\n\n\n- dict: A dictionary representing the compound.
\n
\n", "signature": "(self, row):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.get_all", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.get_all", "kind": "function", "doc": "Retrieves all compounds from the database.
\n\nReturns
\n\n\n- list: A list of dictionaries representing the compounds.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.query_min_max_rt", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.query_min_max_rt", "kind": "function", "doc": "Queries compounds based on retention time range.
\n\nParameters
\n\n\n- min_max_rt (tuple):\nA tuple containing the minimum and maximum retention time values.
\n
\n\nReturns
\n\n\n- list: A list of dictionaries representing the compounds.
\n
\n", "signature": "(self, min_max_rt):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.query_min_max_ri", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.query_min_max_ri", "kind": "function", "doc": "Queries compounds based on RI range.
\n\nParameters
\n\n\n- min_max_ri (tuple):\nA tuple containing the minimum and maximum RI values.
\n
\n", "signature": "(self, min_max_ri):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.query_names_and_rt", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.query_names_and_rt", "kind": "function", "doc": "Queries compounds based on compound names and retention time range.
\n\nParameters
\n\n\n- min_max_rt (tuple):\nA tuple containing the minimum and maximum retention time values.
\n- compound_names (list):\nA list of compound names.
\n
\n\nReturns
\n\n\n- list: A list of dictionaries representing the compounds.
\n
\n", "signature": "(self, min_max_rt, compound_names):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.query_min_max_ri_and_rt", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.query_min_max_ri_and_rt", "kind": "function", "doc": "Queries compounds based on RI range and retention time range.
\n\nParameters
\n\n\n- min_max_ri (tuple):\nA tuple containing the minimum and maximum RI values.
\n- min_max_rt (tuple):\nA tuple containing the minimum and maximum retention time values.
\n
\n\nReturns
\n\n\n- list: A list of dictionaries representing the compounds.
\n
\n", "signature": "(self, min_max_ri, min_max_rt):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.delete_compound", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.delete_compound", "kind": "function", "doc": "Deletes a compound from the database.
\n\nParameters
\n\n\n- compound (LowResolutionEICompound):\nA compound object.
\n
\n", "signature": "(self, compound):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.purge", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.purge", "kind": "function", "doc": "Deletes all compounds from the database table.
\n\nNotes
\n\nCareful, this will delete the entire database table.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.clear_data", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.clear_data", "kind": "function", "doc": "Clears all tables in the database.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.profiled", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "profiled", "kind": "function", "doc": "A context manager for profiling.
\n", "signature": "():", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.insert_database_worker", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "insert_database_worker", "kind": "function", "doc": "Inserts data into the database.
\n", "signature": "(args):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations", "kind": "class", "doc": "A class for generating molecular formula combinations.
\n\nParameters
\n\n\n- molecular_search_settings (object):\nAn object containing user-defined settings.
\n
\n\nAttributes
\n\n\n- sql_db (MolForm_SQL):\nThe SQLite database object.
\n- len_existing_classes (int):\nThe number of existing classes in the SQLite database.
\n- odd_ch_id (list):\nA list of odd carbon and hydrogen atom IDs.
\n- odd_ch_dict (list):\nA list of odd carbon and hydrogen atom dictionaries.
\n- odd_ch_mass (list):\nA list of odd carbon and hydrogen atom masses.
\n- odd_ch_dbe (list):\nA list of odd carbon and hydrogen atom double bond equivalents.
\n- even_ch_id (list):\nA list of even carbon and hydrogen atom IDs.
\n- even_ch_dict (list):\nA list of even carbon and hydrogen atom dictionaries.
\n- even_ch_mass (list):\nA list of even carbon and hydrogen atom masses.
\n- even_ch_dbe (list):\nA list of even carbon and hydrogen atom double bond equivalents.
\n
\n\nMethods
\n\n\n- cProfile_worker(args)
\nA cProfile worker for the get_mol_formulas function. \n- check_database_get_class_list(molecular_search_settings)
\nChecks if the database has all the classes, if not create the missing classes. \n- get_carbonsHydrogens(settings, odd_even)
\nRetrieves carbon and hydrogen atoms from the molecular lookup table based on user-defined settings. \n- add_carbonsHydrogens(settings, existing_classes_objs)
\nAdds carbon and hydrogen atoms to the molecular lookup table based on user-defined settings. \n- runworker(molecular_search_settings)
\nRuns the molecular formula lookup table worker. \n- get_classes_in_order(molecular_search_settings)
\nGets the classes in order. \n- sort_classes(atoms_in_order, combination_dict)
\nSorts the classes in order. \n- get_fixed_initial_number_of_hydrogen(min_h, odd_even)
\nGets the fixed initial number of hydrogen atoms. \n- calc_mz(datadict, class_mass=0)
\nCalculates the mass-to-charge ratio (m/z) of a molecular formula. \n- calc_dbe_class(datadict)
\nCalculates the double bond equivalent (DBE) of a molecular formula. \n- populate_combinations(classe_tuple, settings)
\nPopulates the combinations. \n- get_or_add(SomeClass, kw)
\nGets or adds a class. \n- get_mol_formulas(odd_even_tag, classe_tuple, settings)
\nGets the molecular formulas. \n- get_h_odd_or_even(class_dict)
\nGets the hydrogen odd or even. \n- get_total_halogen_atoms(class_dict)
\nGets the total number of halogen atoms. \n
\n"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.__init__", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.__init__", "kind": "function", "doc": "\n", "signature": "(sql_db=None)"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.cProfile_worker", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.cProfile_worker", "kind": "function", "doc": "cProfile worker for the get_mol_formulas function
\n", "signature": "(self, args):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.check_database_get_class_list", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.check_database_get_class_list", "kind": "function", "doc": "check if the database has all the classes, if not create the missing classes
\n\nParameters
\n\n\n- molecular_search_settings (object):\nAn object containing user-defined settings.
\n
\n\nReturns
\n\n\n- list: list of tuples with the class name and the class dictionary
\n
\n", "signature": "(self, molecular_search_settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_carbonsHydrogens", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_carbonsHydrogens", "kind": "function", "doc": "Retrieve carbon and hydrogen atoms from the molecular lookup table based on user-defined settings.
\n\nParameters
\n\n\n- settings (object):\nAn object containing user-defined settings.
\n- odd_even (str):\nA string indicating whether to retrieve even or odd hydrogen atoms.
\n
\n\nReturns
\n\n\n- list: A list of CarbonHydrogen objects that satisfy the specified conditions.
\n
\n", "signature": "(self, settings, odd_even):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.add_carbonsHydrogens", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.add_carbonsHydrogens", "kind": "function", "doc": "Add carbon and hydrogen atoms to the molecular lookup table based on user-defined settings.
\n\nParameters
\n\n\n- settings (object):\nAn object containing user-defined settings.
\n- existing_classes_objs (list):\nA list of HeteroAtoms objects.
\n
\n", "signature": "(self, settings, existing_classes_objs):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.runworker", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.runworker", "kind": "function", "doc": "Run the molecular formula lookup table worker.
\n\nParameters
\n\n\n- molecular_search_settings (object):\nAn object containing user-defined settings.
\n
\n\nReturns
\n\n\n- list: A list of tuples with the class name and the class dictionary.
\n
\n", "signature": "(*args, **kw):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_classes_in_order", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_classes_in_order", "kind": "function", "doc": "Get the classes in order
\n\nParameters
\n\n\n- molecular_search_settings (object):\nAn object containing user-defined settings.
\n
\n\nReturns
\n\n\n- dict: A dictionary of classes in order.\nstructure is ('HC', {'HC': 1})
\n
\n", "signature": "(self, molecular_search_settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.sort_classes", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.sort_classes", "kind": "function", "doc": "Sort the classes in order
\n\nParameters
\n\n\n- atoms_in_order (list):\nA list of atoms in order.
\n- combination_dict (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- dict: A dictionary of classes in order.
\n
\n", "signature": "(atoms_in_order, combination_dict) -> Dict[str, Dict[str, int]]:", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_fixed_initial_number_of_hydrogen", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_fixed_initial_number_of_hydrogen", "kind": "function", "doc": "Get the fixed initial number of hydrogen atoms
\n\nParameters
\n\n\n- min_h (int):\nThe minimum number of hydrogen atoms.
\n- odd_even (str):\nA string indicating whether to retrieve even or odd hydrogen atoms.
\n
\n", "signature": "(min_h, odd_even):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.calc_mz", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.calc_mz", "kind": "function", "doc": "Calculate the mass-to-charge ratio (m/z) of a molecular formula.
\n\nParameters
\n\n\n- datadict (dict):\nA dictionary of classes.
\n- class_mass (int):\nThe mass of the class.
\n
\n\nReturns
\n\n\n- float: The mass-to-charge ratio (m/z) of a molecular formula.
\n
\n", "signature": "(self, datadict, class_mass=0):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.calc_dbe_class", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.calc_dbe_class", "kind": "function", "doc": "Calculate the double bond equivalent (DBE) of a molecular formula.
\n\nParameters
\n\n\n- datadict (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- float: The double bond equivalent (DBE) of a molecular formula.
\n
\n", "signature": "(self, datadict):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.populate_combinations", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.populate_combinations", "kind": "function", "doc": "Populate the combinations
\n\nParameters
\n\n\n- classe_tuple (tuple):\nA tuple containing the class name, the class dictionary, and the class ID.
\n- settings (object):\nAn object containing user-defined settings.
\n
\n\nReturns
\n\n\n- list: A list of molecular formula data dictionaries.
\n
\n", "signature": "(self, classe_tuple, settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_or_add", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_or_add", "kind": "function", "doc": "Get or add a class
\n\nParameters
\n\n\n- SomeClass (object):\nA class object.
\n- kw (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- object: A class object.
\n
\n", "signature": "(self, SomeClass, kw):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_mol_formulas", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_mol_formulas", "kind": "function", "doc": "Get the molecular formulas
\n\nParameters
\n\n\n\nReturns
\n\n\n- list: A list of molecular formula data dictionaries.
\n
\n", "signature": "(self, odd_even_tag, classe_tuple, settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_h_odd_or_even", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_h_odd_or_even", "kind": "function", "doc": "Get the hydrogen odd or even
\n\nParameters
\n\n\n- class_dict (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- str: A string indicating whether to retrieve even or odd hydrogen atoms.
\n
\n", "signature": "(self, class_dict):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_total_halogen_atoms", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_total_halogen_atoms", "kind": "function", "doc": "Get the total number of halogen atoms
\n\nParameters
\n\n\n- class_dict (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- int: The total number of halogen atoms.
\n
\n", "signature": "(class_dict):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification", "modulename": "corems.molecular_id.factory.classification", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.flatten_list", "modulename": "corems.molecular_id.factory.classification", "qualname": "flatten_list", "kind": "function", "doc": "\n", "signature": "(l):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification", "kind": "class", "doc": "Class for grouping mass spectrum data by heteroatom classes (Nn, Oo, Ss, NnOo, NnSs, etc..)
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- choose_molecular_formula (bool, optional):\nIf True, the molecular formula with the highest abundance is chosen. If False, all molecular formulas are considered. Default is True.
\n
\n\nRaises
\n\n\n- Exception: If no molecular formula is associated with any mspeak objects.
\n
\n\nAttributes
\n\n\n- _ms_grouped_class (dict):\nA dictionary of classes and a list of ms_peak objects.
\n- choose_mf (bool):\nIf True, the molecular formula with the highest abundance is chosen. If False, all molecular formulas are considered.
\n- total_peaks (int):\nThe total number of peaks.
\n- sum_abundance (float):\nThe sum of the abundance of all peaks.
\n- min_max_mz (tuple):\nThe minimum and maximum mz values.
\n- min_max_abundance (tuple):\nThe minimum and maximum abundance values.
\n- min_ppm_error (float):\nThe minimum ppm error.
\n- max_ppm_error (float):\nThe maximum ppm error.
\n- all_identified_atoms (list):\nA list of all identified atoms.
\n
\n\nMethods
\n\n\n- __len__().\nReturns the number of classes.
\n- __getitem__(classe)
\nReturns the molecular formula list for specified class. \n- __iter__().\nReturns an iterator over the keys of the dictionary.
\n- get_classes(threshold_perc=1, isotopologue=True).\nReturns a list of classes with abundance percentile above threshold.
\n- molecular_formula_string(classe).\nReturns a list of molecular formula string for specified class.
\n- molecular_formula(classe).\nReturns a list of molecular formula for specified class.
\n- carbon_number(classe).\nReturns a list of carbon number for specified class.
\n- atom_count(atom, classe).\nReturns a list of atom count for specified class.
\n- dbe(classe).\nReturns a list of DBE for specified class.
\n- atoms_ratio(classe, numerator, denominator).\nReturns a list of atoms ratio for specified class.
\n- mz_exp(classe).\nReturns a list of experimental mz for specified class.
\n- abundance(classe).\nReturns a list of abundance for specified class.
\n- mz_error(classe).\nReturns a list of mz error for specified class.
\n- mz_calc(classe).\nReturns a list of calculated mz for specified class.
\n- peaks_count_percentile(classe).\nReturns the peaks count percentile of a specific class.
\n- abundance_count_percentile(classe).\nReturns the abundance percentile of a specific class.
\n- mz_exp_assigned().\nReturns a list of experimental mz for all assigned classes.
\n- abundance_assigned().\nReturns a list of abundance for all classes.
\n- mz_exp_all().\nReturns a list of mz for all classes.
\n
\n", "bases": "collections.abc.Mapping"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.__init__", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.__init__", "kind": "function", "doc": "\n", "signature": "(mass_spectrum, choose_molecular_formula=True)"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.choose_mf", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.choose_mf", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.total_peaks", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.total_peaks", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.sum_abundance", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.sum_abundance", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.min_max_mz", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.min_max_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.min_max_abundance", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.min_max_abundance", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.min_ppm_error", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.min_ppm_error", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.max_ppm_error", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.max_ppm_error", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.all_identified_atoms", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.all_identified_atoms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.get_classes", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.get_classes", "kind": "function", "doc": "Return a list of classes with abundance percentile above threshold
\n", "signature": "(self, threshold_perc=1, isotopologue=True):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.molecular_formula_string", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.molecular_formula_string", "kind": "function", "doc": "Return a list of molecular formula string for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.molecular_formula", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.molecular_formula", "kind": "function", "doc": "Return a list of molecular formula for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.carbon_number", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.carbon_number", "kind": "function", "doc": "Return a list of carbon number for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.atom_count", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.atom_count", "kind": "function", "doc": "Return a list of atom count for specified class
\n", "signature": "(self, atom, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.dbe", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.dbe", "kind": "function", "doc": "Return a list of DBE for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.atoms_ratio", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.atoms_ratio", "kind": "function", "doc": "Return a list of atoms ratio for specified class
\n", "signature": "(self, classe, numerator, denominator):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_exp", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_exp", "kind": "function", "doc": "Return a list of experimental mz for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.abundance", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.abundance", "kind": "function", "doc": "Return a list of abundance for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_error", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_error", "kind": "function", "doc": "Return a list of mz error for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_calc", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_calc", "kind": "function", "doc": "Return a list of calculated mz for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.peaks_count_percentile", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.peaks_count_percentile", "kind": "function", "doc": "Return the peaks count percentile of a specific class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.abundance_count_percentile", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.abundance_count_percentile", "kind": "function", "doc": "Return the abundance percentile of a specific class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_exp_assigned", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_exp_assigned", "kind": "function", "doc": "Return a list of experimental mz for all assigned classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.abundance_assigned", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.abundance_assigned", "kind": "function", "doc": "Return a list of abundance for all classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_exp_all", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_exp_all", "kind": "function", "doc": "Return a list of mz for all classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_error_all", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_error_all", "kind": "function", "doc": "Return a list of mz error for all classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.carbon_number_all", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.carbon_number_all", "kind": "function", "doc": "Return a list of carbon number for all classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.dbe_all", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.dbe_all", "kind": "function", "doc": "Return a list of DBE for all classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.atoms_ratio_all", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.atoms_ratio_all", "kind": "function", "doc": "Return a list of atoms ratio for all classes
\n", "signature": "(self, numerator, denominator):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.to_dataframe", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.to_dataframe", "kind": "function", "doc": "Return a pandas dataframe with all the data from the class
\n\nParameters
\n\n\n- include_isotopologue (bool, optional):\nInclude isotopologues, by default False
\n- abundance_perc_threshold (int, optional):\nAbundance percentile threshold, by default 5
\n- include_unassigned (bool, optional):\nInclude unassigned peaks, by default False
\n
\n\nReturns
\n\n\n- DataFrame: Pandas dataframe with all the data from the class
\n
\n", "signature": "(\tself,\tinclude_isotopologue=False,\tabundance_perc_threshold=5,\tinclude_unassigned=False):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_ms_assigned_unassigned", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_ms_assigned_unassigned", "kind": "function", "doc": "Plot stick mass spectrum of all classes
\n\nParameters
\n\n\n- assigned_color (str, optional):\nMatplotlib color for the assigned peaks, by default \"b\"
\n- unassigned_color (str, optional):\nMatplotlib color for the unassigned peaks, by default \"r\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n
\n", "signature": "(self, assigned_color='b', unassigned_color='r'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_mz_error", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_mz_error", "kind": "function", "doc": "Plot mz error scatter plot of all classes
\n\nParameters
\n\n\n- color (str, optional):\nMatplotlib color, by default \"g\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n
\n", "signature": "(self, color='g'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_mz_error_class", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_mz_error_class", "kind": "function", "doc": "Plot mz error scatter plot of a specific class
\n\nParameters
\n\n\n- classe (str):\nClass name
\n- color (str, optional):\nMatplotlib color, by default \"g\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n
\n", "signature": "(self, classe, color='g'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_ms_class", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_ms_class", "kind": "function", "doc": "Plot stick mass spectrum of a specific class
\n\nParameters
\n\n\n- classe (str):\nClass name
\n- color (str, optional):\nMatplotlib color, by default \"g\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n
\n", "signature": "(self, classe, color='g'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_van_krevelen", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_van_krevelen", "kind": "function", "doc": "Plot Van Krevelen Diagram
\n\nParameters
\n\n\n- classe (str):\nClass name
\n- max_hc (float, optional):\nMax H/C ratio, by default 2.5
\n- max_oc (float, optional):\nMax O/C ratio, by default 2
\n- ticks_number (int, optional):\nNumber of ticks, by default 5
\n- color (str, optional):\nMatplotlib color, by default \"viridis\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n- abun_perc (float):\nClass percentile of the relative abundance
\n
\n", "signature": "(self, classe, max_hc=2.5, max_oc=2, ticks_number=5, color='viridis'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_dbe_vs_carbon_number", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_dbe_vs_carbon_number", "kind": "function", "doc": "Plot DBE vs Carbon Number
\n\nParameters
\n\n\n- classe (str):\nClass name
\n- max_c (int, optional):\nMax Carbon Number, by default 50
\n- max_dbe (int, optional):\nMax DBE, by default 40
\n- dbe_incr (int, optional):\nDBE increment, by default 5
\n- c_incr (int, optional):\nCarbon Number increment, by default 10
\n- color (str, optional):\nMatplotlib color, by default \"viridis\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n- abun_perc (float):\nClass percentile of the relative abundance
\n
\n", "signature": "(\tself,\tclasse,\tmax_c=50,\tmax_dbe=40,\tdbe_incr=5,\tc_incr=10,\tcolor='viridis'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL", "modulename": "corems.molecular_id.factory.molecularSQL", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.Base", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "Base", "kind": "class", "doc": "The base class of the class hierarchy.
\n\nWhen called, it accepts no arguments and returns a new featureless\ninstance that has no instance attributes and cannot be given any.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.Base.__init__", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "Base.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.molecularSQL.Base.registry", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "Base.registry", "kind": "variable", "doc": "\n", "default_value": "<sqlalchemy.orm.decl_api.registry object>"}, {"fullname": "corems.molecular_id.factory.molecularSQL.Base.metadata", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "Base.metadata", "kind": "variable", "doc": "\n", "default_value": "MetaData()"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms", "kind": "class", "doc": "HeteroAtoms class for the heteroAtoms table in the SQLite database.
\n\nAttributes
\n\n\n- id (int):\nThe primary key for the table.
\n- name (str):\nThe name of the heteroAtoms class.
\n- halogensCount (int):\nThe number of halogens in the heteroAtoms class.
\n- carbonHydrogen (relationship):\nThe relationship to the carbonHydrogen table.
\n
\n\nMethods
\n\n\n- __repr__()\nReturns the string representation of the object.
\n- to_dict()\nReturns the heteroAtoms class as a dictionary.
\n- halogens_count()\nReturns the number of halogens as a float.
\n
\n", "bases": "sqlalchemy.orm.decl_api.Base"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.__init__", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.id", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.name", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.halogensCount", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.halogensCount", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.carbonHydrogen", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.carbonHydrogen", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.halogens_count", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.halogens_count", "kind": "variable", "doc": "Returns the number of halogens as a float.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.to_dict", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.to_dict", "kind": "function", "doc": "Returns the heteroAtoms class as a dictionary.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen", "kind": "class", "doc": "CarbonHydrogen class for the carbonHydrogen table in the SQLite database.
\n\nAttributes
\n\n\n- id (int):\nThe primary key for the table.
\n- C (int):\nThe number of carbon atoms.
\n- H (int):\nThe number of hydrogen atoms.
\n- heteroAtoms (relationship):\nThe relationship to the heteroAtoms table.
\n
\n\nMethods
\n\n\n- __repr__()\nReturns the string representation of the object.
\n- mass()\nReturns the mass of the carbonHydrogen class as a float.
\n- c()\nReturns the number of carbon atoms as a float.
\n- h()\nReturns the number of hydrogen atoms as a float.
\n- dbe()\nReturns the double bond equivalent as a float.
\n
\n", "bases": "sqlalchemy.orm.decl_api.Base"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.__init__", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.id", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.C", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.C", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.H", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.H", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.heteroAtoms", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.heteroAtoms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.mass", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.mass", "kind": "variable", "doc": "Returns the mass of the carbonHydrogen class as a float.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.c", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.c", "kind": "variable", "doc": "Returns the number of carbon atoms as a float.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.h", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.h", "kind": "variable", "doc": "Returns the number of hydrogen atoms as a float.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.dbe", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.dbe", "kind": "variable", "doc": "Returns the double bond equivalent as a float.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink", "kind": "class", "doc": "MolecularFormulaLink class for the molecularformula table in the SQLite database.
\n\nAttributes
\n\n\n- heteroAtoms_id (int):\nThe foreign key for the heteroAtoms table.
\n- carbonHydrogen_id (int):\nThe foreign key for the carbonHydrogen table.
\n- mass (float):\nThe mass of the molecular formula.
\n- DBE (float):\nThe double bond equivalent of the molecular formula.
\n- carbonHydrogen (relationship):\nThe relationship to the carbonHydrogen table.
\n- heteroAtoms (relationship):\nThe relationship to the heteroAtoms table.
\n- C (association_proxy):\nThe association proxy for the carbonHydrogen table.
\n- H (association_proxy):\nThe association proxy for the carbonHydrogen table.
\n- classe (association_proxy):\nThe association proxy for the heteroAtoms table.
\n
\n\nMethods
\n\n\n- __repr__()\nReturns the string representation of the object.
\n- to_dict()\nReturns the molecular formula as a dictionary.
\n- formula_string()\nReturns the molecular formula as a string.
\n- classe_string()\nReturns the heteroAtoms class as a string.
\n- _adduct_mz(ion_charge, adduct_atom)\nReturns the m/z of the adduct ion as a float.
\n- _protonated_mz(ion_charge)\nReturns the m/z of the protonated ion as a float.
\n- _radical_mz(ion_charge)\nReturns the m/z of the radical ion as a float.
\n
\n", "bases": "sqlalchemy.orm.decl_api.Base"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.__init__", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.heteroAtoms_id", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.heteroAtoms_id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.carbonHydrogen_id", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.carbonHydrogen_id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.mass", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.mass", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.DBE", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.DBE", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.carbonHydrogen", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.carbonHydrogen", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.heteroAtoms", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.heteroAtoms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.C", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.C", "kind": "variable", "doc": "A descriptor that presents a read/write view of an object attribute.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.H", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.H", "kind": "variable", "doc": "A descriptor that presents a read/write view of an object attribute.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.classe", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.classe", "kind": "variable", "doc": "A descriptor that presents a read/write view of an object attribute.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.to_dict", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.to_dict", "kind": "function", "doc": "Returns the molecular formula as a dictionary.
\n\nReturns
\n\n\n- dict: The molecular formula as a dictionary.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.formula_string", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.formula_string", "kind": "variable", "doc": "Returns the molecular formula as a string.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.classe_string", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.classe_string", "kind": "variable", "doc": "Returns the heteroAtoms class as a string.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL", "kind": "class", "doc": "MolForm_SQL class for the SQLite database.
\n\nAttributes
\n\n\n- engine (sqlalchemy.engine.base.Engine):\nThe SQLAlchemy engine.
\n- session (sqlalchemy.orm.session.Session):\nThe SQLAlchemy session.
\n- type (str):\nThe type of database.
\n- chunks_count (int):\nThe number of chunks to use when querying the database.
\n
\n\nMethods
\n\n\n- __init__(url=None, echo=False)\nInitializes the database.
\n- __exit__(exc_type, exc_val, exc_tb)\nCloses the database.
\n- initiate_database(url, database_name)\nCreates the database.
\n- commit()\nCommits the session.
\n- init_engine(url)\nInitializes the SQLAlchemy engine.
\n__enter__()
get_dict_by_classes(classes, ion_type, nominal_mzs, ion_charge, molecular_search_settings, adducts=None)\nReturns a dictionary of molecular formulas.
- check_entry(classe, ion_type, molecular_search_settings)\nChecks if a molecular formula is in the database.
\n- get_all_classes()\nReturns a list of all classes in the database.
\n- get_all()\nReturns a list of all molecular formulas in the database.
\n- delete_entry(row)\nDeletes a molecular formula from the database.
\n- purge(cls)\nDeletes all molecular formulas from the database.
\n- clear_data()\nClears the database.
\n- close(commit=True)\nCloses the database.
\n- add_engine_pidguard(engine)\nAdds multiprocessing guards.
\n
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.__init__", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.__init__", "kind": "function", "doc": "\n", "signature": "(url=None, echo=False)"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.engine", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.engine", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.session", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.session", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.initiate_database", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.initiate_database", "kind": "function", "doc": "Creates the database.
\n\nParameters
\n\n\n- url (str):\nThe URL for the database.
\n- database_name (str):\nThe name of the database.
\n
\n", "signature": "(self, url, database_name):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.commit", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.commit", "kind": "function", "doc": "Commits the session.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.init_engine", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.init_engine", "kind": "function", "doc": "Initializes the SQLAlchemy engine.
\n\nParameters
\n\n\n- url (str):\nThe URL for the database.
\n
\n\nReturns
\n\n\n- sqlalchemy.engine.base.Engine: The SQLAlchemy engine.
\n
\n", "signature": "(self, url):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.get_dict_by_classes", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.get_dict_by_classes", "kind": "function", "doc": "Returns a dictionary of molecular formulas.
\n\nParameters
\n\n\n- classes (list):\nThe list of classes.
\n- ion_type (str):\nThe ion type.
\n- nominal_mzs (list):\nThe list of nominal m/z values.
\n- ion_charge (int):\nThe ion charge.
\n- molecular_search_settings (MolecularFormulaSearchSettings):\nThe molecular formula search settings.
\n- adducts (list, optional):\nThe list of adducts. Default is None.
\n
\n\nReturns
\n\n\n- dict: The dictionary of molecular formulas.
\n
\n\nNotes
\n\nKnown issue, when using SQLite:\nif the number of classes and nominal_m/zs are higher than 999 the query will fail\nSolution: use postgres or split query
\n", "signature": "(\tself,\tclasses,\tion_type,\tnominal_mzs,\tion_charge,\tmolecular_search_settings,\tadducts=None):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.check_entry", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.check_entry", "kind": "function", "doc": "Checks if a molecular formula is in the database.
\n\nParameters
\n\n\n- classe (str):\nThe class of the molecular formula.
\n- ion_type (str):\nThe ion type.
\n- molecular_search_settings (MolecularFormulaSearchSettings):\nThe molecular formula search settings.
\n
\n\nReturns
\n\n\n- sqlalchemy.orm.query.Query: The query.
\n
\n", "signature": "(self, classe, ion_type, molecular_search_settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.get_all_classes", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.get_all_classes", "kind": "function", "doc": "Returns a list of all classes in the database.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.get_all", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.get_all", "kind": "function", "doc": "Returns a list of all molecular formulas in the database.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.delete_entry", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.delete_entry", "kind": "function", "doc": "Deletes a molecular formula from the database.
\n", "signature": "(self, row):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.purge", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.purge", "kind": "function", "doc": "Deletes all molecular formulas from the database.
\n\nNotes
\n\nCareful, this will delete the entire database table
\n", "signature": "(self, cls):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.clear_data", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.clear_data", "kind": "function", "doc": "Clears the database.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.close", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.close", "kind": "function", "doc": "Closes the database.
\n\nParameters
\n\n\n- commit (bool, optional):\nWhether to commit the session. Default is True.
\n
\n", "signature": "(self, commit=True):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.add_engine_pidguard", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.add_engine_pidguard", "kind": "function", "doc": "Adds multiprocessing guards.
\n\nForces a connection to be reconnected if it is detected\nas having been shared to a sub-process.
\n\nParameters
\n\n\n- engine (sqlalchemy.engine.base.Engine):\nThe SQLAlchemy engine.
\n
\n", "signature": "(self, engine):", "funcdef": "def"}, {"fullname": "corems.molecular_id.input", "modulename": "corems.molecular_id.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.input.nistMSI", "modulename": "corems.molecular_id.input.nistMSI", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI", "kind": "class", "doc": "A class for reading NIST MSI files and storing the data in a SQLite database.
\n\nParameters
\n\n\n- file_path (str):\nThe path to the NIST MSI file.
\n- url (str, optional):\nThe URL for the SQLite database. Default is 'sqlite://'.
\n
\n\nRaises
\n\n\n- FileExistsError: If the specified file does not exist.
\n
\n\nAttributes
\n\n\n- file_path (str):\nThe path to the NIST MSI file.
\n- url (str):\nThe URL for the SQLite database.
\n- sqlLite_obj (EI_LowRes_SQLite):\nThe SQLite object for storing the compound data.
\n
\n\nMethods
\n\n\n- run().\nRuns the thread and initializes the SQLite object.
\n- get_sqlLite_obj().\nReturns the SQLite object.
\n- get_compound_data_dict_list().\nParses the NIST MSI file and returns a list of compound data dictionaries.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.__init__", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(file_path, url='sqlite://')"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.file_path", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.file_path", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.url", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.url", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.run", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.run", "kind": "function", "doc": "Runs the thread and initializes the SQLite object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.get_sqlLite_obj", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.get_sqlLite_obj", "kind": "function", "doc": "Returns the SQLite object.
\n\nReturns
\n\n\n- EI_LowRes_SQLite: The SQLite object for storing the compound data.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.get_compound_data_dict_list", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.get_compound_data_dict_list", "kind": "function", "doc": "Parses the NIST MSI file and returns a list of compound data dictionaries.
\n\nReturns
\n\n\n- list: A list of compound data dictionaries.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search", "modulename": "corems.molecular_id.search", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.search.compoundSearch", "modulename": "corems.molecular_id.search.compoundSearch", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch", "kind": "class", "doc": "A class representing a low-resolution mass spectral match.
\n\nParameters
\n\n\n- gcms_obj (object):\nThe GC-MS object.
\n- sql_obj (object, optional):\nThe SQL object for database operations. Default is None.
\n- calibration (bool, optional):\nFlag indicating if the match is for calibration. Default is False.
\n
\n\nAttributes
\n\n\n- gcms_obj (object):\nThe GC-MS object.
\n- sql_obj (object):\nThe SQL object for database operations.
\n- calibration (bool):\nFlag indicating if the match is for calibration.
\n
\n\nMethods
\n\n\n- metabolite_detector_score(gc_peak, ref_obj, spectral_simi).\nCalculates the spectral similarity scores and the similarity score for a given GC peak and reference object.
\n- run().\nRuns the low-resolution mass spectral match.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch.__init__", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(gcms_obj, sql_obj=None, calibration=False)"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch.gcms_obj", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch.gcms_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch.calibration", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch.calibration", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch.metabolite_detector_score", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch.metabolite_detector_score", "kind": "function", "doc": "Calculates the spectral similarity scores and the similarity score for a given GC peak and reference object.
\n\nParameters
\n\n\n- gc_peak (object):\nThe GC peak object.
\n- ref_obj (object):\nThe reference object.
\n- spectral_simi (object):\nThe spectral similarity object.
\n
\n\nReturns
\n\n\n- tuple: A tuple containing the spectral similarity scores, RI score, and similarity score.
\n
\n", "signature": "(self, gc_peak, ref_obj, spectral_simi):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch.run", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch.run", "kind": "function", "doc": "Runs the low-resolution mass spectral match.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks", "modulename": "corems.molecular_id.search.findOxygenPeaks", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks", "kind": "class", "doc": "Class to find Oxygen peaks in a mass spectrum for formula assignment search
\n\nClass to walk 14Da units over oxygen space for negative ion mass spectrum of natural organic matter\nReturns a list of MSPeak class containing the possible Molecular Formula class objects.
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpec class):\nThis is where we store MassSpec class obj,
\n- lookupTableSettings (MolecularLookupTableSettings class):\nThis is where we store MolecularLookupTableSettings class obj
\n- min_O , max_O (int):\nminium and maximum of Oxygen to allow the software to look for\nit will override the settings at lookupTableSettings.usedAtoms\ndefault min = 1, max = 22
\n
\n\nAttributes
\n\n\n- mass_spectrum_obj (MassSpec class):\nThis is where we store MassSpec class obj,
\n- lookupTableSettings (MolecularLookupTableSettings class):\nThis is where we store MolecularLookupTableSettings class obj
\n
\n\nMethods
\n\n\n- run().\nwill be called when the instantiated class method start is called
\n- get_list_found_peaks().\nreturns a list of MSpeaks classes cotaining all the MolecularFormula candidates inside the MSPeak\nfor more details of the structure see MSPeak class and MolecularFormula class
\n- set_mass_spec_indexes_by_found_peaks().\nset the mass spectrum to interate over only the selected indexes
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.__init__", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(\tmass_spectrum_obj,\tsql_db: bool = False,\tmin_O: int = 1,\tmax_O: int = 22)"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.mass_spectrum_obj", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.mass_spectrum_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.min_0", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.min_0", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.max_O", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.max_O", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.run", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.run", "kind": "function", "doc": "Run the thread
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.find_most_abundant_formula", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.find_most_abundant_formula", "kind": "function", "doc": "Find the most abundant formula in the mass spectrum
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpec class):\nMass spectrum object
\n
\n\nReturns
\n\n\n- MolecularFormula class obj: most abundant MolecularFormula with the lowest mass error
\n
\n", "signature": "(self, mass_spectrum_obj):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.find_most_abundant_formula_test", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.find_most_abundant_formula_test", "kind": "function", "doc": "[Test function] Find the most abundant formula in the mass spectrum
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpec class):\nMass spectrum object
\n- settings (MolecularSearchSettings class):\nMolecular search settings object
\n
\n\nReturns
\n\n\n- MolecularFormula class obj: most abundant MolecularFormula with the lowest mass error
\n
\n", "signature": "(self, mass_spectrum_obj, settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.find_series_mspeaks", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.find_series_mspeaks", "kind": "function", "doc": "Find a series of abundant peaks in the mass spectrum for a given molecular formula
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpec class):\nMass spectrum object
\n- molecular_formula_obj_reference (MolecularFormula class):\nMolecular formula object
\n- deltamz (float):\ndelta m/z to look for peaks
\n
\n\nReturns
\n\n\n- list: list of MSpeak class objects
\n
\n", "signature": "(self, mass_spectrum_obj, molecular_formula_obj_reference, deltamz=14):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.get_list_found_peaks", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.get_list_found_peaks", "kind": "function", "doc": "Get the list of found peaks
\n\nReturns
\n\n\n- list: list of MSpeak class objects
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.set_mass_spec_indexes_by_found_peaks", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.set_mass_spec_indexes_by_found_peaks", "kind": "function", "doc": "Set the mass spectrum to interate over only the selected indexes.
\n\nNotes
\n\nWarning!!!!\nset the mass spectrum to interate over only the selected indexes\ndon not forget to call mass_spectrum_obj.reset_indexes after the job is done
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.last_error", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "last_error", "kind": "variable", "doc": "\n", "default_value": "0"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.last_dif", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "last_dif", "kind": "variable", "doc": "\n", "default_value": "0"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.closest_error", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "closest_error", "kind": "variable", "doc": "\n", "default_value": "0"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.error_average", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "error_average", "kind": "variable", "doc": "\n", "default_value": "0"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.nbValues", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "nbValues", "kind": "variable", "doc": "\n", "default_value": "0"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas", "kind": "class", "doc": "Class for searching molecular formulas in a mass spectrum.
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- sql_db (MolForm_SQL, optional):\nThe SQL database object, by default None.
\n- first_hit (bool, optional):\nFlag to indicate whether to skip peaks that already have a molecular formula assigned, by default False.
\n- find_isotopologues (bool, optional):\nFlag to indicate whether to find isotopologues, by default True.
\n
\n\nAttributes
\n\n\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- sql_db (MolForm_SQL):\nThe SQL database object.
\n- first_hit (bool):\nFlag to indicate whether to skip peaks that already have a molecular formula assigned.
\n- find_isotopologues (bool):\nFlag to indicate whether to find isotopologues.
\n
\n\nMethods
\n\n\n- run_search().\nRun the molecular formula search.
\n- run_worker_mass_spectrum().\nRun the molecular formula search on the mass spectrum object.
\n- run_worker_ms_peaks().\nRun the molecular formula search on the given list of mass spectrum peaks.
\n- database_to_dict().\nConvert the database results to a dictionary.
\n- run_molecular_formula().\nRun the molecular formula search on the given list of mass spectrum peaks.
\n- search_mol_formulas().\nSearch for molecular formulas in the mass spectrum.
\n
\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.__init__", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.__init__", "kind": "function", "doc": "\n", "signature": "(\tmass_spectrum_obj,\tsql_db=None,\tfirst_hit: bool = False,\tfind_isotopologues: bool = True)"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.first_hit", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.first_hit", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.find_isotopologues", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.find_isotopologues", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.mass_spectrum_obj", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.mass_spectrum_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.run_search", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.run_search", "kind": "function", "doc": "Run the molecular formula search.
\n\nParameters
\n\n\n- mspeaks (list of MSPeak):\nThe list of mass spectrum peaks.
\n- query (dict):\nThe query dictionary containing the possible molecular formulas.
\n- min_abundance (float):\nThe minimum abundance threshold.
\n- ion_type (str):\nThe ion type.
\n- ion_charge (int):\nThe ion charge.
\n- adduct_atom (str, optional):\nThe adduct atom, by default None.
\n
\n", "signature": "(\tself,\tmspeaks: list,\tquery: dict,\tmin_abundance: float,\tion_type: str,\tion_charge: int,\tadduct_atom=None):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.run_worker_mass_spectrum", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.run_worker_mass_spectrum", "kind": "function", "doc": "Run the molecular formula search on the mass spectrum object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.run_worker_ms_peaks", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.run_worker_ms_peaks", "kind": "function", "doc": "Run the molecular formula search on the given list of mass spectrum peaks.
\n\nParameters
\n\n\n- ms_peaks (list of MSPeak):\nThe list of mass spectrum peaks.
\n
\n", "signature": "(self, ms_peaks):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.database_to_dict", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.database_to_dict", "kind": "function", "doc": "Convert the database results to a dictionary.
\n\nParameters
\n\n\n- classe_str_list (list):\nThe list of class strings.
\n- nominal_mzs (list):\nThe list of nominal m/z values.
\n- mf_search_settings (MolecularFormulaSearchSettings):\nThe molecular formula search settings.
\n- ion_charge (int):\nThe ion charge.
\n
\n\nReturns
\n\n\n- dict: The dictionary containing the database results.
\n
\n", "signature": "(classe_str_list, nominal_mzs, mf_search_settings, ion_charge):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.run_molecular_formula", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.run_molecular_formula", "kind": "function", "doc": "Run the molecular formula search on the given list of mass spectrum peaks.
\n\nParameters
\n\n\n- ms_peaks (list of MSPeak):\nThe list of mass spectrum peaks.
\n
\n", "signature": "(*args, **kw):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.search_mol_formulas", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.search_mol_formulas", "kind": "function", "doc": "Search for molecular formulas in the mass spectrum.
\n\nParameters
\n\n\n- possible_formulas_list (list of MolecularFormula):\nThe list of possible molecular formulas.
\n- ion_type (str):\nThe ion type.
\n- neutral_molform (bool, optional):\nFlag to indicate whether the molecular formulas are neutral, by default True.
\n- find_isotopologues (bool, optional):\nFlag to indicate whether to find isotopologues, by default True.
\n- adduct_atom (str, optional):\nThe adduct atom, by default None.
\n
\n\nReturns
\n\n\n- list of MSPeak: The list of mass spectrum peaks with assigned molecular formulas.
\n
\n", "signature": "(\tself,\tpossible_formulas_list: List[corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormula],\tion_type: str,\tneutral_molform=True,\tfind_isotopologues=True,\tadduct_atom=None) -> List[corems.ms_peak.factory.MSPeakClasses._MSPeak]:", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker", "kind": "class", "doc": "Class for searching molecular formulas in a mass spectrum.
\n\nParameters
\n\n\n- find_isotopologues (bool, optional):\nFlag to indicate whether to find isotopologues, by default True.
\n
\n\nAttributes
\n\n\n- find_isotopologues (bool):\nFlag to indicate whether to find isotopologues.
\n
\n\nMethods
\n\n\n- reset_error().\nReset the error variables.
\n- set_last_error().\nSet the last error.
\n- find_formulas().\nFind the formulas.
\n- calc_error().\nCalculate the error.
\n
\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.__init__", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.__init__", "kind": "function", "doc": "\n", "signature": "(find_isotopologues=True)"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.find_isotopologues", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.find_isotopologues", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.reset_error", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.reset_error", "kind": "function", "doc": "Reset the error variables.
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n
\n", "signature": "(self, mass_spectrum_obj):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.set_last_error", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.set_last_error", "kind": "function", "doc": "Set the last error.
\n\nParameters
\n\n\n- error (float):\nThe error.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n
\n", "signature": "(self, error, mass_spectrum_obj):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.calc_error", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.calc_error", "kind": "function", "doc": "Calculate the error.
\n\nParameters
\n\n\n- mz_exp (float):\nThe experimental m/z value.
\n- mz_calc (float):\nThe calculated m/z value.
\n- method (str, optional):\nThe method, by default 'ppm'.
\n
\n\nRaises
\n\n\n- Exception: If the method is not ppm or ppb.
\n
\n\nReturns
\n\n\n", "signature": "(mz_exp, mz_calc, method='ppm'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.find_formulas", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.find_formulas", "kind": "function", "doc": "Find the formulas.
\n\nParameters
\n\n\n- formulas (list of MolecularFormula):\nThe list of molecular formulas.
\n- min_abundance (float):\nThe minimum abundance threshold.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- ms_peak (MSPeak):\nThe mass spectrum peak.
\n- ion_type (str):\nThe ion type.
\n- ion_charge (int):\nThe ion charge.
\n- adduct_atom (str, optional):\nThe adduct atom, by default None.
\n
\n\nReturns
\n\n\n- list of MSPeak: The list of mass spectrum peaks with assigned molecular formulas.
\n
\n\nNotes
\n\nUses the closest error the next search (this is not ideal, it needs to use confidence \nmetric to choose the right candidate then propagate the error using the error from the best candidate).\nIt needs to add s/n to the equation.\nIt need optimization to define the mz_error_range within a m/z unit since it is directly proportional \nwith the mass, and inversely proportional to the rp. It's not linear, i.e., sigma mass.\nThe idea it to correlate sigma to resolving power, signal to noise and sample complexity per mz unit.\nMethod='distance'
\n", "signature": "(\tself,\tformulas,\tmin_abundance,\tmass_spectrum_obj,\tms_peak,\tion_type,\tion_charge,\tadduct_atom=None):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC", "kind": "class", "doc": "Class for searching molecular formulas in a LC object.
\n\nParameters
\n\n\n- lcms_obj (LC):\nThe LC object.
\n- sql_db (MolForm_SQL, optional):\nThe SQL database object, by default None.
\n- first_hit (bool, optional):\nFlag to indicate whether to skip peaks that already have a molecular formula assigned, by default False.
\n- find_isotopologues (bool, optional):\nFlag to indicate whether to find isotopologues, by default True.
\n
\n\nMethods
\n\n\n- run_untargeted_worker_ms1().\nRun untargeted molecular formula search on the ms1 mass spectrum.
\n- run_target_worker_ms1().\nRun targeted molecular formula search on the ms1 mass spectrum.
\n
\n", "bases": "SearchMolecularFormulas"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.__init__", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.__init__", "kind": "function", "doc": "\n", "signature": "(lcms_obj, sql_db=None, first_hit=False, find_isotopologues=True)"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.first_hit", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.first_hit", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.find_isotopologues", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.find_isotopologues", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.lcms_obj", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.lcms_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.run_untargeted_worker_ms1", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.run_untargeted_worker_ms1", "kind": "function", "doc": "Run untargeted molecular formula search on the ms1 mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.run_target_worker_ms1", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.run_target_worker_ms1", "kind": "function", "doc": "Run targeted molecular formula search on the ms1 mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment", "modulename": "corems.molecular_id.search.priorityAssignment", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment", "kind": "class", "doc": "A class for assigning priority to oxygen classes in a molecular search.
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- sql_db (bool, optional):\nWhether to use an SQL database. The default is False.
\n
\n\nAttributes
\n\n\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- sql_db (MolForm_SQL):\nThe SQL database object.
\n
\n\nMethods
\n\n\n- run().\nRun the priority assignment process.
\n- create_data_base().\nCreate the molecular database for the specified heteroatomic classes.
\n- run_worker_mass_spectrum(assign_classes_order_tuples).\nRun the molecular formula search for each class in the specified order.
\n- get_dict_molecular_database(classe_str_list).\nGet the molecular database as a dictionary.
\n- ox_classes_and_peaks_in_order_().\nGet the oxygen classes and associated peaks in order.
\n- get_classes_in_order(dict_ox_class_and_ms_peak)
\nGet the classes in order. \n
\n", "bases": "threading.Thread"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.__init__", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(mass_spectrum_obj, sql_db=False)"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.mass_spectrum_obj", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.mass_spectrum_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.run", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.run", "kind": "function", "doc": "Run the priority assignment process.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.create_data_base", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.create_data_base", "kind": "function", "doc": "Create the molecular database for the specified heteroatomic classes.
\n\nReturns
\n\n\n- assign_classes_order_str_dict_tuple_ (list):\nA list of tuples containing the class names and dictionaries of class attributes.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.run_worker_mass_spectrum", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.run_worker_mass_spectrum", "kind": "function", "doc": "Run the molecular formula search for each class in the specified order.
\n\nParameters
\n\n\n- assign_classes_order_tuples (list):\nA list of tuples containing the class names and dictionaries of class attributes.
\n
\n", "signature": "(self, assign_classes_order_tuples):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.get_dict_molecular_database", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.get_dict_molecular_database", "kind": "function", "doc": "Get the molecular database as a dictionary.
\n\nParameters
\n\n\n- classe_str_list (list):\nA list of class names.
\n
\n\nReturns
\n\n\n- dict: A dictionary containing the molecular database.
\n
\n", "signature": "(self, classe_str_list):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.ox_classes_and_peaks_in_order_", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.ox_classes_and_peaks_in_order_", "kind": "function", "doc": "Get the oxygen classes and associated peaks in order.
\n\nReturns
\n\n\n- dict: A dictionary containing the oxygen classes and associated peaks.
\n
\n", "signature": "(self) -> dict:", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.get_classes_in_order", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.get_classes_in_order", "kind": "function", "doc": "Get the classes in order.
\n\nParameters
\n\n\n- dict_ox_class_and_ms_peak (dict):\nA dictionary containing the oxygen classes and associated peaks.
\n
\n\nReturns
\n\n\n- list: A list of tuples containing the class names and dictionaries of class attributes.
\n
\n\nNotes
\n\nstructure is \n ('HC', {'HC': 1})
\n", "signature": "(self, dict_ox_class_and_ms_peak) -> [(<class 'str'>, <class 'dict'>)]:", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.get_class_strings_dict", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.get_class_strings_dict", "kind": "function", "doc": "Get the class strings and dictionaries.
\n\nParameters
\n\n\n- all_atoms_tuples (tuple):\nA tuple containing the atoms.
\n- atoms_in_order (list):\nA list of atoms in order.
\n
\n\nReturns
\n\n\n- list: A list of tuples containing the class strings and dictionaries.
\n
\n", "signature": "(all_atoms_tuples, atoms_in_order) -> [(<class 'str'>, <class 'dict'>)]:", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.combine_ox_class_with_other", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.combine_ox_class_with_other", "kind": "function", "doc": "Combine the oxygen classes with other classes.
\n\nParameters
\n\n\n\nReturns
\n\n\n- list: A list of dictionaries.
\n
\n", "signature": "(\tatoms_in_order,\tclasses_strings_dict_tuples,\tdict_ox_class_and_ms_peak) -> [<class 'dict'>]:", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.sort_classes", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.sort_classes", "kind": "function", "doc": "Sort the classes.
\n\nParameters
\n\n\n- atoms_in_order (list):\nA list of atoms in order.
\n- combination_tuples (list):
\n
\n\nReturns
\n\n\n- list: A list of tuples containing the class strings and dictionaries.
\n
\n", "signature": "(atoms_in_order, combination_tuples) -> [(<class 'str'>, <class 'dict'>)]:", "funcdef": "def"}, {"fullname": "corems.ms_peak", "modulename": "corems.ms_peak", "kind": "module", "doc": "\n"}, {"fullname": "corems.ms_peak.calc", "modulename": "corems.ms_peak.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc", "modulename": "corems.ms_peak.calc.MSPeakCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation", "kind": "class", "doc": "Class to perform calculations on MSPeak objects.
\n\nThis class provides methods to perform various calculations on MSPeak objects, such as calculating Kendrick Mass Defect (KMD) and Kendrick Mass (KM), calculating peak area, and fitting peak lineshape using different models.
\n\nParameters
\n\n\n\nAttributes
\n\n\n- _ms_parent (MSParent):\nThe parent MSParent object associated with the MSPeakCalculation object.
\n- mz_exp (float):\nThe experimental m/z value of the peak.
\n- start_scan (int):\nThe start scan index of the peak.
\n- final_scan (int):\nThe final scan index of the peak.
\n- resolving_power (float):\nThe resolving power of the peak.
\n
\n\nMethods
\n\n\n- _calc_kmd(dict_base).\nCalculate the Kendrick Mass Defect (KMD) and Kendrick Mass (KM) for a given base formula.
\n- calc_area().\nCalculate the peak area using numpy's trapezoidal fit.
\n- fit_peak(mz_extend=6, delta_rp=0, model='Gaussian').\nPerform lineshape analysis on a peak using lmfit module.
\n- voigt_pso(w, r, yoff, width, loc, a).\nCalculate the Voigt function for particle swarm optimization (PSO) fitting.
\n- objective_pso(x, w, u).\nCalculate the objective function for PSO fitting.
\n- minimize_pso(lower, upper, w, u).\nMinimize the objective function using the particle swarm optimization algorithm.
\n- fit_peak_pso(mz_extend=6, upsample_multiplier=5).\nPerform lineshape analysis on a peak using particle swarm optimization (PSO) fitting.
\n- voigt(oversample_multiplier=1, delta_rp=0, mz_overlay=1).\n[Legacy] Perform voigt lineshape analysis on a peak.
\n- pseudovoigt(oversample_multiplier=1, delta_rp=0, mz_overlay=1, fraction=0.5).\n[Legacy] Perform pseudovoigt lineshape analysis on a peak.
\n- lorentz(oversample_multiplier=1, delta_rp=0, mz_overlay=1).\n[Legacy] Perform lorentz lineshape analysis on a peak.
\n- gaussian(oversample_multiplier=1, delta_rp=0, mz_overlay=1).\n[Legacy] Perform gaussian lineshape analysis on a peak.
\n- get_mz_domain(oversample_multiplier, mz_overlay).\n[Legacy] Resample/interpolate datapoints for lineshape analysis.
\n- number_possible_assignments().\nReturn the number of possible molecular formula assignments for the peak.
\n- molecular_formula_lowest_error().\nReturn the molecular formula with the smallest absolute mz error.
\n- molecular_formula_highest_prob_score().\nReturn the molecular formula with the highest confidence score.
\n- molecular_formula_earth_filter(lowest_error=True).\nFilter molecular formula using the 'Earth' filter.
\n- molecular_formula_water_filter(lowest_error=True).\nFilter molecular formula using the 'Water' filter.
\n- molecular_formula_air_filter(lowest_error=True).\nFilter molecular formula using the 'Air' filter.
\n- cia_score_S_P_error().\nCompound Identification Algorithm SP Error - Assignment Filter.
\n- cia_score_N_S_P_error().\nCompound Identification Algorithm NSP Error - Assignment Filter.
\n
\n"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.calc_area", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.calc_area", "kind": "function", "doc": "Calculate the peak area using numpy's trapezoidal fit
\n\nuses provided mz_domain to accurately integrate areas independent of digital resolution
\n\nReturns
\n\n\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.fit_peak", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.fit_peak", "kind": "function", "doc": "Lineshape analysis on a peak using lmfit module.
\n\nModel and fit peak lineshape by defined function - using lmfit module\nDoes not oversample/resample/interpolate data points \nBetter to go back to time domain and perform more zero filling - if possible.
\n\nParameters
\n\n\n- mz_extend (int):\nextra points left and right of peak definition to include in fitting
\n- delta_rp (float):\ndelta resolving power to add to resolving power
\n- model (str):\nType of lineshape model to use.\nModels allowed: Gaussian, Lorentz, Voigt
\n
\n\nReturns
\n\n\n- mz_domain (ndarray):\nx-axis domain for fit
\n- fit_peak (lmfit object):\nfit results object from lmfit module
\n
\n\nNotes
\n\nReturns the calculated mz domain, initial defined abundance profile, and the fit peak results object from lmfit module\nmz_extend here extends the x-axis domain so that we have sufficient points either side of the apex to fit.\nTakes about 10ms per peak
\n", "signature": "(self, mz_extend=6, delta_rp=0, model='Gaussian'):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.voigt_pso", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.voigt_pso", "kind": "function", "doc": "Voigt function for particle swarm optimisation (PSO) fitting
\n\nFrom https://github.com/pnnl/nmrfit/blob/master/nmrfit/equations.py.\nCalculates a Voigt function over w based on the relevant properties of the distribution.
\n\nParameters
\n\n\n- w (ndarray):\nArray over which the Voigt function will be evaluated.
\n- r (float):\nRatio between the Guassian and Lorentzian functions.
\n- yoff (float):\nY-offset of the Voigt function.
\n- width (float):\nThe width of the Voigt function.
\n- loc (float):\nCenter of the Voigt function.
\n- a (float):\nArea of the Voigt function.
\n
\n\nReturns
\n\n\n- V (ndarray):\nArray defining the Voigt function over w.
\n
\n\nReferences
\n\n\n- https://github.com/pnnl/nmrfit
\n
\n\nNotes
\n\nParticle swarm optimisation (PSO) fitting function can be significantly more computationally expensive than lmfit, with more parameters to optimise.
\n", "signature": "(self, w, r, yoff, width, loc, a):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.objective_pso", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.objective_pso", "kind": "function", "doc": "Objective function for particle swarm optimisation (PSO) fitting
\n\nThe objective function used to fit supplied data. Evaluates sum of squared differences between the fit and the data.
\n\nParameters
\n\n\n- x (list of floats):\nParameter vector.
\n- w (ndarray):\nArray of frequency data.
\n- u (ndarray):\nArray of data to be fit.
\n
\n\nReturns
\n\n\n- rmse (float):\nRoot mean square error between the data and fit.
\n
\n\nReferences
\n\n\n- https://github.com/pnnl/nmrfit
\n
\n", "signature": "(self, x, w, u):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.minimize_pso", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.minimize_pso", "kind": "function", "doc": "Minimization function for particle swarm optimisation (PSO) fitting
\n\nMinimizes the objective function using the particle swarm optimization algorithm.\nMinimization function based on defined parameters
\n\nParameters
\n\n\n- lower (list of floats):\nLower bounds for the parameters.
\n- upper (list of floats):\nUpper bounds for the parameters.
\n- w (ndarray):\nArray of frequency data.
\n- u (ndarray):\nArray of data to be fit.
\n
\n\nNotes
\n\nParticle swarm optimisation (PSO) fitting function can be significantly more computationally expensive than lmfit, with more parameters to optimise.\nCurrent parameters take ~2 seconds per peak.
\n\nReferences
\n\n\n- https://github.com/pnnl/nmrfit
\n
\n", "signature": "(self, lower, upper, w, u):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.fit_peak_pso", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.fit_peak_pso", "kind": "function", "doc": "Lineshape analysis on a peak using particle swarm optimisation (PSO) fitting
\n\nFunction to fit a Voigt peakshape using particle swarm optimisation (PSO).\nShould return better results than lmfit, but much more computationally expensive
\n\nParameters
\n\n\n- mz_extend (int, optional):\nextra points left and right of peak definition to include in fitting. Defaults to 6.
\n- upsample_multiplier (int, optional):\nfactor to increase x-axis points by for simulation of fitted lineshape function. Defaults to 5.
\n
\n\nReturns
\n\n\n- xopt (array):\nvariables describing the voigt function.\nG/L ratio, width (fwhm), apex (x-axis), area.\ny-axis offset is fixed at 0
\n- fopt (float):\nobjective score (rmse)
\n- psfit (array):\nrecalculated y values based on function and optimised fit
\n- psfit_hdp (tuple of arrays):\n0 - linspace x-axis upsampled grid\n1 - recalculated y values based on function and upsampled x-axis grid\nDoes not change results, but aids in visualisation of the 'true' voigt lineshape
\n
\n\nNotes
\n\nParticle swarm optimisation (PSO) fitting function can be significantly more computationally expensive than lmfit, with more parameters to optimise.
\n", "signature": "(self, mz_extend: int = 6, upsample_multiplier: int = 5):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.voigt", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.voigt", "kind": "function", "doc": "[Legacy] Voigt lineshape analysis function\nLegacy function for voigt lineshape analysis
\n\nParameters
\n\n\n- oversample_multiplier (int):\nfactor to increase x-axis points by for simulation of fitted lineshape function
\n- delta_rp (float):\ndelta resolving power to add to resolving power
\n- mz_overlay (int):\nextra points left and right of peak definition to include in fitting
\n
\n\nReturns
\n\n\n- mz_domain (ndarray):\nx-axis domain for fit
\n- calc_abundance (ndarray):\ncalculated abundance profile based on voigt function
\n
\n", "signature": "(self, oversample_multiplier=1, delta_rp=0, mz_overlay=1):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.pseudovoigt", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.pseudovoigt", "kind": "function", "doc": "[Legacy] pseudovoigt lineshape function
\n\nLegacy function for pseudovoigt lineshape analysis. \nNote - Code may not be functional currently.
\n\nParameters
\n\n\n- oversample_multiplier (int, optional):\nfactor to increase x-axis points by for simulation of fitted lineshape function. Defaults to 1.
\n- delta_rp (float, optional):\ndelta resolving power to add to resolving power. Defaults to 0.
\n- mz_overlay (int, optional):\nextra points left and right of peak definition to include in fitting. Defaults to 1.
\n- fraction (float, optional):\nfraction of gaussian component in pseudovoigt function. Defaults to 0.5.
\n
\n", "signature": "(\tself,\toversample_multiplier=1,\tdelta_rp=0,\tmz_overlay=1,\tfraction=0.5):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.lorentz", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.lorentz", "kind": "function", "doc": "[Legacy] Lorentz lineshape analysis function
\n\nLegacy function for lorentz lineshape analysis
\n\nParameters
\n\n\n- oversample_multiplier (int):\nfactor to increase x-axis points by for simulation of fitted lineshape function
\n- delta_rp (float):\ndelta resolving power to add to resolving power
\n- mz_overlay (int):\nextra points left and right of peak definition to include in fitting
\n
\n\nReturns
\n\n\n- mz_domain (ndarray):\nx-axis domain for fit
\n- calc_abundance (ndarray):\ncalculated abundance profile based on lorentz function
\n
\n", "signature": "(self, oversample_multiplier=1, delta_rp=0, mz_overlay=1):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.gaussian", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.gaussian", "kind": "function", "doc": "[Legacy] Gaussian lineshape analysis function\nLegacy gaussian lineshape analysis function
\n\nParameters
\n\n\n- oversample_multiplier (int):\nfactor to increase x-axis points by for simulation of fitted lineshape function
\n- delta_rp (float):\ndelta resolving power to add to resolving power
\n- mz_overlay (int):\nextra points left and right of peak definition to include in fitting
\n
\n\nReturns
\n\n\n- mz_domain (ndarray):\nx-axis domain for fit
\n- calc_abundance (ndarray):\ncalculated abundance profile based on gaussian function
\n
\n", "signature": "(self, oversample_multiplier=1, delta_rp=0, mz_overlay=1):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.get_mz_domain", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.get_mz_domain", "kind": "function", "doc": "[Legacy] function to resample/interpolate datapoints for lineshape analysis
\n\nThis code is used for the legacy line fitting functions and not recommended.\nLegacy function to support expanding mz domain for legacy lineshape functions
\n\nParameters
\n\n\n- oversample_multiplier (int):\nfactor to increase x-axis points by for simulation of fitted lineshape function
\n- mz_overlay (int):\nextra points left and right of peak definition to include in fitting
\n
\n\nReturns
\n\n\n- mz_domain (ndarray):\nx-axis domain for fit
\n
\n", "signature": "(self, oversample_multiplier, mz_overlay):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.number_possible_assignments", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.number_possible_assignments", "kind": "variable", "doc": "\n"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.molecular_formula_lowest_error", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.molecular_formula_lowest_error", "kind": "function", "doc": "Return the molecular formula with the smallest absolute mz error
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.molecular_formula_highest_prob_score", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.molecular_formula_highest_prob_score", "kind": "function", "doc": "Return the molecular formula with the highest confidence score score
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.molecular_formula_earth_filter", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.molecular_formula_earth_filter", "kind": "function", "doc": "Filter molecular formula using the 'Earth' filter
\n\nThis function applies the Formularity-esque 'Earth' filter to possible molecular formula assignments.\nEarth Filter:\n O > 0 AND N <= 3 AND P <= 2 AND 3P <= O
\n\nIf the lowest_error method is also used, it will return the single formula annotation with the smallest absolute error which also fits the Earth filter. \nOtherwise, it will return all Earth-filter compliant formulas.
\n\nParameters
\n\n\n- lowest_error (bool, optional.):\nReturn only the lowest error formula which also fits the Earth filter. \nIf False, return all Earth-filter compliant formulas. Default is True.
\n
\n\nReturns
\n\n\n- list: List of molecular formula objects which fit the Earth filter
\n
\n\nReferences
\n\n\n- Nikola Tolic et al., \"Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra\"\nAnal. Chem. 2017, 89, 23, 12659\u201312665\ndoi: 10.1021/acs.analchem.7b03318
\n
\n", "signature": "(self, lowest_error=True):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.molecular_formula_water_filter", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.molecular_formula_water_filter", "kind": "function", "doc": "Filter molecular formula using the 'Water' filter
\n\nThis function applies the Formularity-esque 'Water' filter to possible molecular formula assignments.\nWater Filter:\n O > 0 AND N <= 3 AND S <= 2 AND P <= 2
\n\nIf the lowest_error method is also used, it will return the single formula annotation with the smallest absolute error which also fits the Water filter.\nOtherwise, it will return all Water-filter compliant formulas.
\n\nParameters
\n\n\n- lowest_error (bool, optional):\nReturn only the lowest error formula which also fits the Water filter.\nIf False, return all Water-filter compliant formulas. Defaults to 2
\n
\n\nReturns
\n\nlist\n List of molecular formula objects which fit the Water filter
\n\nReferences
\n\n\n- Nikola Tolic et al., \"Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra\"\nAnal. Chem. 2017, 89, 23, 12659\u201312665\ndoi: 10.1021/acs.analchem.7b03318
\n
\n", "signature": "(self, lowest_error=True):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.molecular_formula_air_filter", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.molecular_formula_air_filter", "kind": "function", "doc": "Filter molecular formula using the 'Air' filter
\n\nThis function applies the Formularity-esque 'Air' filter to possible molecular formula assignments.\nAir Filter:\n O > 0 AND N <= 3 AND S <= 1 AND P = 0 AND 3(S+N) <= O
\n\nIf the lowest_error method is also used, it will return the single formula annotation with the smallest absolute error which also fits the Air filter.\nOtherwise, it will return all Air-filter compliant formulas.
\n\nParameters
\n\n\n- lowest_error (bool, optional):\nReturn only the lowest error formula which also fits the Air filter.\nIf False, return all Air-filter compliant formulas. Defaults to True.
\n
\n\nReturns
\n\n\n- list: List of molecular formula objects which fit the Air filter
\n
\n\nReferences
\n\n\n- Nikola Tolic et al., \"Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra\"\nAnal. Chem. 2017, 89, 23, 12659\u201312665\ndoi: 10.1021/acs.analchem.7b03318
\n
\n", "signature": "(self, lowest_error=True):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.cia_score_S_P_error", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.cia_score_S_P_error", "kind": "function", "doc": "Compound Identification Algorithm SP Error - Assignment Filter
\n\nThis function applies the Compound Identification Algorithm (CIA) SP Error filter to possible molecular formula assignments.
\n\nIt takes the molecular formula with the lowest S+P count, and returns the formula with the lowest absolute error from this subset.
\n\nReturns
\n\n\n- MolecularFormula: A single molecular formula which fits the rules of the CIA SP Error filter
\n
\n\nReferences
\n\n\n- Elizabeth B. Kujawinski and Mark D. Behn, \"Automated Analysis of Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectra of Natural Organic Matter\"\nAnal. Chem. 2006, 78, 13, 4363\u20134373\ndoi: 10.1021/ac0600306
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.cia_score_N_S_P_error", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.cia_score_N_S_P_error", "kind": "function", "doc": "Compound Identification Algorithm NSP Error - Assignment Filter
\n\nThis function applies the Compound Identification Algorithm (CIA) NSP Error filter to possible molecular formula assignments.
\n\nIt takes the molecular formula with the lowest N+S+P count, and returns the formula with the lowest absolute error from this subset.
\n\nReturns
\n\n\n- MolecularFormula: A single molecular formula which fits the rules of the CIA NSP Error filter
\n
\n\nReferences
\n\n\n- Elizabeth B. Kujawinski and Mark D. Behn, \"Automated Analysis of Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectra of Natural Organic Matter\"\nAnal. Chem. 2006, 78, 13, 4363\u20134373\ndoi: 10.1021/ac0600306
\n
\n\nRaises
\n\n\n- Exception: If no molecular formula are associated with mass spectrum peak.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.factory", "modulename": "corems.ms_peak.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses", "modulename": "corems.ms_peak.factory.MSPeakClasses", "kind": "module", "doc": "\n"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.ICRMassPeak", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "ICRMassPeak", "kind": "class", "doc": "A class representing a peak in an ICR mass spectrum.
\n", "bases": "_MSPeak"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.ICRMassPeak.__init__", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "ICRMassPeak.__init__", "kind": "function", "doc": "\n", "signature": "(*args, ms_parent=None, exp_freq=None)"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.ICRMassPeak.resolving_power_calc", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "ICRMassPeak.resolving_power_calc", "kind": "function", "doc": "Calculate the theoretical resolving power of the peak.
\n\nParameters
\n\n\n- T (float):\ntransient time
\n- B (float):\nMagnetic Filed Strength (Tesla)
\n
\n\nReturns
\n\n\n- float: Theoretical resolving power of the peak.
\n
\n\nReferences
\n\n\n- Marshall et al. (Mass Spectrom Rev. 1998 Jan-Feb;17(1):1-35.)\nDOI: 10.1002/(SICI)1098-2787(1998)17:1<1::AID-MAS1>3.0.CO;2-K
\n
\n", "signature": "(self, B, T):", "funcdef": "def"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.ICRMassPeak.set_calc_resolving_power", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "ICRMassPeak.set_calc_resolving_power", "kind": "function", "doc": "Set the resolving power of the peak to the calculated one.
\n", "signature": "(self, B: float, T: float):", "funcdef": "def"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.TOFMassPeak", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "TOFMassPeak", "kind": "class", "doc": "A class representing a peak in a TOF mass spectrum.
\n", "bases": "_MSPeak"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.TOFMassPeak.__init__", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "TOFMassPeak.__init__", "kind": "function", "doc": "\n", "signature": "(*args, exp_freq=None)"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.TOFMassPeak.set_calc_resolving_power", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "TOFMassPeak.set_calc_resolving_power", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.OrbiMassPeak", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "OrbiMassPeak", "kind": "class", "doc": "A class representing a peak in an Orbitrap mass spectrum.
\n", "bases": "_MSPeak"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.OrbiMassPeak.__init__", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "OrbiMassPeak.__init__", "kind": "function", "doc": "\n", "signature": "(*args, exp_freq=None)"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.OrbiMassPeak.set_calc_resolving_power", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "OrbiMassPeak.set_calc_resolving_power", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient", "modulename": "corems.transient", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.calc", "modulename": "corems.transient.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.calc.TransientCalc", "modulename": "corems.transient.calc.TransientCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations", "kind": "class", "doc": "Transient Calculations
\n\nParameters
\n\n\n- parameters (corems.transient.parameters.TransientParameters):\nThe transient parameters
\n- bandwidth (float):\nThe bandwidth of the transient (Hz)
\n- number_data_points (int):\nThe number of data points of the transient
\n- exc_low_freq (float):\nThe low frequency of the excitation (Hz)
\n- exc_high_freq (float):\nThe high frequency of the excitation (Hz)
\n
\n\nAttributes
\n\n\n- parameters (corems.transient.parameters.TransientParameters):\nThe transient parameters
\n- bandwidth (float):\nThe bandwidth of the transient (Hz)
\n- number_data_points (int):\nThe number of data points of the transient
\n- exc_low_freq (float):\nThe low frequency of the excitation (Hz)
\n- exc_high_freq (float):\nThe high frequency of the excitation (Hz)
\n
\n\nMethods
\n\n\n- cal_transient_time().\nCalculate the time domain length of the transient
\n- zero_fill(transient).\nZero fill the transient
\n- truncation(transient).\nTruncate the transient
\n- apodization(transient).
\nApodization of the transient \n- calculate_frequency_domain(number_data_points).\nCalculate the frequency domain (axis) of the transient
\n- cut_freq_domain(freqdomain_X, freqdomain_Y).\nCut the frequency domain of the transient
\n- phase_and_absorption_mode_ft().\n[Not Functional] Produce a phased absorption mode FT spectrum
\n- magnitude_mode_ft(transient).\nPerform magnitude mode FT of the transient
\n- correct_dc_offset().\n[Not Yet Implemented] Correct the DC offset of the transient
\n
\n"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.cal_transient_time", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.cal_transient_time", "kind": "function", "doc": "Calculate the time domain length of the transient
\n\nReturns
\n\n\n- float: The time domain length of the transient (s)
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.zero_fill", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.zero_fill", "kind": "function", "doc": "Zero fill the transient
\n\nParameters
\n\n\n- transient (numpy.ndarray):\nThe transient data points
\n
\n\nReturns
\n\n\n- numpy.ndarray: The transient data points zerofilled
\n
\n\nNotes
\n\nThe number of zero fills is defined by the transient parameter number_of_zero_fills.\nThe function first calculate the next power of two of the transient length and zero fills to that length, to take advantage of FFT algorithm.\n If the parameter next_power_of_two is set to False, the function will zero fill to the length of the original transient times the number of zero fills
\n", "signature": "(self, transient):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.truncation", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.truncation", "kind": "function", "doc": "Truncate the transient
\n\nParameters
\n\n\n- transient (numpy.ndarray):\nThe transient data points
\n
\n\nReturns
\n\n\n- numpy.ndarray: The truncated transient data points
\n
\n\nNotes
\n\nThe number of truncations is defined by the transient parameter number_of_truncations
\n", "signature": "(self, transient):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.apodization", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.apodization", "kind": "function", "doc": "Apodization of the transient
\n\nParameters
\n\n\n- transient (numpy.ndarray):\nThe transient data points
\n
\n\nReturns
\n\n\n- numpy.ndarray: The apodized transient data points
\n
\n\nNotes
\n\nThe apodization method is defined by the transient parameter apodization_method.\nThe following apodization methods are available:\n Hamming,\n Hanning,\n Blackman,\n Full-Sine,\n Half-Sine,\n Kaiser,\n Half-Kaiser.
\n\nFor Kaiser and Half-Kaiser, an additional parameter 'beta' is required, set by the transient parameter kaiser_beta.
\n", "signature": "(self, transient):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.calculate_frequency_domain", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.calculate_frequency_domain", "kind": "function", "doc": "Calculate the frequency domain (axis) of the transient
\n\nParameters
\n\n\n- number_data_points (int):\nThe number of data points of the transient
\n
\n\nReturns
\n\n\n- numpy.ndarray: The frequency domain of the transient (Hz)
\n
\n", "signature": "(self, number_data_points):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.cut_freq_domain", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.cut_freq_domain", "kind": "function", "doc": "Cut the frequency domain of the transient
\n\nParameters
\n\n\n- freqdomain_X (numpy.ndarray):\nThe frequency domain of the transient (Hz)
\n- freqdomain_Y (numpy.ndarray):\nThe frequency domain of the transient (Hz)
\n
\n\nReturns
\n\n\n- numpy.ndarray: The frequency domain of the transient (Hz)
\n- numpy.ndarray: The frequency domain of the transient (Hz)
\n
\n", "signature": "(self, freqdomain_X, freqdomain_Y):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.phase_and_absorption_mode_ft", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.phase_and_absorption_mode_ft", "kind": "function", "doc": "[Not Functional] Produce a phased absorption mode FT spectrum
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.perform_magniture_mode_ft", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.perform_magniture_mode_ft", "kind": "function", "doc": "Perform magnitude mode FT of the transient
\n\nParameters
\n\ntransient : numpy.ndarray\n The transient data points
\n\nReturns
\n\n\n- numpy.ndarray: The frequency domain of the transient (Hz)
\n- numpy.ndarray: The magnitude of the transient (a.u.)
\n
\n", "signature": "(self, transient):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.correct_dc_offset", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.correct_dc_offset", "kind": "function", "doc": "[Not Yet Implemented] Correct the DC offset of the transient
\n\nA simple baseline correction to compensate for a DC offset in the recorded transient.\nNot implemented.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient.factory", "modulename": "corems.transient.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses", "modulename": "corems.transient.factory.TransientClasses", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient", "kind": "class", "doc": "The Transient object contains the transient data and the parameters used to process it
\n\nParameters
\n\n\n- data (numpy.ndarray):\nArray with the transient data
\n- d_params (dict):\nDictionary with the parameters to be set
\n
\n\nAttributes
\n\n\n- calibration_terms (tuple):\nTuple with the calibration terms (A, B, C)
\n- bandwidth (float):\nThe bandwidth of the transient (Hz)
\n- number_data_points (int):\nThe number of data points of the transient
\n- polarity (int):\nThe polarity of the transient
\n- transient_time (float):\nThe time domain length of the transient
\n- d_params (dict):\nDictionary with the parameters to be set
\n- frequency_domain (numpy.ndarray):\nArray with the frequency domain
\n- magnitude (numpy.ndarray):\nArray with the magnitude
\n- _full_filename_path (str):\nThe full path of the transient file
\n- _exc_high_freq (float):\nThe high frequency of the excitation (Hz)
\n- _exc_low_freq (float):\nThe low frequency of the excitation (Hz)
\n- _parameters (corems.transient.parameters.TransientParameters):\nThe transient parameters
\n- _transient_data (numpy.ndarray):\nArray with the transient data
\n
\n\nMethods
\n\n\n- get_frequency_domain(plot_result=True).\nGet the frequency domain and magnitude from the transient data
\n- get_mass_spectrum(auto_process=True, plot_result=True, keep_profile=True).
\nGet the mass spectrum from the transient data \n- set_processing_parameter(apodization_method, number_of_truncations, number_of_zero_fills).
\nSet the processing parameters \n- scale_plot_size(factor=1.5).\nScale the plot size by a factor
\n- plot_transient(ax=None, c='k').\nPlot the transient data
\n- plot_zerofilled_transient(ax=None, c='k').\nPlot the transient data with zero fill
\n- plot_apodized_transient(ax=None, c='k').\nPlot the transient data with apodization
\n- plot_frequency_domain(ax=None, c='k').\nPlot the frequency domain and magnitude
\n- set_parameter_from_toml(parameters_path).\nSet the processing parameters from a toml file
\n- set_parameter_from_json(parameters_path).\nSet the processing parameters from a json file
\n
\n", "bases": "corems.transient.calc.TransientCalc.TransientCalculations"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.__init__", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.__init__", "kind": "function", "doc": "\n", "signature": "(data, d_params)"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.d_params", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.d_params", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.frequency_domain", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.frequency_domain", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.magnitude", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.magnitude", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.scale_plot_size", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.scale_plot_size", "kind": "function", "doc": "Scale the plot size by a factor
\n\nParameters
\n\n\n- factor (float, optional):\nThe factor to scale the plot size, by default 1.5
\n
\n", "signature": "(self, factor=1.5):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.set_processing_parameter", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.set_processing_parameter", "kind": "function", "doc": "Set the processing parameters
\n\nParameters
\n\n\n- apodization_method (str):\nApodization method to be used
\n- number_of_truncations (int):\nNumber of truncations to be used
\n- number_of_zero_fills (int):\nNumber of zero fills to be used
\n
\n", "signature": "(\tself,\tapodization_method: str,\tnumber_of_truncations: int,\tnumber_of_zero_fills: int):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.parameters", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.parameters", "kind": "variable", "doc": "The transient parameters
\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.set_parameter_from_toml", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.set_parameter_from_toml", "kind": "function", "doc": "Set the processing parameters from a toml file
\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.set_parameter_from_json", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.set_parameter_from_json", "kind": "function", "doc": "Set the processing parameters from a json file
\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.get_frequency_domain", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.get_frequency_domain", "kind": "function", "doc": "Get the frequency domain and magnitude from the transient data
\n\nParameters
\n\n\n- plot_result (bool, optional):\nPlot the frequency domain and magnitude, by default True
\n
\n\nReturns
\n\n\n- frequency_domain (numpy.ndarray):\nArray with the frequency domain
\n- magnitude (numpy.ndarray):\nArray with the magnitude
\n
\n", "signature": "(self, plot_result=True):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.get_mass_spectrum", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.get_mass_spectrum", "kind": "function", "doc": "Get the mass spectrum from the transient data
\n\nParameters
\n\n\n- auto_process (bool, optional):\nProcess the transient data, by default True
\n- plot_result (bool, optional):\nPlot the frequency domain and magnitude, by default True
\n- keep_profile (bool, optional):\nKeep the profile data, by default True
\n
\n\nReturns
\n\n\n- MassSpecfromFreq: Mass spectrum object
\n
\n", "signature": "(\tself,\tauto_process: bool = True,\tplot_result: bool = True,\tkeep_profile: bool = True) -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq:", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.filename", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.filename", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.dir_location", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.dir_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.A_therm", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.A_therm", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.B_therm", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.B_therm", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.C_therm", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.C_therm", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.plot_transient", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.plot_transient", "kind": "function", "doc": "Plot the transient data
\n\nParameters
\n\n\n- ax (matplotlib.axes, optional):\nMatplotlib axes object, by default None
\n- c (str, optional):\nColor, by default 'k'
\n
\n\nReturns
\n\n\n- matplotlib.axes: Matplotlib axes object
\n
\n", "signature": "(self, ax=None, c='k'):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.plot_zerofilled_transient", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.plot_zerofilled_transient", "kind": "function", "doc": "Plot the transient data with zero fill
\n\nParameters
\n\n\n- ax (matplotlib.axes, optional):\nMatplotlib axes object, by default None
\n- c (str, optional):\nColor, by default 'k'
\n
\n\nReturns
\n\n\n- matplotlib.axes: Matplotlib axes object
\n
\n", "signature": "(self, ax=None, c='k'):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.plot_apodized_transient", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.plot_apodized_transient", "kind": "function", "doc": "Plot the transient data with apodization
\n\nParameters
\n\n\n- ax (matplotlib.axes, optional):\nMatplotlib axes object, by default None
\n- c (str, optional):\nColor, by default 'k'
\n
\n\nReturns
\n\n\n- matplotlib.axes: Matplotlib axes object
\n
\n", "signature": "(self, ax=None, c='k'):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.plot_frequency_domain", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.plot_frequency_domain", "kind": "function", "doc": "Plot the frequency domain and magnitude
\n\nParameters
\n\n\n- ax (matplotlib.axes, optional):\nMatplotlib axes object, by default None
\n- c (str, optional):\nColor, by default 'k'
\n
\n\nReturns
\n\n\n- matplotlib.axes: Matplotlib axes object
\n
\n", "signature": "(self, ax=None, c='k'):", "funcdef": "def"}, {"fullname": "corems.transient.input", "modulename": "corems.transient.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.input.brukerSolarix", "modulename": "corems.transient.input.brukerSolarix", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix", "kind": "class", "doc": "A class used to Read a single Transient from Bruker's FT-MS acquisition station (fid, or ser)
\n\nParameters
\n\n\n- d_directory_location (str):\nthe full path of the .d folder
\n
\n\nAttributes
\n\n\n- d_directory_location (str):\nthe full path of the .d folder
\n- file_location (str):\nthe full path of the .d folder
\n- parameter_filename_location (str):\nthe full path of the apexAcquisition.method file
\n- transient_data_path (str):\nthe full path of the fid or ser file
\n- scan_attr (str):\nthe full path of the scan.xml file
\n
\n\nMethods
\n\n\n- get_transient().\nRead the data and settings returning a Transient class
\n- get_scan_attr().\nRead the scan retention times, TIC values and scan indices.
\n- locate_file(folder, type_file_name).\nFind the full path of a specific file within the acquisition .d folder or subfolders
\n- parse_parameters(parameters_filename).\nOpen the given file and retrieve all parameters from apexAcquisition.method
\n- fix_freq_limits(d_parameters).\nRead and set the correct frequency limits for the spectrum
\n- get_excite_sweep_range(filename).\nDetermine excitation sweep range from ExciteSweep file
\n
\n"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.__init__", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.__init__", "kind": "function", "doc": "\n", "signature": "(d_directory_location)"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.d_directory_location", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.d_directory_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.file_location", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.get_scan_attr", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.get_scan_attr", "kind": "function", "doc": "Function to get the scan retention times, TIC values and scan indices.
\n\nGets information from scan.xml file in the bruker .d folder.\nNote this file is only present in some .d format - e.g. for imaging mode data, it is not present.
\n\nReturns
\n\n\n- dict_scan_rt_tic (dict):\na dictionary with scan number as key and rt and tic as values
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.get_transient", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.get_transient", "kind": "function", "doc": "Function to get the transient data and parameters from a Bruker Solarix .d folder.
\n\nParameters
\n\n\n- scan_number (int):\nthe scan number to be read. Default is 1.
\n
\n\nReturns
\n\n\n- Transient: a transient object
\n
\n", "signature": "(self, scan_number=1):", "funcdef": "def"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.fix_freq_limits", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.fix_freq_limits", "kind": "function", "doc": "Function to read and set the correct frequency limits for the spectrum
\n\nNotes
\n\nThis is using the excitation limits from the apexAcquisition.method file,\nwhich may not match the intended detection limits in edge cases. \nIn default acquisitions, excitation and detection are the same. \nBut, they may not be in some cases with selective excitation, custom excite waveforms, or in 2DMS applications.
\n\nParameters
\n\n\n- d_parameters (dict):\na dictionary with the parameters from the apexAcquisition.method file
\n
\n", "signature": "(self, d_parameters):", "funcdef": "def"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.get_excite_sweep_range", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.get_excite_sweep_range", "kind": "function", "doc": "Function to determine excitation sweep range from ExciteSweep file
\n\nThis looks at the first and last rows of the ExciteSweep file to determine the excitation frequency range.\nNote that this assumes the excitation sweep was linear and the first and last rows are the lowest and highest frequencies.\nThis is presumably always true, but again may be incorrect for edge cases with custom excitation waveforms.
\n\nParameters
\n\n\n- filename (str):\nthe full path to the ExciteSweep file
\n
\n", "signature": "(filename):", "funcdef": "def"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.locate_file", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.locate_file", "kind": "function", "doc": "Function to locate a file in a folder
\n\nFind the full path of a specific file within the acquisition .d folder or subfolders
\n\nParameters
\n\n\n- folder (str):\nthe full path to the folder
\n- type_file_name (str):\nthe name of the file to be located\nExpected options: ExciteSweep or apexAcquisition.method
\n
\n\nReturns
\n\n\n- str: the full path to the file
\n
\n\nNotes
\n\nadapted from code from SPIKE library, https://github.com/spike-project/spike
\n", "signature": "(folder, type_file_name):", "funcdef": "def"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.parse_parameters", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.parse_parameters", "kind": "function", "doc": "Function to parse the parameters from apexAcquisition.method file
\n\nOpen the given file and retrieve all parameters from apexAcquisition.method\n None is written when no value for value is found
\n\nstructure : <param name = \"AMS_ActiveExclusion\"><value>0</value></param>\n
\n\nParameters
\n\n\n- parameters_filename (str):\nthe full path to the apexAcquisition.method file
\n
\n\nReturns
\n\n\n- dict: a dictionary with the parameters and values
\n
\n\nNotes
\n\nAdapted from code from SPIKE library, https://github.com/spike-project/spike.\nCode may not handle all possible parameters, but should be sufficient for most common use cases
\n", "signature": "(parameters_filename):", "funcdef": "def"}, {"fullname": "corems.transient.input.midasDatFile", "modulename": "corems.transient.input.midasDatFile", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile", "kind": "class", "doc": "[Not Implemented] Reads MIDAS .dat files (binary transient data)
\n\nThis class will read .dat binary format transient data, e.g. midas format from Predator or Thermo datastations\nThis code is not yet implemented and is not fully functional.
\n\nParameters
\n\n\n- filename_path (str):\nThe path to the .dat file
\n
\n\nAttributes
\n\n\n- filename_path (str):\nThe path to the .dat file
\n- d_params (dict):\nA dictionary with the parameters of the .dat file
\n- transient_data (numpy.ndarray):\nThe transient data
\n
\n\nMethods
\n\n\n- read_file().\nReads the .dat file and returns the transient data and the parameters
\n- get_transient_data(data_file, d_params).\nReads the transient data from the .dat file
\n- parse_parameter(f).\nParses the parameters from the .dat file
\n
\n\nRaises
\n\n\n- NotImplementedError: This class is not yet implemented.
\n
\n"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile.__init__", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile.__init__", "kind": "function", "doc": "\n", "signature": "(filename_path)"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile.filename_path", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile.filename_path", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile.read_file", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile.read_file", "kind": "function", "doc": "Reads the .dat file and returns the transient data and the parameters
\n\nReturns
\n\n\n- transient_data (numpy.ndarray):\nThe transient data
\n- d_params (dict):\nA dictionary with the parameters of the .dat file
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile.get_transient_data", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile.get_transient_data", "kind": "function", "doc": "Reads the transient data from the .dat file
\n\nParameters
\n\n\n- data_file (file):\nThe .dat file
\n- d_params (dict):\nA dictionary with the parameters of the .dat file
\n
\n\nReturns
\n\n\n- myarray (numpy.ndarray):\nThe transient data
\n
\n", "signature": "(self, data_file, d_params):", "funcdef": "def"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile.parse_parameter", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile.parse_parameter", "kind": "function", "doc": "Parses the parameters from the .dat file
\n\nParameters
\n\n\n- f (file):\nThe .dat file
\n
\n\nReturns
\n\n\n- output_parameters (dict):\nA dictionary with the parameters of the .dat file
\n
\n", "signature": "(self, f):", "funcdef": "def"}];
+ /** pdoc search index */const docs = [{"fullname": "corems", "modulename": "corems", "kind": "module", "doc": "\n\n
\n
\n
\n
\n
\n\nTable of Contents
\n\n\n- Introduction\n
\n- Installation
\n \nExecution:
\n\nSibling Projects:
\n\n
\n\nCoreMS
\n\nCoreMS is a comprehensive mass spectrometry framework for software development and data analysis of small molecules analysis.
\n\nData handling and software development for modern mass spectrometry (MS) is an interdisciplinary endeavor requiring skills in computational science and a deep understanding of MS. To enable scientific software development to keep pace with fast improvements in MS technology, we have developed a Python software framework named CoreMS. The goal of the framework is to provide a fundamental, high-level basis for working with all mass spectrometry data types, allowing custom workflows for data signal processing, annotation, and curation. The data structures were designed with an intuitive, mass spectrometric hierarchical structure, thus allowing organized and easy access to the data and calculations. Moreover, CoreMS supports direct access for almost all vendors\u2019 data formats, allowing for the centralization and automation of all data processing workflows from the raw signal to data annotation and curation.
\n\nCoreMS aims to provide
\n\n\n- logical mass spectrometric data structure
\n- self-containing data and metadata storage
\n- modern molecular formulae assignment algorithms
\n- dynamic molecular search space database search and generator
\n
\n\nCurrent Version
\n\n2.0
\n\nMain Developers/Contact
\n\n\n\n\n\n\n\n\n- Bruker Solarix (CompassXtract)
\n- Bruker Solarix transients, ser and fid (FT magnitude mode only)
\n- ThermoFisher (.raw)
\n- Spectroswiss signal booster data-acquisition station (.hdf5)
\n- MagLab ICR data-acquisition station (FT and magnitude mode) (.dat)
\n- ANDI NetCDF for GC-MS (.cdf)
\n- Generic mass list in profile and centroid mde (include all delimiters types and Excel formats)
\n- CoreMS exported processed mass list files(excel, .csv, .txt, pandas dataframe as .pkl)
\n- CoreMS self-containing Hierarchical Data Format (.hdf5)
\n- Pandas Dataframe
\n- Support for cloud Storage using s3path.S3path(see examples of usage here: S3 Support)
\n
\n\n\n\n\n- Pandas data frame (can be saved using pickle, h5, etc)
\n- Text Files (.csv, tab separated .txt, etc)
\n- Microsoft Excel (xlsx)
\n- Automatic JSON for metadata storage and reuse
\n- Self-containing Hierarchical Data Format (.hdf5) including raw data and ime-series data-point for processed data-sets with all associated metadata stored as json attributes
\n
\n\nData structure types
\n\n\n- LC-MS
\n- GC-MS
\n- Transient
\n- Mass Spectra
\n- Mass Spectrum
\n- Mass Spectral Peak
\n- Molecular Formula
\n
\n\nIn progress data structures
\n\n\n- IMS-MS
\n- LC-IMS-MS
\n- Collections
\n- Molecular Structure
\n
\n\n
\n\nAvailable features
\n\n\n\n\n- Apodization, Zerofilling, and Magnitude mode FT
\n- Manual and automatic noise threshold calculation
\n- Peak picking using apex quadratic fitting
\n- Experimental resolving power calculation
\n- Frequency and m/z domain calibration functions:
\n- LedFord equation
\n- Linear equation
\n- Quadratic equation
\n- Automatic search most abundant Ox homologue series
\n- Automatic local (SQLite) or external (PostgreSQL) database check, generation, and search
\n- Automatic molecular formulae assignments algorithm for ESI(-) MS for natural organic matter analysis
\n- Automatic fine isotopic structure calculation and search for all isotopes
\n- Flexible Kendrick normalization base
\n- Kendrick filter using density-based clustering
\n- Kendrick classification
\n- Heteroatoms classification and visualization
\n
\n\nGC-MS Signal Processing, Calibration, and Compound Identification
\n\n\n- Baseline detection, subtraction, smoothing
\n- m/z based Chromatogram Peak Deconvolution,
\n- Manual and automatic noise threshold calculation
\n- First and second derivatives peak picking methods
\n- Peak Area Calculation
\n- Retention Index Calibration
\n- Automatic local (SQLite) or external (MongoDB or PostgreSQL) database check, generation, and search
\n- Automatic molecular match algorithm with all spectral similarity methods
\n
\n\nHigh Resolution Mass Spectrum Simulations
\n\n\n- Peak shape (Lorentz, Gaussian, Voigt, and pseudo-Voigt)
\n- Peak fitting for peak shape definition
\n- Peak position in function of data points, signal to noise and resolving power (Lorentz and Gaussian)
\n- Prediction of mass error distribution
\n- Calculated ICR Resolving Power based on magnetic field (B), and transient time(T)
\n
\n\n
\n\nInstallation
\n\n\n\nBy default the molecular formula database will be generated using SQLite
\n\nTo use Postgresql the easiest way is to build a docker container:
\n\n\n
docker-compose up -d\n
\n
\n- Change the url_database on MSParameters.molecular_search.url_database to: \"postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp\"
\n- Set the url_database env variable COREMS_DATABASE_URL to: \"postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp\"
\n
\n\nThermo Raw File Access:
\n\nTo be able to open thermo file a installation of pythonnet is needed:
\n\n\n- Windows: \n
\n
pip install pythonnet\n
\n
\n
\n\n\n- Mac and Linux:\n
\n
brew install mono\npip install pythonnet \n
\n
\n
\n\n
\n\nDocker stack
\n\nAnother option to use CoreMS is to run the docker stack that will start the CoreMS containers
\n\nMolecular Database and Jupyter Notebook Docker Containers
\n\nA docker container containing:
\n\n\n- A custom python distribution will all dependencies installed
\n- A Jupyter notebook server with workflow examples
\n- A PostgreSQL database for the molecular formulae assignment
\n
\n\nIf you don't have docker installed, the easiest way is to install docker for desktop
\n\n\nStart the containers using docker-compose (easiest way):
\n\nOn docker-compose-jupyter.yml there is a volume mapping for the tests_data directory with the data provided for testing, to change to your data location:
\n\n\nlocate the volumes on docker-compose-jupyter.yml:
\n\n\n
volumes:\n - ./tests/tests_data:/home/CoreMS/data\n
\n
change \"./tests/tests_data\" to your data directory location
\n\n\n
volumes:\n - path_to_your_data_directory:/home/corems/data\n
\n
save the file and then call:
\n\n\n
docker-compose -f docker-compose-jupyter.yml up\n
\n
Another option is to manually build the containers:
\n\n\nBuild the corems image:
\n\n\n
docker build -t corems:local .\n
\n
Start the database container:
\n\n\n
docker-compose up -d \n
\n
Start the Jupyter Notebook:
\n\n\n
docker run --rm -v ./data:/home/CoreMS/data corems:local\n
\n
Open your browser, copy and past the URL address provided in the terminal: http://localhost:8888/?token=<token>.
Open the CoreMS-Tutorial.ipynb
\n\n
\n\nSimple Script Example
\n\nMore examples can be found under the directory examples/scripts, examples/notebooks
\n\n\n- Basic functionality example
\n
\n\n\n
from corems.transient.input.brukerSolarix import ReadBrukerSolarix\nfrom corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas\nfrom corems.mass_spectrum.output.export import HighResMassSpecExport\nfrom matplotlib import pyplot\n\nfile_path= 'tests/tests_data/ftms/ESI_NEG_SRFA.d'\n\n# Instatiate the Bruker Solarix reader with the filepath\nbruker_reader = ReadBrukerSolarix(file_path)\n\n# Use the reader to instatiate a transient object\nbruker_transient_obj = bruker_reader.get_transient()\n\n# Calculate the transient duration time\nT = bruker_transient_obj.transient_time\n\n# Use the transient object to instatitate a mass spectrum object\nmass_spectrum_obj = bruker_transient_obj.get_mass_spectrum(plot_result=False, auto_process=True)\n\n# The following SearchMolecularFormulas function does the following\n# - searches monoisotopic molecular formulas for all mass spectral peaks\n# - calculates fine isotopic structure based on monoisotopic molecular formulas found and current dynamic range\n# - searches molecular formulas of correspondent calculated isotopologues\n# - settings are stored at SearchConfig.json and can be changed directly on the file or inside the framework class\n\nSearchMolecularFormulas(mass_spectrum_obj, first_hit=False).run_worker_mass_spectrum()\n\n# Iterate over mass spectral peaks objs within the mass_spectrum_obj\nfor mspeak in mass_spectrum_obj.sort_by_abundance():\n\n # If there is at least one molecular formula associated, mspeak returns True\n if mspeak:\n\n # Get the molecular formula with the highest mass accuracy\n molecular_formula = mspeak.molecular_formula_lowest_error\n\n # Plot mz and peak height\n pyplot.plot(mspeak.mz_exp, mspeak.abundance, 'o', c='g')\n\n # Iterate over all molecular formulas associated with the ms peaks obj\n for molecular_formula in mspeak:\n\n # Check if the molecular formula is a isotopologue\n if molecular_formula.is_isotopologue:\n\n # Access the molecular formula text representation and print\n print (molecular_formula.string)\n\n # Get 13C atoms count\n print (molecular_formula['13C'])\n else:\n # Get mz and peak height\n print(mspeak.mz_exp,mspeak.abundance)\n\n# Save data\n## to a csv file\nmass_spectrum_obj.to_csv("filename")\nmass_spectrum_obj.to_hdf("filename")\n# to pandas Datarame pickle\nmass_spectrum_obj.to_pandas("filename")\n\n# Extract data as a pandas Dataframe\ndf = mass_spectrum_obj.to_dataframe()\n
\n
UML Diagrams
\n\nUML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS classes can be found here.
\n\nCiting CoreMS
\n\nIf you use CoreMS in your work, please use the following citation:\nVersion 2.0 Release on GitHub, archived on Zenodo:
\n\n
\n\nYuri E. Corilo, William R. Kew, Lee Ann McCue (2021, March 27). EMSL-Computing/CoreMS: CoreMS 2.0 (Version v2.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641552\n
\n\nThis material was prepared as an account of work sponsored by an agency of the\nUnited States Government. Neither the United States Government nor the United\nStates Department of Energy, nor Battelle, nor any of their employees, nor any\njurisdiction or organization that has cooperated in the development of these\nmaterials, makes any warranty, express or implied, or assumes any legal\nliability or responsibility for the accuracy, completeness, or usefulness or\nany information, apparatus, product, software, or process disclosed, or\nrepresents that its use would not infringe privately owned rights.
\n\nReference herein to any specific commercial product, process, or service by\ntrade name, trademark, manufacturer, or otherwise does not necessarily\nconstitute or imply its endorsement, recommendation, or favoring by the United\nStates Government or any agency thereof, or Battelle Memorial Institute. The\nviews and opinions of authors expressed herein do not necessarily state or\nreflect those of the United States Government or any agency thereof.
\n\n PACIFIC NORTHWEST NATIONAL LABORATORY\n operated by\n BATTELLE\n for the\n UNITED STATES DEPARTMENT OF ENERGY\n under Contract DE-AC05-76RL01830\n
\n"}, {"fullname": "corems.timeit", "modulename": "corems", "qualname": "timeit", "kind": "function", "doc": "\n", "signature": "(method):", "funcdef": "def"}, {"fullname": "corems.SuppressPrints", "modulename": "corems", "qualname": "SuppressPrints", "kind": "class", "doc": "\n"}, {"fullname": "corems.get_filenames", "modulename": "corems", "qualname": "get_filenames", "kind": "function", "doc": "\n", "signature": "(app=None):", "funcdef": "def"}, {"fullname": "corems.get_filename", "modulename": "corems", "qualname": "get_filename", "kind": "function", "doc": "\n", "signature": "(app=None):", "funcdef": "def"}, {"fullname": "corems.get_dirname", "modulename": "corems", "qualname": "get_dirname", "kind": "function", "doc": "\n", "signature": "(app=None):", "funcdef": "def"}, {"fullname": "corems.get_dirnames", "modulename": "corems", "qualname": "get_dirnames", "kind": "function", "doc": "\n", "signature": "(app=None):", "funcdef": "def"}, {"fullname": "corems.chunks", "modulename": "corems", "qualname": "chunks", "kind": "function", "doc": "Yield successive n-sized chunks from lst.
\n", "signature": "(lst, n):", "funcdef": "def"}, {"fullname": "corems.corems_md5", "modulename": "corems", "qualname": "corems_md5", "kind": "function", "doc": "\n", "signature": "(fname):", "funcdef": "def"}, {"fullname": "corems.chroma_peak", "modulename": "corems.chroma_peak", "kind": "module", "doc": "\n"}, {"fullname": "corems.chroma_peak.calc", "modulename": "corems.chroma_peak.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.chroma_peak.calc.ChromaPeakCalc", "modulename": "corems.chroma_peak.calc.ChromaPeakCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.chroma_peak.calc.ChromaPeakCalc.GCPeakCalculation", "modulename": "corems.chroma_peak.calc.ChromaPeakCalc", "qualname": "GCPeakCalculation", "kind": "class", "doc": "Class for performing peak calculations in GC chromatography.
\n\nMethods
\n\n\ncalc_area(self, tic: List[float], dx: float) -> None: Calculate the area under the curve of the chromatogram.linear_ri(self, right_ri: float, left_ri: float, left_rt: float, right_rt: float) -> float: Calculate the retention index using linear interpolation.calc_ri(self, rt_ri_pairs: List[Tuple[float, float]]) -> int: Calculate the retention index based on the given retention time - retention index pairs.
\n"}, {"fullname": "corems.chroma_peak.calc.ChromaPeakCalc.GCPeakCalculation.calc_area", "modulename": "corems.chroma_peak.calc.ChromaPeakCalc", "qualname": "GCPeakCalculation.calc_area", "kind": "function", "doc": "Calculate the area under the curve of the chromatogram.
\n\nParameters
\n\n\n- tic (List[float]):\nThe total ion current (TIC) values.
\n- dx (float):\nThe spacing between data points.
\n
\n", "signature": "(self, tic: list[float], dx: float) -> None:", "funcdef": "def"}, {"fullname": "corems.chroma_peak.calc.ChromaPeakCalc.GCPeakCalculation.linear_ri", "modulename": "corems.chroma_peak.calc.ChromaPeakCalc", "qualname": "GCPeakCalculation.linear_ri", "kind": "function", "doc": "Calculate the retention index using linear interpolation.
\n\nParameters
\n\n\n- right_ri (float):\nThe retention index at the right reference point.
\n- left_ri (float):\nThe retention index at the left reference point.
\n- left_rt (float):\nThe retention time at the left reference point.
\n- right_rt (float):\nThe retention time at the right reference point.
\n
\n\nReturns
\n\n\n- float: The calculated retention index.
\n
\n", "signature": "(\tself,\tright_ri: float,\tleft_ri: float,\tleft_rt: float,\tright_rt: float) -> float:", "funcdef": "def"}, {"fullname": "corems.chroma_peak.calc.ChromaPeakCalc.GCPeakCalculation.calc_ri", "modulename": "corems.chroma_peak.calc.ChromaPeakCalc", "qualname": "GCPeakCalculation.calc_ri", "kind": "function", "doc": "Calculate the retention index based on the given retention time - retention index pairs.
\n\nParameters
\n\n\n- rt_ri_pairs (List[Tuple[float, float]]):\nThe list of retention time - retention index pairs.
\n
\n", "signature": "(self, rt_ri_pairs: list[tuple[float, float]]) -> None:", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory", "modulename": "corems.chroma_peak.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "kind": "module", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase", "kind": "class", "doc": "Base class for chromatographic peak (ChromaPeak) objects.
\n\nParameters
\n\n\n- chromatogram_parent (Chromatogram):\nThe parent chromatogram object.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- start_index (int):\nThe start index of the peak.
\n- index (int):\nThe index of the peak.
\n- final_index (int):\nThe final index of the peak.
\n
\n\nAttributes
\n\n\n- start_scan (int):\nThe start scan of the peak.
\n- final_scan (int):\nThe final scan of the peak.
\n- apex_scan (int):\nThe apex scan of the peak.
\n- chromatogram_parent (Chromatogram):\nThe parent chromatogram object.
\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- _area (float):\nThe area of the peak.
\n
\n\nProperties
\n\n\n- retention_time : float. \nThe retention time of the peak.
\n- tic : float. \nThe total ion current of the peak.
\n- area : float. \nThe area of the peak.
\n- rt_list : list. \nThe list of retention times within the peak.
\n- tic_list : list.\nThe list of total ion currents within the peak.
\n
\n\nMethods
\n\n\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.__init__", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.__init__", "kind": "function", "doc": "\n", "signature": "(\tchromatogram_parent,\tmass_spectrum_obj,\tstart_index,\tindex,\tfinal_index)"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.start_scan", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.start_scan", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.final_scan", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.final_scan", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.apex_scan", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.apex_scan", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.chromatogram_parent", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.chromatogram_parent", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.mass_spectrum", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.retention_time", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.retention_time", "kind": "variable", "doc": "Retention Time
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.tic", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.tic", "kind": "variable", "doc": "Total Ion Current
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.area", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.area", "kind": "variable", "doc": "Peak Area
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.rt_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.rt_list", "kind": "variable", "doc": "Retention Time List
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.ChromaPeakBase.tic_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "ChromaPeakBase.tic_list", "kind": "variable", "doc": "Total Ion Current List
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak", "kind": "class", "doc": "Data dependent peak (DataDependentPeak) object.
\n\nParameters
\n\n\n- chromatogram_parent (Chromatogram):\nThe parent chromatogram object.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- peak_indexes (tuple):\nThe start, apex and final indexes of the peak.
\n- eic_data (EIC_Data):\nThe EIC data object.
\n- Attributes
\n- --------
\n- _eic_data (EIC_Data):\nThe EIC data object.
\n- _possible_molecular_formulae (list):\nThe list of possible molecular formulas.
\n
\n\nProperties
\n\n\n- eic_rt_list : list. \nEIC retention time list.
\n- eic_list : list.\nEIC list.
\n- targeted_molecular_formulas : list.\nThe list of possible molecular formulas.
\n
\n\nMethods
\n\n\n- add_dependent_mass_spectrum(mass_spectrum).
\nAdd a dependent mass spectrum to the peak. \n- add_molecular_formula(molfform).
\nAdd a molecular formula to the peak. \n
\n", "bases": "ChromaPeakBase"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.__init__", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.__init__", "kind": "function", "doc": "\n", "signature": "(\tchromatogram_parent,\tmass_spectrum_obj,\tpeak_indexes,\teic_data: corems.mass_spectra.factory.LC_Temp.EIC_Data,\tpossible_molform=None)"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.add_dependent_mass_spectrum", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.add_dependent_mass_spectrum", "kind": "function", "doc": "Add a dependent mass spectrum to the peak.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.add_molecular_formula", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.add_molecular_formula", "kind": "function", "doc": "Add a molecular formula to the peak.
\n\nParameters
\n\n\n- molfform (str):\nThe molecular formula.
\n
\n", "signature": "(self, molfform):", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.eic_rt_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.eic_rt_list", "kind": "variable", "doc": "EIC Retention Time List
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.eic_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.eic_list", "kind": "variable", "doc": "EIC List
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.DataDependentPeak.targeted_molecular_formulas", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "DataDependentPeak.targeted_molecular_formulas", "kind": "variable", "doc": "Targeted Molecular Formulas
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak", "kind": "class", "doc": "Class representing a peak in a gas chromatography (GC) chromatogram.
\n\nParameters
\n\n\n- chromatogram_parent (Chromatogram):\nThe parent chromatogram object.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object associated with the peak.
\n- indexes (tuple):\nThe indexes of the peak in the chromatogram.
\n
\n\nAttributes
\n\n\n- _compounds (list):\nList of compounds associated with the peak.
\n- _ri (float or None):\nRetention index of the peak.
\n
\n\nMethods
\n\n\n- __len__(). Returns the number of compounds associated with the peak.
\n- __getitem__(position). Returns the compound at the specified position.
\n- remove_compound(compounds_obj). Removes the specified compound from the peak.
\n- clear_compounds(). Removes all compounds from the peak.
\n- add_compound(compounds_dict, spectral_similarity_scores, ri_score=None, similarity_score=None). Adds a compound to the peak with the specified attributes.
\n- ri(). Returns the retention index of the peak.
\n- highest_ss_compound(). Returns the compound with the highest spectral similarity score.
\n- highest_score_compound(). Returns the compound with the highest similarity score.
\n- compound_names(). Returns a list of names of compounds associated with the peak.
\n
\n", "bases": "ChromaPeakBase, corems.chroma_peak.calc.ChromaPeakCalc.GCPeakCalculation"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.__init__", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.__init__", "kind": "function", "doc": "\n", "signature": "(chromatogram_parent, mass_spectrum_obj, indexes)"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.remove_compound", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.remove_compound", "kind": "function", "doc": "\n", "signature": "(self, compounds_obj):", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.clear_compounds", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.clear_compounds", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.add_compound", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.add_compound", "kind": "function", "doc": "Adds a compound to the peak with the specified attributes.
\n\nParameters
\n\n\n- compounds_dict (dict):\nDictionary containing the compound information.
\n- spectral_similarity_scores (dict):\nDictionary containing the spectral similarity scores.
\n- ri_score (float or None, optional):\nThe retention index score of the compound. Default is None.
\n- similarity_score (float or None, optional):\nThe similarity score of the compound. Default is None.
\n
\n", "signature": "(\tself,\tcompounds_dict,\tspectral_similarity_scores,\tri_score=None,\tsimilarity_score=None):", "funcdef": "def"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.ri", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.ri", "kind": "variable", "doc": "Returns the retention index of the peak.
\n\nReturns
\n\n\n- float or None: The retention index of the peak.
\n
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.highest_ss_compound", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.highest_ss_compound", "kind": "variable", "doc": "Returns the compound with the highest spectral similarity score.
\n\nReturns
\n\n\n- LowResCompoundRef or None: The compound with the highest spectral similarity score.
\n
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.highest_score_compound", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.highest_score_compound", "kind": "variable", "doc": "Returns the compound with the highest similarity score.
\n\nReturns
\n\n\n- LowResCompoundRef or None: The compound with the highest similarity score.
\n
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeak.compound_names", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeak.compound_names", "kind": "variable", "doc": "Returns a list of names of compounds associated with the peak.
\n\nReturns
\n\n\n- list: List of names of compounds associated with the peak.
\n
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeakDeconvolved", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeakDeconvolved", "kind": "class", "doc": "Represents a deconvolved peak in a chromatogram.
\n\nParameters
\n\n\n- chromatogram_parent (Chromatogram):\nThe parent chromatogram object.
\n- mass_spectra (list):\nList of mass spectra associated with the peak.
\n- apex_index (int):\nIndex of the apex mass spectrum in the
mass_spectra list. \n- rt_list (list):\nList of retention times.
\n- tic_list (list):\nList of total ion currents.
\n
\n", "bases": "GCPeak"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeakDeconvolved.__init__", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeakDeconvolved.__init__", "kind": "function", "doc": "\n", "signature": "(chromatogram_parent, mass_spectra, apex_index, rt_list, tic_list)"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeakDeconvolved.mass_spectra", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeakDeconvolved.mass_spectra", "kind": "variable", "doc": "\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeakDeconvolved.rt_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeakDeconvolved.rt_list", "kind": "variable", "doc": "Get the list of retention times.
\n\nReturns
\n\n\n- list: The list of retention times.
\n
\n"}, {"fullname": "corems.chroma_peak.factory.ChromaPeakClasses.GCPeakDeconvolved.tic_list", "modulename": "corems.chroma_peak.factory.ChromaPeakClasses", "qualname": "GCPeakDeconvolved.tic_list", "kind": "variable", "doc": "Get the list of total ion currents.
\n\nReturns
\n\n\n- list: The list of total ion currents.
\n
\n"}, {"fullname": "corems.collection", "modulename": "corems.collection", "kind": "module", "doc": "\n"}, {"fullname": "corems.collection.factory", "modulename": "corems.collection.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.collection.input", "modulename": "corems.collection.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.collection.output", "modulename": "corems.collection.output", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation", "modulename": "corems.encapsulation", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.constant", "modulename": "corems.encapsulation.constant", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.constant.Labels", "modulename": "corems.encapsulation.constant", "qualname": "Labels", "kind": "class", "doc": "Class for Labels used in CoreMS
\n\nThese labels are used to define:
\n\n\n- types of columns in plaintext data inputs,
\n- types of data/mass spectra
\n- types of assignment for ions
\n
\n"}, {"fullname": "corems.encapsulation.constant.Labels.mz", "modulename": "corems.encapsulation.constant", "qualname": "Labels.mz", "kind": "variable", "doc": "\n", "default_value": "'m/z'"}, {"fullname": "corems.encapsulation.constant.Labels.abundance", "modulename": "corems.encapsulation.constant", "qualname": "Labels.abundance", "kind": "variable", "doc": "\n", "default_value": "'Peak Height'"}, {"fullname": "corems.encapsulation.constant.Labels.rp", "modulename": "corems.encapsulation.constant", "qualname": "Labels.rp", "kind": "variable", "doc": "\n", "default_value": "'Resolving Power'"}, {"fullname": "corems.encapsulation.constant.Labels.s2n", "modulename": "corems.encapsulation.constant", "qualname": "Labels.s2n", "kind": "variable", "doc": "\n", "default_value": "'S/N'"}, {"fullname": "corems.encapsulation.constant.Labels.label", "modulename": "corems.encapsulation.constant", "qualname": "Labels.label", "kind": "variable", "doc": "\n", "default_value": "'label'"}, {"fullname": "corems.encapsulation.constant.Labels.bruker_profile", "modulename": "corems.encapsulation.constant", "qualname": "Labels.bruker_profile", "kind": "variable", "doc": "\n", "default_value": "'Bruker_Profile'"}, {"fullname": "corems.encapsulation.constant.Labels.thermo_profile", "modulename": "corems.encapsulation.constant", "qualname": "Labels.thermo_profile", "kind": "variable", "doc": "\n", "default_value": "'Thermo_Profile'"}, {"fullname": "corems.encapsulation.constant.Labels.simulated_profile", "modulename": "corems.encapsulation.constant", "qualname": "Labels.simulated_profile", "kind": "variable", "doc": "\n", "default_value": "'Simulated Profile'"}, {"fullname": "corems.encapsulation.constant.Labels.booster_profile", "modulename": "corems.encapsulation.constant", "qualname": "Labels.booster_profile", "kind": "variable", "doc": "\n", "default_value": "'Booster Profile'"}, {"fullname": "corems.encapsulation.constant.Labels.bruker_frequency", "modulename": "corems.encapsulation.constant", "qualname": "Labels.bruker_frequency", "kind": "variable", "doc": "\n", "default_value": "'Bruker_Frequency'"}, {"fullname": "corems.encapsulation.constant.Labels.midas_frequency", "modulename": "corems.encapsulation.constant", "qualname": "Labels.midas_frequency", "kind": "variable", "doc": "\n", "default_value": "'Midas_Frequency'"}, {"fullname": "corems.encapsulation.constant.Labels.thermo_centroid", "modulename": "corems.encapsulation.constant", "qualname": "Labels.thermo_centroid", "kind": "variable", "doc": "\n", "default_value": "'Thermo_Centroid'"}, {"fullname": "corems.encapsulation.constant.Labels.corems_centroid", "modulename": "corems.encapsulation.constant", "qualname": "Labels.corems_centroid", "kind": "variable", "doc": "\n", "default_value": "'CoreMS_Centroid'"}, {"fullname": "corems.encapsulation.constant.Labels.gcms_centroid", "modulename": "corems.encapsulation.constant", "qualname": "Labels.gcms_centroid", "kind": "variable", "doc": "\n", "default_value": "'Thermo_Centroid'"}, {"fullname": "corems.encapsulation.constant.Labels.unassigned", "modulename": "corems.encapsulation.constant", "qualname": "Labels.unassigned", "kind": "variable", "doc": "\n", "default_value": "'unassigned'"}, {"fullname": "corems.encapsulation.constant.Labels.radical_ion", "modulename": "corems.encapsulation.constant", "qualname": "Labels.radical_ion", "kind": "variable", "doc": "\n", "default_value": "'RADICAL'"}, {"fullname": "corems.encapsulation.constant.Labels.protonated_de_ion", "modulename": "corems.encapsulation.constant", "qualname": "Labels.protonated_de_ion", "kind": "variable", "doc": "\n", "default_value": "'DE_OR_PROTONATED'"}, {"fullname": "corems.encapsulation.constant.Labels.protonated", "modulename": "corems.encapsulation.constant", "qualname": "Labels.protonated", "kind": "variable", "doc": "\n", "default_value": "'protonated'"}, {"fullname": "corems.encapsulation.constant.Labels.de_protonated", "modulename": "corems.encapsulation.constant", "qualname": "Labels.de_protonated", "kind": "variable", "doc": "\n", "default_value": "'de-protonated'"}, {"fullname": "corems.encapsulation.constant.Labels.adduct_ion", "modulename": "corems.encapsulation.constant", "qualname": "Labels.adduct_ion", "kind": "variable", "doc": "\n", "default_value": "'ADDUCT'"}, {"fullname": "corems.encapsulation.constant.Labels.neutral", "modulename": "corems.encapsulation.constant", "qualname": "Labels.neutral", "kind": "variable", "doc": "\n", "default_value": "'neutral'"}, {"fullname": "corems.encapsulation.constant.Labels.ion_type", "modulename": "corems.encapsulation.constant", "qualname": "Labels.ion_type", "kind": "variable", "doc": "\n", "default_value": "'IonType'"}, {"fullname": "corems.encapsulation.constant.Labels.ion_type_translate", "modulename": "corems.encapsulation.constant", "qualname": "Labels.ion_type_translate", "kind": "variable", "doc": "\n", "default_value": "{'protonated': 'DE_OR_PROTONATED', 'de-protonated': 'DE_OR_PROTONATED', 'radical': 'RADICAL', 'adduct': 'ADDUCT'}"}, {"fullname": "corems.encapsulation.constant.Atoms", "modulename": "corems.encapsulation.constant", "qualname": "Atoms", "kind": "class", "doc": "Class for Atoms in CoreMS
\n\nThis class includes key properties of atoms (and the electron) and isotopes, including their exact masses, relative abundances, and covalences. \nIt also associates which isotopes are for the same element, and provides an ordering of elements.
\n\nIUPAC definition of monoisotopic mass is based on the most abundant isotopes of each element present.\nHere, we will use atom symbols with isotope numbers for all isotopes excluding the most abundant one.\nThis list has been corrected up to Iodine.
\n\nReferences
\n\n\n- NIST - Last Accessed 2019-06-12\nhttps://www.nist.gov/pml/atomic-weights-and-isotopic-compositions-relative-atomic-masses
\n
\n"}, {"fullname": "corems.encapsulation.constant.Atoms.electron_mass", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.electron_mass", "kind": "variable", "doc": "\n", "default_value": "0.000548579909065"}, {"fullname": "corems.encapsulation.constant.Atoms.atomic_masses", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.atomic_masses", "kind": "variable", "doc": "\n", "default_value": "{'H': 1.00782503223, 'D': 2.01410177812, 'T': 3.0160492779, '3He': 3.0160293201, 'He': 4.00260325413, '6Li': 6.0151228874, 'Li': 7.0160034366, 'Be': 9.012183065, '10B': 10.01293695, 'B': 11.00930536, 'C': 12.0, '13C': 13.00335483507, '14C': 14.0032419884, 'N': 14.00307400443, '15N': 15.00010889888, 'O': 15.99491461957, '17O': 16.9991317565, '18O': 17.99915961286, 'F': 18.99840316273, 'Ne': 19.9924401762, '21Ne': 20.993846685, '22Ne': 21.991385114, 'Na': 22.989769282, 'Mg': 23.985041697, '25Mg': 24.985836976, '26Mg': 25.982592968, 'Al': 26.98153853, 'Si': 27.97692653465, '29Si': 28.9764946649, '30Si': 29.973770136, 'P': 30.97376199842, 'S': 31.9720711744, '33S': 32.9714589098, '34S': 33.967867004, '36S': 35.96708071, 'Cl': 34.968852682, '37Cl': 36.965902602, '36Ar': 35.967545105, '38Ar': 37.96273211, 'Ar': 39.9623831237, 'K': 38.9637064864, '40K': 39.963998166, '41K': 40.9618252579, 'Ca': 39.962590863, '42Ca': 41.95861783, '43Ca': 42.95876644, '44Ca': 43.95548156, '46Ca': 45.953689, '48Ca': 47.95252276, 'Sc': 44.95590828, '46Ti': 45.95262772, '47Ti': 46.95175879, 'Ti': 47.94794198, '49Ti': 48.94786568, '50Ti': 49.94478689, '50V': 49.94715601, 'V': 50.94395704, '50Cr': 49.94604183, 'Cr': 51.94050623, '53Cr': 52.94064815, '54Cr': 53.93887916, 'Mn': 54.93804391, '54Fe': 53.93960899, 'Fe': 55.93493633, '57Fe': 56.93539284, '58Fe': 57.93327443, 'Co': 58.93319429, 'Ni': 57.93534241, '60Ni': 59.93078588, '61Ni': 60.93105557, '62Ni': 61.92834537, '64Ni': 63.92796682, 'Cu': 62.92959772, '65Cu': 64.9277897, 'Zn': 63.92914201, '66Zn': 65.92603381, '67Zn': 66.92712775, '68Zn': 67.92484455, '70Zn': 69.9253192, 'Ga': 68.9255735, '71Ga': 70.92470258, '70Ge': 69.92424875, '72Ge': 71.922075826, '73Ge': 72.923458956, 'Ge': 73.921177761, '76Ge': 75.921402726, 'As': 74.92159457, '74Se': 73.922475934, '76Se': 75.919213704, '77Se': 76.919914154, '78Se': 77.91730928, 'Se': 79.9165218, '82Se': 81.9166995, 'Br': 78.9183376, '81Br': 80.9162897, '78Kr': 77.92036494, '80Kr': 79.91637808, '82Kr': 81.91348273, '83Kr': 82.91412716, 'Kr': 83.9114977282, '86Kr': 85.9106106269, 'Rb': 84.9117897379, '87Rb': 86.909180531, '84Sr': 83.9134191, '86Sr': 85.9092606, '87Sr': 86.9088775, 'Sr': 87.9056125, 'Y': 88.9058403, 'Zr': 89.9046977, '91Zr': 90.9056396, '92Zr': 91.9050347, '94Zr': 93.9063108, '96Zr': 95.9082714, 'Nb': 92.906373, '92Mo': 91.90680796, '94Mo': 93.9050849, '95Mo': 94.90583877, '96Mo': 95.90467612, '97Mo': 96.90601812, 'Mo': 97.90540482, '100Mo': 99.9074718, 'Tc': 98.9062508, '96Ru': 95.90759025, '98Ru': 97.9052868, '99Ru': 98.9059341, '100Ru': 99.9042143, '101Ru': 100.9055769, 'Ru': 101.9043441, '104Ru': 103.9054275, 'Rh': 102.905498, '102Pd': 101.9056022, '104Pd': 103.9040305, '105Pd': 104.9050796, 'Pd': 105.9034804, '108Pd': 107.9038916, '110Pd': 109.9051722, 'Ag': 106.9050916, '109Ag': 108.9047553, '106Cd': 105.9064599, '108Cd': 107.9041834, '110Cd': 109.90300661, '111Cd': 110.90418287, 'Cd': 111.90276287, '113Cd': 112.90440813, '114Cd': 113.90336509, '116Cd': 115.90476315, '113In': 112.90406184, 'In': 114.903878776, '112Sn': 111.90482387, '114Sn': 113.9027827, '115Sn': 114.903344699, '116Sn': 115.9017428, '117Sn': 116.90295398, '118Sn': 117.90160657, '119Sn': 118.90331117, 'Sn': 119.90220163, '122Sn': 121.9034438, '124Sn': 123.9052766, 'Sb': 120.903812, '123Sb': 122.9042132, '120Te': 119.9040593, '122Te': 121.9030435, '123Te': 122.9042698, '124Te': 123.9028171, '125Te': 124.9044299, '126Te': 125.9033109, '128Te': 127.90446128, 'Te': 129.906222748, 'I': 126.9044719, '124Xe': 123.905892, '126Xe': 125.9042983, '128Xe': 127.903531, '129Xe': 128.9047808611, '130Xe': 129.903509349, '131Xe': 130.90508406, 'Xe': 131.9041550856, '134Xe': 133.90539466, '136Xe': 135.907214484, 'Cs': 132.905451961, '130Ba': 129.9063207, '132Ba': 131.9050611, '134Ba': 133.90450818, '135Ba': 134.90568838, '136Ba': 135.90457573, '137Ba': 136.90582714, 'Ba': 137.905247, '138La': 137.9071149, 'La': 138.9063563, '136Ce': 135.90712921, '138Ce': 137.905991, 'Ce': 139.9054431, '142Ce': 141.9092504, 'Pr': 140.9076576, 'Nd': 141.907729, '143Nd': 142.90982, '144Nd': 143.910093, '145Nd': 144.9125793, '146Nd': 145.9131226, '148Nd': 147.9168993, '150Nd': 149.9209022, '145Pm': 144.9127559, '147Pm': 146.915145, '144Sm': 143.9120065, '147Sm': 146.9149044, '148Sm': 147.9148292, '149Sm': 148.9171921, '150Sm': 149.9172829, 'Sm': 151.9197397, '154Sm': 153.9222169, '151Eu': 150.9198578, 'Eu': 152.921238, '152Gd': 151.9197995, '154Gd': 153.9208741, '155Gd': 154.9226305, '156Gd': 155.9221312, '157Gd': 156.9239686, 'Gd': 157.9241123, '160Gd': 159.9270624, 'Tb': 158.9253547, '156Dy': 155.9242847, '158Dy': 157.9244159, '160Dy': 159.9252046, '161Dy': 160.9269405, '162Dy': 161.9268056, '163Dy': 162.9287383, 'Dy': 163.9291819, 'Ho': 164.9303288, '162Er': 161.9287884, '164Er': 163.9292088, 'Er': 165.9302995, '167Er': 166.9320546, '168Er': 167.9323767, '170Er': 169.9354702, 'Tm': 168.9342179, '168Yb': 167.9338896, '170Yb': 169.9347664, '171Yb': 170.9363302, '172Yb': 171.9363859, '173Yb': 172.9382151, 'Yb': 173.9388664, '176Yb': 175.9425764, 'Lu': 174.9407752, '176Lu': 175.9426897, '174Hf': 173.9400461, '176Hf': 175.9414076, '177Hf': 176.9432277, '178Hf': 177.9437058, '179Hf': 178.9458232, 'Hf': 179.946557, '180Ta': 179.9474648, 'Ta': 180.9479958, '180W': 179.9467108, '182W': 181.94820394, '183W': 182.95022275, 'W': 183.95093092, '186W': 185.9543628, '185Re': 184.9529545, 'Re': 186.9557501, '184Os': 183.9524885, '186Os': 185.953835, '187Os': 186.9557474, '188Os': 187.9558352, '189Os': 188.9581442, '190Os': 189.9584437, '192Os': 191.961477, '191Ir': 190.9605893, 'Ir': 192.9629216, '190Pt': 189.9599297, '192Pt': 191.9610387, '194Pt': 193.9626809, 'Pt': 194.9647917, '196Pt': 195.96495209, '198Pt': 197.9678949, 'Au': 196.96656879, '196Hg': 195.9658326, '198Hg': 197.9667686, '199Hg': 198.96828064, '200Hg': 199.96832659, '201Hg': 200.97030284, 'Hg': 201.9706434, '204Hg': 203.97349398, '203Tl': 202.9723446, 'Tl': 204.9744278, '204Pb': 203.973044, '206Pb': 205.9744657, '207Pb': 206.9758973, 'Pb': 207.9766525, 'Bi': 208.9803991, '209Po': 208.9824308, '210Po': 209.9828741, '210At': 209.9871479, '211At': 210.9874966, '211Rn': 210.9906011, '220Rn': 220.0113941, '222Rn': 222.0175782, '223Fr': 223.019736, '223Ra': 223.0185023, '224Ra': 224.020212, '226Ra': 226.0254103, '228Ra': 228.0310707, '227Ac': 227.0277523, '230Th': 230.0331341, 'Th': 232.0380558, 'Pa': 231.0358842, '233U': 233.0396355, '234U': 234.0409523, '235U': 235.0439301, '236U': 236.0455682, 'U': 238.0507884, '236Np': 236.04657, '237Np': 237.0481736, '238Pu': 238.0495601, '239Pu': 239.0521636, '240Pu': 240.0538138, '241Pu': 241.0568517, '242Pu': 242.0587428, '244Pu': 244.0642053, '241Am': 241.0568293, '243Am': 243.0613813, '243Cm': 243.0613893, '244Cm': 244.0627528, '245Cm': 245.0654915, '246Cm': 246.0672238, '247Cm': 247.0703541, '248Cm': 248.0723499, '247Bk': 247.0703073, '249Bk': 249.0749877, '249Cf': 249.0748539, '250Cf': 250.0764062, '251Cf': 251.0795886, '252Cf': 252.0816272, '252Es': 252.08298, '257Fm': 257.0951061, '258Md': 258.0984315, '260Md': 260.10365, '259No': 259.10103, '262Lr': 262.10961, '267Rf': 267.12179, '268Db': 268.12567, '271Sg': 271.13393, '272Bh': 272.13826, '270Hs': 270.13429, '276Mt': 276.15159, '281Ds': 281.16451, '280Rg': 280.16514, '285Cn': 285.17712, '284Nh': 284.17873, '289Fl': 289.19042, '288Mc': 288.19274, '293Lv': 293.20449, '292Ts': 292.20746, '294Og': 294.21392}"}, {"fullname": "corems.encapsulation.constant.Atoms.atoms_order", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.atoms_order", "kind": "variable", "doc": "\n", "default_value": "['C', 'H', 'O', 'N', 'P', 'S', 'F', 'Cl', 'Br', 'I', 'At', 'Li', 'Na', 'K', 'Rb', 'Cs', 'Fr', 'He', 'Ne', 'Ar', 'Kr', 'Xe', 'Rn', 'Be', 'B', 'Mg', 'Al', 'Si', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'Ba', 'La', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'Ra', 'Ac', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'D', '6Li', '10B', '13C', '15N', '17O', '18O', '22Ne', '25Mg', '26Mg', '29Si', '30Si', '33S', '34S', '36S', '37Cl', '40Ca', '41K', '44Ca', '46Ti', '47Ti', '49Ti', '50Cr', '50Ti', '50V', '53Cr', '54Cr', '54Fe', '57Fe', '58Fe', '60Ni', '61Ni', '62Ni', '65Cu', '66Zn', '67Zn', '68Zn', '70Ge', '71Ga', '72Ge', '73Ge', '76Ge', '76Se', '77Se', '78Se', '81Br', '80Kr', '82Kr', '82Se', '83Kr', '85Rb', '86Kr', '86Sr', '87Rb', '87Sr', '88Sr', '91Zr', '92Mo', '92Zr', '94Mo', '94Zr', '95Mo', '96Mo', '96Ru', '96Zr', '97Mo', '98Ru', '99Ru', '100Mo', '100Ru', '101Ru', '102Pd', '104Pd', '104Ru', '105Pd', '106Cd', '106Pd', '108Cd', '108Pd', '109Ag', '110Cd', '110Pd', '111Cd', '112Cd', '112Sn', '113Cd', '113In', '114Cd', '114Sn', '115In', '115Sn', '116Cd', '116Sn', '117Sn', '118Sn', '119Sn', '120Sn', '120Te', '121Sb', '122Sn', '122Te', '123Sb', '123Te', '124Sn', '124Te', '124Xe', '125Te', '126Te', '126Xe', '128Te', '128Xe', '129Xe', '130Ba', '130Te', '130Xe', '131Xe', '132Ba', '132Xe', '134Ba', '134Xe', '135Ba', '136Ba', '136Xe', '137Ba', '138Ba', '174Hf', '176Hf', '177Hf', '178Hf', '179Hf', '180Hf', '180W', '182W', '183W', '184Os', '184W', '185Re', '186Os', '186W', '187Os', '187Re', '188Os', '189Os', '190Os', '190Pt', '191Ir', '192Ir', '192Os', '192Pt', '194Pt', '195Pt', '196Hg', '196Pt', '198Hg', '198Pt', '199Hg', '200Hg', '201Hg', '202Hg', '203Tl', '204Hg', '204Pb', '205Tl', '206Pb', '207Pb', '208Pb']"}, {"fullname": "corems.encapsulation.constant.Atoms.atoms_covalence", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.atoms_covalence", "kind": "variable", "doc": "\n", "default_value": "{'C': 4, '13C': 4, 'N': 3, 'O': 2, 'S': 2, 'H': 1, 'F': (1, 0), 'Cl': (1, 0), 'Br': (1, 0), 'I': (1, 0), 'At': 1, 'Li': (1, 0), 'Na': (1, 0), 'K': (1, 0), 'Rb': 1, 'Cs': 1, 'Fr': 1, 'B': (4, 3, 2, 1), 'In': (3, 2, 1), 'Al': (3, 1, 2), 'P': (3, 5, 4, 2, 1), 'Ga': (3, 1, 2), 'Mg': (2, 1), 'Be': (2, 1), 'Ca': (2, 1), 'Sr': (2, 1), 'Ba': 2, 'Ra': 2, 'V': (5, 4, 3, 2, 1), 'Fe': (3, 2, 4, 5, 6), 'Si': (4, 3, 2), 'Sc': (3, 2, 1), 'Ti': (4, 3, 2, 1), 'Cr': (1, 2, 3, 4, 5, 6), 'Mn': (1, 2, 3, 4, 5, 6, 7), 'Co': (1, 2, 3, 4, 5), 'Ni': (1, 2, 3, 4), 'Cu': (2, 1, 3, 4), 'Zn': (2, 1), 'Ge': (4, 3, 2, 1), 'As': (5, 3, 2, 1), 'Se': (6, 4, 2, 1), 'Y': (3, 2, 1), 'Zr': (4, 3, 2, 1), 'Nb': (5, 4, 3, 2, 1), 'Mo': (6, 5, 4, 3, 2, 1), 'Tc': (7, 6, 5, 4, 3, 2, 1), 'Ru': (8, 7, 6, 5, 4, 3, 2, 1), 'Rh': (6, 5, 4, 3, 2, 1), 'Pd': (4, 2, 1), 'Ag': (0, 1, 2, 3, 4), 'Cd': (2, 1), 'Sn': (4, 2), 'Sb': (5, 3), 'Te': (6, 5, 4, 2), 'La': (3, 2), 'Hf': (4, 3, 2), 'Ta': (5, 4, 3, 2), 'W': (6, 5, 4, 3, 2, 1), 'Re': (4, 7, 6, 5, 3, 2, 1), 'Os': (4, 8, 7, 6, 5, 3, 2, 1), 'Ir': (4, 8, 6, 5, 3, 2, 1), 'Pt': (4, 6, 5, 3, 2, 1), 'Au': (3, 5, 2, 1), 'Hg': (1, 2, 4), 'Tl': (3, 1), 'Pb': (4, 2), 'Bi': (3, 1, 5), 'Po': (2, 4, 6), 'Ac': (3, 2)}"}, {"fullname": "corems.encapsulation.constant.Atoms.isotopic_abundance", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.isotopic_abundance", "kind": "variable", "doc": "\n", "default_value": "{'H': 0.999885, 'D': 0.000115, 'T': 0, '3He': 1.34e-06, 'He': 0.99999866, '6Li': 0.0759, 'Li': 0.9241, 'Be': 1.0, '10B': 0.199, 'B': 0.801, 'C': 0.9893, '13C': 0.0107, '14C': 0, 'N': 0.99636, '15N': 0.00364, 'O': 0.99757, '17O': 0.00038, '18O': 0.00205, 'F': 1.0, 'Ne': 0.9048, '21Ne': 0.0027, '22Ne': 0.0925, 'Na': 1.0, 'Mg': 0.7899, '25Mg': 0.1, '26Mg': 0.1101, 'Al': 1.0, 'Si': 0.92223, '29Si': 0.04685, '30Si': 0.03092, 'P': 1.0, 'S': 0.9499, '33S': 0.0075, '34S': 0.0425, '36S': 0.0001, 'Cl': 0.7576, '37Cl': 0.2424, '36Ar': 0.003336, '38Ar': 0.000629, 'Ar': 0.996035, 'K': 0.932581, '40K': 0.000117, '41K': 0.067302, 'Ca': 0.96941, '42Ca': 0.00647, '43Ca': 0.00135, '44Ca': 0.02086, '46Ca': 4e-05, '48Ca': 0.001872, 'Sc': 1.0, '46Ti': 0.0825, '47Ti': 0.0744, 'Ti': 0.7372, '49Ti': 0.0541, '50Ti': 0.0518, '50V': 0.0025, 'V': 0.9975, '50Cr': 0.04345, 'Cr': 0.83789, '53Cr': 0.09501, '54Cr': 0.02365, 'Mn': 1.0, '54Fe': 0.05845, 'Fe': 0.91754, '57Fe': 0.02119, '58Fe': 0.00282, 'Co': 1.0, 'Ni': 0.68077, '60Ni': 0.26223, '61Ni': 0.011399, '62Ni': 0.036346, '64Ni': 0.009255, 'Cu': 0.6915, '65Cu': 0.3085, 'Zn': 0.4917, '66Zn': 0.2773, '67Zn': 0.0404, '68Zn': 0.1845, '70Zn': 0.0061, 'Ga': 0.60108, '71Ga': 0.39892, '70Ge': 0.2057, '72Ge': 0.2745, '73Ge': 0.0775, 'Ge': 0.365, '76Ge': 0.0773, 'As': 1.0, '74Se': 0.0089, '76Se': 0.0937, '77Se': 0.0763, '78Se': 0.2377, 'Se': 0.4961, '82Se': 0.0873, 'Br': 0.5069, '81Br': 0.4931, '78Kr': 0.00355, '80Kr': 0.02286, '82Kr': 0.11593, '83Kr': 0.115, 'Kr': 0.56987, '86Kr': 0.17279, 'Rb': 0.7217, '87Rb': 0.2783, '84Sr': 0.0056, '86Sr': 0.0986, '87Sr': 0.07, 'Sr': 0.8258, 'Y': 1.0, 'Zr': 0.5145, '91Zr': 0.1122, '92Zr': 0.1715, '94Zr': 0.1738, '96Zr': 0.028, 'Nb': 1.0, '92Mo': 0.1453, '94Mo': 0.0915, '95Mo': 0.1584, '96Mo': 0.1667, '97Mo': 0.096, 'Mo': 0.2439, '100Mo': 0.0982, '99Tc': 0, '96Ru': 0.0554, '98Ru': 0.0187, '99Ru': 0.1276, '100Ru': 0.126, '101Ru': 0.1706, 'Ru': 0.3155, '104Ru': 0.1862, 'Rh': 1.0, '102Pd': 0.0102, '104Pd': 0.1114, '105Pd': 0.2233, 'Pd': 0.2733, '108Pd': 0.2646, '110Pd': 0.1172, 'Ag': 0.51839, '109Ag': 0.48161, '106Cd': 0.0125, '108Cd': 0.0089, '110Cd': 0.1249, '111Cd': 0.128, 'Cd': 0.2413, '113Cd': 0.1222, '114Cd': 0.2873, '116Cd': 0.0749, '113In': 0.0429, 'In': 0.9571, '112Sn': 0.0097, '114Sn': 0.0066, '115Sn': 0.0034, '116Sn': 0.1454, '117Sn': 0.0768, '118Sn': 0.2422, '119Sn': 0.0859, 'Sn': 0.3258, '122Sn': 0.0463, '124Sn': 0.0579, 'Sb': 0.5721, '123Sb': 0.4279, '120Te': 0.0009, '122Te': 0.0255, '123Te': 0.0089, '124Te': 0.0474, '125Te': 0.0707, '126Te': 0.1884, '128Te': 0.3174, 'Te': 0.3408, 'I': 1.0, '124Xe': 0.000952, '126Xe': 0.00089, '128Xe': 0.019102, '129Xe': 0.264006, '130Xe': 0.04071, '131Xe': 0.212324, 'Xe': 0.269086, '134Xe': 0.104357, '136Xe': 0.088573, 'Cs': 1.0, '130Ba': 0.00106, '132Ba': 0.00101, '134Ba': 0.02417, '135Ba': 0.06592, '136Ba': 0.07854, '137Ba': 0.11232, 'Ba': 0.71698, '138La': 0.0008881, 'La': 0.9991119, '136Ce': 0.00185, '138Ce': 0.00251, 'Ce': 0.8845, '142Ce': 0.11114, 'Pr': 1.0, 'Nd': 0.27152, '143Nd': 0.12174, '144Nd': 0.23798, '145Nd': 0.08293, '146Nd': 0.17189, '148Nd': 0.05756, '150Nd': 0.05638, '145Pm': 0, '147Pm': 0, '144Sm': 0.0307, '147Sm': 0.1499, '148Sm': 0.1124, '149Sm': 0.1382, '150Sm': 0.0738, 'Sm': 0.2675, '154Sm': 0.2275, '151Eu': 0.4781, 'Eu': 0.5219, '152Gd': 0.002, '154Gd': 0.0218, '155Gd': 0.148, '156Gd': 0.2047, '157Gd': 0.1565, 'Gd': 0.2484, '160Gd': 0.2186, 'Tb': 1.0, '156Dy': 0.00056, '158Dy': 0.00095, '160Dy': 0.02329, '161Dy': 0.18889, '162Dy': 0.25475, '163Dy': 0.24896, 'Dy': 0.2826, 'Ho': 1.0, '162Er': 0.00139, '164Er': 0.01601, 'Er': 0.33503, '167Er': 0.22869, '168Er': 0.26978, '170Er': 0.1491, 'Tm': 1.0, '168Yb': 0.00123, '170Yb': 0.02982, '171Yb': 0.1409, '172Yb': 0.2168, '173Yb': 0.16103, 'Yb': 0.32026, '176Yb': 0.12996, 'Lu': 0.97401, '176Lu': 0.02599, '174Hf': 0.0016, '176Hf': 0.0526, '177Hf': 0.186, '178Hf': 0.2728, '179Hf': 0.1362, 'Hf': 0.3508, '180Ta': 0.0001201, 'Ta': 0.9998799, '180W': 0.0012, '182W': 0.265, '183W': 0.1431, 'W': 0.3064, '186W': 0.2843, '185Re': 0.374, 'Re': 0.626, '184Os': 0.0002, '186Os': 0.0159, '187Os': 0.0196, '188Os': 0.1324, '189Os': 0.1615, '190Os': 0.2626, 'Os': 0.4078, '191Ir': 0.373, 'Ir': 0.627, '190Pt': 0.00012, '192Pt': 0.00782, '194Pt': 0.3286, 'Pt': 0.3378, '196Pt': 0.2521, '198Pt': 0.07356, 'Au': 1.0, '196Hg': 0.0015, '198Hg': 0.0997, '199Hg': 0.16872, '200Hg': 0.231, '201Hg': 0.1318, 'Hg': 0.2986, '204Hg': 0.0687, '203Tl': 0.2952, 'Tl': 0.7048, '204Pb': 0.014, '206Pb': 0.241, '207Pb': 0.221, 'Pb': 0.524, 'Bi': 1.0, '209Po': 0, '210Po': 0, '210At': 0, '211At': 0, '211Rn': 0, '220Rn': 0, '222Rn': 0, '223Fr': 0, '223Ra': 0, '224Ra': 0, '226Ra': 0, '228Ra': 0, '227Ac': 0, '230Th': 0, 'Th': 1.0, 'Pa': 1.0, '233U': 0, '234U': 5.4e-05, '235U': 0.007204, '236U': 0, 'U': 0.992742, '236Np': 0, '237Np': 0, '238Pu': 0, '239Pu': 0, '240Pu': 0, '241Pu': 0, '242Pu': 0, '244Pu': 0, '241Am': 0, '243Am': 0, '243Cm': 0, '244Cm': 0, '245Cm': 0, '246Cm': 0, '247Cm': 0, '248Cm': 0, '247Bk': 0, '249Bk': 0, '249Cf': 0, '250Cf': 0, '251Cf': 0, '252Cf': 0, '252Es': 0, '257Fm': 0, '258Md': 0, '260Md': 0, '259No': 0, '262Lr': 0, '267Rf': 0, '268Db': 0, '271Sg': 0, '272Bh': 0, '270Hs': 0, '276Mt': 0, '281Ds': 0, '280Rg': 0, '285Cn': 0, '284Nh': 0, '289Fl': 0, '288Mc': 0, '293Lv': 0, '292Ts': 0, '294Og': 0}"}, {"fullname": "corems.encapsulation.constant.Atoms.isotopes", "modulename": "corems.encapsulation.constant", "qualname": "Atoms.isotopes", "kind": "variable", "doc": "\n", "default_value": "{'H': ['Hydrogen', ['D', 'T']], 'He': ['Helium', ['3He']], 'Li': ['Lithium', ['6Li']], 'Be': ['Beryllium', [None]], 'B': ['Boron', ['10B']], 'C': ['Carbon', ['13C']], 'N': ['Nitrogen', ['15N']], 'O': ['Oxygen', ['18O', '17O']], 'F': ['Fluorine', [None]], 'Ne': ['Neon', ['22Ne', '21Ne']], 'Na': ['Sodium', [None]], 'Mg': ['Magnesium', ['26Mg', '25Mg']], 'Al': ['Aluminum', [None]], 'Si': ['Silicon', ['29Si', '30Si']], 'P': ['Phosphorus', [None]], 'S': ['Sulfur', ['34S', '33S', '36S']], 'Cl': ['Chlorine', ['37Cl']], 'Ar': ['Argon', ['36Ar', '38Ar']], 'K': ['Potassium', ['41K', '40K']], 'Ca': ['Calcium', ['44Ca', '48Ca', '43Ca', '42Ca', '46Ca']], 'Sc': ['Scandium', [None]], 'Ti': ['Titanium', ['46Ti', '47Ti', '49Ti', '50Ti']], 'V': ['Vanadium', ['50V']], 'Cr': ['Chromium', ['53Cr', '50Cr', '54Cr']], 'Mn': ['Manganese', [None]], 'Fe': ['Iron', ['54Fe', '57Fe', '58Fe']], 'Co': ['Cobalt', [None]], 'Ni': ['Nickel', ['60Ni', '62Ni', '61Ni', '64Ni']], 'Cu': ['Copper', ['65Cu']], 'Zn': ['Zinc', ['66Zn', '68Zn', '67Zn', '70Zn']], 'Ga': ['Gallium', ['71Ga']], 'Ge': ['Germanium', ['72Ge', '70Ge', '73Ge', '76Ge']], 'As': ['Arsenic', [None]], 'Se': ['Selenium', ['78Se', '76Se', '82Se', '77Se', '74Se']], 'Br': ['Bromine', ['81Br']], 'Kr': ['Krypton', ['86Kr', '82Kr', '83Kr', '80Kr']], 'Rb': ['Rubidium', ['87Rb']], 'Sr': ['Strontium', ['86Sr', '87Sr', '84Sr']], 'Y': ['Yttrium', [None]], 'Zr': ['Zirconium', ['94Zr', '92Zr', '91Zr', '96Zr']], 'Nb': ['Niobium', [None]], 'Mo': ['Molybdenum', ['96Mo', '95Mo', '92Mo', '100Mo', '97Mo', '94Mo']], 'Tc': ['Technetium', [None]], 'Ru': ['Ruthenium', ['104Ru', '101Ru', '99Ru', '100Ru', '96Ru', '98Ru']], 'Rh': ['Rhodium', [None]], 'Pd': ['Palladium', ['108Pd', '105Pd', '110Pd', '104Pd', '102Pd']], 'Ag': ['Silver', ['109Ag']], 'Cd': ['Cadmium', ['114Cd', '111Cd', '110Cd', '113Cd', '116Cd', '106Cd', '108Cd']], 'In': ['Indium', ['113In']], 'Sn': ['Tin', ['118Sn', '116Sn', '119Sn', '117Sn', '124Sn', '122Sn', '112Sn', '114Sn', '115Sn']], 'Sb': ['Antimony', ['123Sb']], 'Te': ['Tellurium', ['128Te', '126Te', '125Te', '124Te', '122Te', '123Te', '120Te']], 'I': ['Iodine', [None]], 'Xe': ['Xenon', ['129Xe', '131Xe', '134Xe', '136Xe', '130Xe', '128Xe']], 'Cs': ['Cesium', [None]], 'Ba': ['Barium', ['137Ba', '136Ba', '135Ba', '134Ba']], 'La': ['Lanthanum', ['138La']], 'Hf': ['Hafnium', ['178Hf', '177Hf', '179Hf', '176Hf']], 'Ta': ['Tantalum', ['180Ta']], 'W': ['Tungsten', ['186W', '182W', '183W']], 'Re': ['Rhenium', ['185Re']], 'Os': ['Osmium', ['190Os', '189Os', '188Os', '187Os', '186Os']], 'Ir': ['Iridium', ['191Ir']], 'Pt': ['Platinum', ['194Pt', '196Pt', '198Pt', '192Pt']], 'Au': ['Gold', [None]], 'Hg': ['Mercury', ['200Hg', '199Hg', '201Hg', '198Hg', '204Hg']], 'Tl': ['Thallium', ['203Tl']], 'Pb': ['Lead', ['206Pb', '207Pb', '204Pb']], 'Bi': ['Bismuth', [None]], 'Po': ['Polonium', [None]], 'At': ['Astatine', [None]], 'Rn': ['Radon', [None]], 'Fr': ['Francium', [None]], 'Ra': ['Radium', [None]], 'Ac': ['Actinium', [None]], 'Rf': ['Rutherfordium', [None]], 'Db': ['Dubnium', [None]], 'Sg': ['Seaborgium', [None]], 'Bh': ['Bohrium', [None]], 'Hs': ['Hassium', [None]], 'Mt': ['Meitnerium', [None]], 'Ds': ['Darmstadtium', [None]], 'Rg': ['Roentgenium', [None]], 'Cn': ['Copernicium', [None]], 'Nh': ['Nihonium', [None]], 'Fl': ['Flerovium', [None]], 'Mc': ['Moscovium', [None]], 'Lv': ['Livermorium', [None]], 'Ts': ['Tennessine', [None]], 'Og': ['Oganesson', [None]], 'Ce': ['Cerium', ['142Ce', '138Ce136Ce']], 'Pr': ['Praseodymium', [None]], 'Nd': ['Neodymium', [None]], 'Pm': ['Promethium', [None]], 'Sm': ['Samarium', [None]], 'Eu': ['Europium', [None]], 'Gd': ['Gadolinium', [None]], 'Tb': ['Terbium', [None]], 'Dy': ['Dysprosium', [None]], 'Ho': ['Holmium', [None]], 'Er': ['Erbium', [None]], 'Tm': ['Thulium', [None]], 'Yb': ['Ytterbium', [None]], 'Lu': ['Lutetium', ['176Lu']], 'Th': ['Thorium', [None]], 'Pa': ['Protactinium', [None]], 'U': ['Uranium', ['235U', '234U']], 'Np': ['Neptunium', [None]], 'Pu': ['Plutonium', [None]], 'Am': ['Americium', [None]], 'Cm': ['Curium', [None]], 'Bk': ['Berkelium', [None]], 'Cf': ['Californium', [None]], 'Es': ['Einsteinium', [None]], 'Fm': ['Fermium', [None]], 'Md': ['Mendelevium', [None]], 'No': ['Nobelium', [None]], 'Lr': ['Lawrencium', [None]]}"}, {"fullname": "corems.encapsulation.factory", "modulename": "corems.encapsulation.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.parameters", "modulename": "corems.encapsulation.factory.parameters", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters", "kind": "class", "doc": "MSParameters class is used to store the parameters used for the processing of the mass spectrum
\n\nEach attibute is a class that contains the parameters for the processing of the mass spectrum, see the corems.encapsulation.factory.processingSetting module for more details.
\n\nAttributes
\n\n\n- molecular_search (MolecularFormulaSearchSettings):\nMolecularFormulaSearchSettings object
\n- transient (TransientSetting):\nTransientSetting object
\n- mass_spectrum (MassSpectrumSetting):\nMassSpectrumSetting object
\n- ms_peak (MassSpecPeakSetting):\nMassSpecPeakSetting object
\n- data_input (DataInputSetting):\nDataInputSetting object
\n
\n"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters.molecular_search", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters.molecular_search", "kind": "variable", "doc": "\n", "default_value": "MolecularFormulaSearchSettings(use_isotopologue_filter=False, isotopologue_filter_threshold=33.0, isotopologue_filter_atoms=('Cl', 'Br'), use_runtime_kendrick_filter=False, use_min_peaks_filter=True, min_peaks_per_class=15, url_database='postgresql+psycopg2://coremsappdb:coremsapppnnl@molformdb:5432/coremsapp', db_jobs=3, db_chunk_size=300, ion_charge=-1, min_hc_filter=0.3, max_hc_filter=3.0, min_oc_filter=0.0, max_oc_filter=1.2, min_op_filter=2.0, use_pah_line_rule=False, min_dbe=0.0, max_dbe=40.0, mz_error_score_weight=0.6, isotopologue_score_weight=0.4, adduct_atoms_neg=('Cl', 'Br'), adduct_atoms_pos=('Na', 'K'), score_methods=('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error'), score_method='prob_score', output_min_score=0.1, output_score_method='All Candidates', isRadical=False, isProtonated=True, isAdduct=False, usedAtoms={'C': (1, 100), 'H': (1, 200)}, ionization_type='ESI', min_ppm_error=-10.0, max_ppm_error=10.0, min_abun_error=-100.0, max_abun_error=100.0, mz_error_range=1.5, error_method='None', mz_error_average=0.0, used_atom_valences={'C': 4, '13C': 4, 'N': 3, 'O': 2, 'S': 2, 'H': 1, 'F': 1, 'Cl': 1, 'Br': 1, 'I': 1, 'At': 1, 'Li': 1, 'Na': 1, 'K': 1, 'Rb': 1, 'Cs': 1, 'Fr': 1, 'B': 4, 'In': 3, 'Al': 3, 'P': 3, 'Ga': 3, 'Mg': 2, 'Be': 2, 'Ca': 2, 'Sr': 2, 'Ba': 2, 'Ra': 2, 'V': 5, 'Fe': 3, 'Si': 4, 'Sc': 3, 'Ti': 4, 'Cr': 1, 'Mn': 1, 'Co': 1, 'Ni': 1, 'Cu': 2, 'Zn': 2, 'Ge': 4, 'As': 5, 'Se': 6, 'Y': 3, 'Zr': 4, 'Nb': 5, 'Mo': 6, 'Tc': 7, 'Ru': 8, 'Rh': 6, 'Pd': 4, 'Ag': 0, 'Cd': 2, 'Sn': 4, 'Sb': 5, 'Te': 6, 'La': 3, 'Hf': 4, 'Ta': 5, 'W': 6, 'Re': 4, 'Os': 4, 'Ir': 4, 'Pt': 4, 'Au': 3, 'Hg': 1, 'Tl': 3, 'Pb': 4, 'Bi': 3, 'Po': 2, 'Ac': 3})"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters.transient", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters.transient", "kind": "variable", "doc": "\n", "default_value": "TransientSetting(implemented_apodization_function=('Hamming', 'Hanning', 'Blackman', 'Full-Sine', 'Half-Sine', 'Kaiser', 'Half-Kaiser'), apodization_method='Hanning', number_of_truncations=0, number_of_zero_fills=1, next_power_of_two=False, kaiser_beta=8.6)"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters.mass_spectrum", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters.mass_spectrum", "kind": "variable", "doc": "\n", "default_value": "MassSpectrumSetting(noise_threshold_method='log', noise_threshold_methods_implemented=('minima', 'signal_noise', 'relative_abundance', 'absolute_abundance', 'log'), noise_threshold_min_std=6, noise_threshold_min_s2n=4.0, noise_threshold_min_relative_abundance=6.0, noise_threshold_absolute_abundance=1000000.0, noise_threshold_log_nsigma=6, noise_threshold_log_nsigma_corr_factor=0.463, noise_threshold_log_nsigma_bins=500, noise_min_mz=50.0, noise_max_mz=1200.0, min_picking_mz=50.0, max_picking_mz=1200.0, picking_point_extrapolate=3, calib_minimize_method='Powell', calib_pol_order=2, max_calib_ppm_error=1.0, min_calib_ppm_error=-1.0, calib_sn_threshold=2.0, do_calibration=True)"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters.ms_peak", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters.ms_peak", "kind": "variable", "doc": "\n", "default_value": "MassSpecPeakSetting(kendrick_base={'C': 1, 'H': 2}, kendrick_rounding_method='floor', implemented_kendrick_rounding_methods=('floor', 'ceil', 'round'), peak_derivative_threshold=0.0, peak_min_prominence_percent=0.1, min_peak_datapoints=5.0, peak_max_prominence_percent=0.1, peak_height_max_percent=10.0, legacy_resolving_power=True)"}, {"fullname": "corems.encapsulation.factory.parameters.MSParameters.data_input", "modulename": "corems.encapsulation.factory.parameters", "qualname": "MSParameters.data_input", "kind": "variable", "doc": "\n", "default_value": "DataInputSetting(header_translate={'m/z': 'm/z', 'mOz': 'm/z', 'Mass': 'm/z', 'Resolving Power': 'Resolving Power', 'Res.': 'Resolving Power', 'Intensity': 'Peak Height', 'I': 'Peak Height', 'Abundance': 'Peak Height', 'Signal/Noise': 'S/N', 'S/N': 'S/N', 'abs_abu': 'Peak Height', 'sn': 'S/N', 'resolution': 'Resolving Power'})"}, {"fullname": "corems.encapsulation.factory.parameters.GCMSParameters", "modulename": "corems.encapsulation.factory.parameters", "qualname": "GCMSParameters", "kind": "class", "doc": "GCMSParameters class is used to store the parameters used for the processing of the gas chromatograph mass spectrum
\n\nEach attibute is a class that contains the parameters for the processing of the data, see the corems.encapsulation.factory.processingSetting module for more details.
\n\nAttributes
\n\n\n- molecular_search (MolecularFormulaSearchSettings):\nMolecularFormulaSearchSettings object
\n- gc_ms (GasChromatographSetting):\nGasChromatographSetting object
\n
\n"}, {"fullname": "corems.encapsulation.factory.parameters.GCMSParameters.molecular_search", "modulename": "corems.encapsulation.factory.parameters", "qualname": "GCMSParameters.molecular_search", "kind": "variable", "doc": "\n", "default_value": "CompoundSearchSettings(url_database='sqlite:///db/pnnl_lowres_gcms_compounds.sqlite', ri_search_range=35.0, rt_search_range=1.0, correlation_threshold=0.5, score_threshold=0.0, ri_spacing=200.0, ri_std=3.0, ri_calibration_compound_names=['Methyl Caprylate', 'Methyl Caprate', 'Methyl Pelargonate', 'Methyl Laurate', 'Methyl Myristate', 'Methyl Palmitate', 'Methyl Stearate', 'Methyl Eicosanoate', 'Methyl Docosanoate', 'Methyl Linocerate', 'Methyl Hexacosanoate', 'Methyl Octacosanoate', 'Methyl Triacontanoate'], exploratory_mode=False, score_methods=('highest_sim_score', 'highest_ss'), output_score_method='All')"}, {"fullname": "corems.encapsulation.factory.parameters.GCMSParameters.gc_ms", "modulename": "corems.encapsulation.factory.parameters", "qualname": "GCMSParameters.gc_ms", "kind": "variable", "doc": "\n", "default_value": "GasChromatographSetting(use_deconvolution=False, implemented_smooth_method=('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'), smooth_window=5, smooth_method='savgol', savgol_pol_order=2, peak_derivative_threshold=0.0005, peak_height_max_percent=10.0, peak_max_prominence_percent=1.0, min_peak_datapoints=5.0, max_peak_width=0.1, noise_threshold_method='manual_relative_abundance', noise_threshold_methods_implemented=('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative'), std_noise_threshold=3, peak_height_min_percent=0.1, peak_min_prominence_percent=0.1, eic_signal_threshold=0.01, max_rt_distance=0.025)"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters", "kind": "class", "doc": "LCMSParameters class is used to store the parameters used for the processing of the liquid chromatograph mass spectrum
\n\nEach attibute is a class that contains the parameters for the processing of the data, see the corems.encapsulation.factory.processingSetting module for more details.
\n\nAttributes
\n\n\n- lc_ms (LiquidChromatographSetting):\nLiquidChromatographSetting object
\n- mass_spectrum (MassSpectrumSetting):\nMassSpectrumSetting object
\n- ms_peak (MassSpecPeakSetting):\nMassSpecPeakSetting object
\n- ms1_molecular_search (MolecularFormulaSearchSettings):\nMolecularFormulaSearchSettings object
\n- ms2_molecular_search (MolecularFormulaSearchSettings):\nMolecularFormulaSearchSettings object
\n
\n"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters.lc_ms", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters.lc_ms", "kind": "variable", "doc": "\n", "default_value": "LiquidChromatographSetting(scans=(0, 1), eic_tolerance_ppm=5.0, enforce_target_ms2=True, average_target_mz=True, smooth_window=5, smooth_method='savgol', implemented_smooth_method=('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'), savgol_pol_order=2, peak_height_max_percent=10.0, peak_max_prominence_percent=1.0, peak_derivative_threshold=0.0005, min_peak_datapoints=5.0, noise_threshold_method='manual_relative_abundance', noise_threshold_methods_implemented=('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative'), std_noise_threshold=3, peak_height_min_percent=0.1, eic_signal_threshold=0.01)"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters.mass_spectrum", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters.mass_spectrum", "kind": "variable", "doc": "\n", "default_value": "MassSpectrumSetting(noise_threshold_method='log', noise_threshold_methods_implemented=('minima', 'signal_noise', 'relative_abundance', 'absolute_abundance', 'log'), noise_threshold_min_std=6, noise_threshold_min_s2n=4.0, noise_threshold_min_relative_abundance=6.0, noise_threshold_absolute_abundance=1000000.0, noise_threshold_log_nsigma=6, noise_threshold_log_nsigma_corr_factor=0.463, noise_threshold_log_nsigma_bins=500, noise_min_mz=50.0, noise_max_mz=1200.0, min_picking_mz=50.0, max_picking_mz=1200.0, picking_point_extrapolate=3, calib_minimize_method='Powell', calib_pol_order=2, max_calib_ppm_error=1.0, min_calib_ppm_error=-1.0, calib_sn_threshold=2.0, do_calibration=True)"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters.ms_peak", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters.ms_peak", "kind": "variable", "doc": "\n", "default_value": "MassSpecPeakSetting(kendrick_base={'C': 1, 'H': 2}, kendrick_rounding_method='floor', implemented_kendrick_rounding_methods=('floor', 'ceil', 'round'), peak_derivative_threshold=0.0, peak_min_prominence_percent=0.1, min_peak_datapoints=5.0, peak_max_prominence_percent=0.1, peak_height_max_percent=10.0, legacy_resolving_power=True)"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters.ms1_molecular_search", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters.ms1_molecular_search", "kind": "variable", "doc": "\n", "default_value": "MolecularFormulaSearchSettings(use_isotopologue_filter=False, isotopologue_filter_threshold=33.0, isotopologue_filter_atoms=('Cl', 'Br'), use_runtime_kendrick_filter=False, use_min_peaks_filter=True, min_peaks_per_class=15, url_database='postgresql+psycopg2://coremsappdb:coremsapppnnl@molformdb:5432/coremsapp', db_jobs=3, db_chunk_size=300, ion_charge=-1, min_hc_filter=0.3, max_hc_filter=3.0, min_oc_filter=0.0, max_oc_filter=1.2, min_op_filter=2.0, use_pah_line_rule=False, min_dbe=0.0, max_dbe=40.0, mz_error_score_weight=0.6, isotopologue_score_weight=0.4, adduct_atoms_neg=('Cl', 'Br'), adduct_atoms_pos=('Na', 'K'), score_methods=('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error'), score_method='prob_score', output_min_score=0.1, output_score_method='All Candidates', isRadical=False, isProtonated=True, isAdduct=False, usedAtoms={'C': (1, 100), 'H': (1, 200)}, ionization_type='ESI', min_ppm_error=-10.0, max_ppm_error=10.0, min_abun_error=-100.0, max_abun_error=100.0, mz_error_range=1.5, error_method='None', mz_error_average=0.0, used_atom_valences={'C': 4, '13C': 4, 'N': 3, 'O': 2, 'S': 2, 'H': 1, 'F': 1, 'Cl': 1, 'Br': 1, 'I': 1, 'At': 1, 'Li': 1, 'Na': 1, 'K': 1, 'Rb': 1, 'Cs': 1, 'Fr': 1, 'B': 4, 'In': 3, 'Al': 3, 'P': 3, 'Ga': 3, 'Mg': 2, 'Be': 2, 'Ca': 2, 'Sr': 2, 'Ba': 2, 'Ra': 2, 'V': 5, 'Fe': 3, 'Si': 4, 'Sc': 3, 'Ti': 4, 'Cr': 1, 'Mn': 1, 'Co': 1, 'Ni': 1, 'Cu': 2, 'Zn': 2, 'Ge': 4, 'As': 5, 'Se': 6, 'Y': 3, 'Zr': 4, 'Nb': 5, 'Mo': 6, 'Tc': 7, 'Ru': 8, 'Rh': 6, 'Pd': 4, 'Ag': 0, 'Cd': 2, 'Sn': 4, 'Sb': 5, 'Te': 6, 'La': 3, 'Hf': 4, 'Ta': 5, 'W': 6, 'Re': 4, 'Os': 4, 'Ir': 4, 'Pt': 4, 'Au': 3, 'Hg': 1, 'Tl': 3, 'Pb': 4, 'Bi': 3, 'Po': 2, 'Ac': 3})"}, {"fullname": "corems.encapsulation.factory.parameters.LCMSParameters.ms2_molecular_search", "modulename": "corems.encapsulation.factory.parameters", "qualname": "LCMSParameters.ms2_molecular_search", "kind": "variable", "doc": "\n", "default_value": "MolecularFormulaSearchSettings(use_isotopologue_filter=False, isotopologue_filter_threshold=33.0, isotopologue_filter_atoms=('Cl', 'Br'), use_runtime_kendrick_filter=False, use_min_peaks_filter=True, min_peaks_per_class=15, url_database='postgresql+psycopg2://coremsappdb:coremsapppnnl@molformdb:5432/coremsapp', db_jobs=3, db_chunk_size=300, ion_charge=-1, min_hc_filter=0.3, max_hc_filter=3.0, min_oc_filter=0.0, max_oc_filter=1.2, min_op_filter=2.0, use_pah_line_rule=False, min_dbe=0.0, max_dbe=40.0, mz_error_score_weight=0.6, isotopologue_score_weight=0.4, adduct_atoms_neg=('Cl', 'Br'), adduct_atoms_pos=('Na', 'K'), score_methods=('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error'), score_method='prob_score', output_min_score=0.1, output_score_method='All Candidates', isRadical=False, isProtonated=True, isAdduct=False, usedAtoms={'C': (1, 100), 'H': (1, 200)}, ionization_type='ESI', min_ppm_error=-10.0, max_ppm_error=10.0, min_abun_error=-100.0, max_abun_error=100.0, mz_error_range=1.5, error_method='None', mz_error_average=0.0, used_atom_valences={'C': 4, '13C': 4, 'N': 3, 'O': 2, 'S': 2, 'H': 1, 'F': 1, 'Cl': 1, 'Br': 1, 'I': 1, 'At': 1, 'Li': 1, 'Na': 1, 'K': 1, 'Rb': 1, 'Cs': 1, 'Fr': 1, 'B': 4, 'In': 3, 'Al': 3, 'P': 3, 'Ga': 3, 'Mg': 2, 'Be': 2, 'Ca': 2, 'Sr': 2, 'Ba': 2, 'Ra': 2, 'V': 5, 'Fe': 3, 'Si': 4, 'Sc': 3, 'Ti': 4, 'Cr': 1, 'Mn': 1, 'Co': 1, 'Ni': 1, 'Cu': 2, 'Zn': 2, 'Ge': 4, 'As': 5, 'Se': 6, 'Y': 3, 'Zr': 4, 'Nb': 5, 'Mo': 6, 'Tc': 7, 'Ru': 8, 'Rh': 6, 'Pd': 4, 'Ag': 0, 'Cd': 2, 'Sn': 4, 'Sb': 5, 'Te': 6, 'La': 3, 'Hf': 4, 'Ta': 5, 'W': 6, 'Re': 4, 'Os': 4, 'Ir': 4, 'Pt': 4, 'Au': 3, 'Hg': 1, 'Tl': 3, 'Pb': 4, 'Bi': 3, 'Po': 2, 'Ac': 3})"}, {"fullname": "corems.encapsulation.factory.parameters.default_parameters", "modulename": "corems.encapsulation.factory.parameters", "qualname": "default_parameters", "kind": "function", "doc": "Generate parameters dictionary with the default parameters for data processing\n To gather parameters from instrument data during the data parsing step, a parameters dictionary with the default parameters needs to be generated.\n This dictionary acts as a placeholder and is later used as an argument for all the class constructor methods during instantiation. \n The data gathered from the instrument is added to the class properties.
\n\nParameters
\n\n\n- file_location (str):\npath to the file
\n
\n\nReturns
\n\n\n- parameters (dict):\ndictionary with the default parameters for data processing
\n
\n", "signature": "(file_location):", "funcdef": "def"}, {"fullname": "corems.encapsulation.factory.processingSetting", "modulename": "corems.encapsulation.factory.processingSetting", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting", "kind": "class", "doc": "Transient processing settings class
\n\nAttributes
\n\n\n- implemented_apodization_function (tuple):\nAvailable apodization functions
\n- apodization_method (str):\nApodization function to use. Hanning is a good default for Fourier transform magnitude mode. For absorption mode processing, Half-Sine or Half-Kaiser may be more appropriate.
\n- number_of_truncations (int):\nHow many times to truncate the transient prior to Fourier transform
\n- number_of_zero_fills (int):\nHow many times to zero fille the transient prior to Fourier transform.
\n- next_power_of_two (bool):\nIf True, zero fill to the next power of two after the new length of len(transient)+(number_of_zero_fills*len(transient)).
\n- kaiser_beta (float):\nBeta parameter for Kaiser or Half-Kaiser apodisation function. 0 is rectangular, 5 is similar to Hamming,\n6 is similar to hanning, and 8.6 is similar to Blackman (from numpy docs)
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.__init__", "kind": "function", "doc": "\n", "signature": "(\timplemented_apodization_function: tuple = ('Hamming', 'Hanning', 'Blackman', 'Full-Sine', 'Half-Sine', 'Kaiser', 'Half-Kaiser'),\tapodization_method: str = 'Hanning',\tnumber_of_truncations: int = 0,\tnumber_of_zero_fills: int = 1,\tnext_power_of_two: bool = False,\tkaiser_beta: float = 8.6)"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.implemented_apodization_function", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.implemented_apodization_function", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('Hamming', 'Hanning', 'Blackman', 'Full-Sine', 'Half-Sine', 'Kaiser', 'Half-Kaiser')"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.apodization_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.apodization_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'Hanning'"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.number_of_truncations", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.number_of_truncations", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "0"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.number_of_zero_fills", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.number_of_zero_fills", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "1"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.next_power_of_two", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.next_power_of_two", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.TransientSetting.kaiser_beta", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "TransientSetting.kaiser_beta", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "8.6"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting", "kind": "class", "doc": "Data input settings class
\n\nAttributes
\n\n\n- header_translate (dict):\nDictionary with the header labels to be translated to the corems labels. For example, {'m/z':'m/z', 'Resolving Power':'Resolving Power', 'Abundance':'Abundance' , 'S/N':'S/N'}
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.__init__", "kind": "function", "doc": "\n", "signature": "(header_translate: dict = <factory>)"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.header_translate", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.header_translate", "kind": "variable", "doc": "\n", "annotation": ": dict"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.add_mz_label", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.add_mz_label", "kind": "function", "doc": "Add a label to the header_translate dictionary to be translated to the corems label for mz.
\n", "signature": "(self, label):", "funcdef": "def"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.add_peak_height_label", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.add_peak_height_label", "kind": "function", "doc": "Add a label to the header_translate dictionary to be translated to the corems label for peak height.
\n", "signature": "(self, label):", "funcdef": "def"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.add_sn_label", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.add_sn_label", "kind": "function", "doc": "Add a label to the header_translate dictionary to be translated to the corems label for signal to noise.
\n", "signature": "(self, label):", "funcdef": "def"}, {"fullname": "corems.encapsulation.factory.processingSetting.DataInputSetting.add_resolving_power_label", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "DataInputSetting.add_resolving_power_label", "kind": "function", "doc": "Add a label to the header_translate dictionary to be translated to the corems label for resolving power.
\n", "signature": "(self, label):", "funcdef": "def"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting", "kind": "class", "doc": "Liquid chromatograph processing settings class
\n\nAttributes
\n\n\n- scans (list or tuple, optional):\nList of select scan to average or a tuple containing the range to average. Default is (0, 1).
\n- eic_tolerance_ppm (float, optional):\nMass tolerance in ppm for extracted ion chromatogram peak detection. Default is 5.
\n- correct_eic_baseline (bool, optional):\nIf True, correct the baseline of the extracted ion chromatogram. Default is True.
\n- enforce_target_ms2 (bool, optional):\nOnly extract EICs for target_mz if the m/z was selected as precursor for ms2. Default is True.
\n- average_target_mz (bool, optional):\nIf True, average the target_mz EICs. Default is True.
\n- smooth_window (int, optional):\nWindow size for smoothing the ion chromatogram. Default is 5.
\n- smooth_method (str, optional):\nSmoothing method to use. Default is 'savgol'. Other options are 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'.
\n- implemented_smooth_method (tuple, optional):\nSmoothing methods that can be implemented. Values are ('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar').
\n- savgol_pol_order (int, optional):\nPolynomial order for Savitzky-Golay smoothing. Default is 2.
\n- peak_height_max_percent (float, optional):\n1-100 % used for baseline detection use 0.1 for second_derivative and 10 for other methods. Default is 10.
\n- peak_max_prominence_percent (float, optional):\n1-100 % used for baseline detection. Default is 1.
\n- peak_derivative_threshold (float, optional):\nThreshold for defining derivative crossing. Default is 0.0005.
\n- min_peak_datapoints (float, optional):\nminimum data point to define a chromatografic peak. Default is 5.
\n- noise_threshold_method (str, optional):\nMethod for detecting noise threshold. Default is 'manual_relative_abundance'.
\n- noise_threshold_methods_implemented (tuple, optional):\nMethods for detected noise threshold that can be implemented. Default is ('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative').
\n- std_noise_threshold (int, optional):\nthe amount of standard deviations used to calculate noise thresould, average + (std_noise_threshold * noise). Default is 3.
\n- peak_height_min_percent (float, optional):\n0-100 % used for peak detection. Default is 0.1.
\n- eic_signal_threshold (float, optional):\n0-100 % used for extracted ion chromatogram peak detection. Default is 0.01.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.__init__", "kind": "function", "doc": "\n", "signature": "(\tscans: list | tuple = (0, 1),\teic_tolerance_ppm: float = 5,\tenforce_target_ms2: bool = True,\taverage_target_mz: bool = True,\tsmooth_window: int = 5,\tsmooth_method: str = 'savgol',\timplemented_smooth_method: tuple = ('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'),\tsavgol_pol_order: int = 2,\tpeak_height_max_percent: float = 10,\tpeak_max_prominence_percent: float = 1,\tpeak_derivative_threshold: float = 0.0005,\tmin_peak_datapoints: float = 5,\tnoise_threshold_method: str = 'manual_relative_abundance',\tnoise_threshold_methods_implemented: tuple = ('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative'),\tstd_noise_threshold: int = 3,\tpeak_height_min_percent: float = 0.1,\teic_signal_threshold: float = 0.01)"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.scans", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.scans", "kind": "variable", "doc": "\n", "annotation": ": list | tuple", "default_value": "(0, 1)"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.eic_tolerance_ppm", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.eic_tolerance_ppm", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.correct_eic_baseline", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.correct_eic_baseline", "kind": "variable", "doc": "\n", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.enforce_target_ms2", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.enforce_target_ms2", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.average_target_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.average_target_mz", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.smooth_window", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.smooth_window", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.smooth_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.smooth_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'savgol'"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.implemented_smooth_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.implemented_smooth_method", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar')"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.savgol_pol_order", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.savgol_pol_order", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "2"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.peak_height_max_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.peak_height_max_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "10"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.peak_max_prominence_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.peak_max_prominence_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.peak_derivative_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.peak_derivative_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0005"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.min_peak_datapoints", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.min_peak_datapoints", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.noise_threshold_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.noise_threshold_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'manual_relative_abundance'"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.noise_threshold_methods_implemented", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.noise_threshold_methods_implemented", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative')"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.std_noise_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.std_noise_threshold", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.peak_height_min_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.peak_height_min_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.LiquidChromatographSetting.eic_signal_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "LiquidChromatographSetting.eic_signal_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.01"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting", "kind": "class", "doc": "Mass spectrum processing settings class
\n\nAttributes
\n\n\n- noise_threshold_method (str, optional):\nMethod for detecting noise threshold. Default is 'log'.
\n- noise_threshold_methods_implemented (tuple, optional):\nMethods for detected noise threshold that can be implemented. Default is ('minima', 'signal_noise', 'relative_abundance', 'absolute_abundance', 'log').
\n- noise_threshold_min_std (int, optional):\nMinumum value for noise thresholding when using 'minima' noise threshold method. Default is 6.
\n- noise_threshold_min_s2n (float, optional):\nMinimum value for noise thresholding when using 'signal_noise' noise threshold method. Default is 4.
\n- noise_threshold_min_relative_abundance (float, optional):\nMinimum value for noise thresholding when using 'relative_abundance' noise threshold method. Default is 6.
\n- noise_threshold_absolute_abundance (float, optional):\nMinimum value for noise thresholding when using 'absolute_abundance' noise threshold method. Default is 1_000_000.
\n- noise_threshold_log_nsigma (int, optional):\nNumber of standard deviations to use when using 'log' noise threshold method. Default is 6.
\n- noise_threshold_log_nsigma_corr_factor (float, optional):\nCorrection factor for log noise threshold method. Default is 0.463.
\n- noise_threshold_log_nsigma_bins (int, optional):\nNumber of bins to use for histogram when using 'log' noise threshold method. Default is 500.
\n- noise_min_mz (float, optional):\nMinimum m/z to use for noise thresholding. Default is 50.0.
\n- noise_max_mz (float, optional):\nMaximum m/z to use for noise thresholding. Default is 1200.0.
\n- min_picking_mz (float, optional):\nMinimum m/z to use for peak picking. Default is 50.0.
\n- max_picking_mz (float, optional):\nMaximum m/z to use for peak picking. Default is 1200.0.
\n- picking_point_extrapolate (int, optional):\nHow many data points (in each direction) to extrapolate the mz axis and 0 pad the abundance axis. Default is 3.
\n- calib_minimize_method (str, optional):\nMinimization method to use for calibration. Default is 'Powell'.
\n- calib_pol_order (int, optional):\nPolynomial order to use for calibration. Default is 2.
\n- max_calib_ppm_error (float, optional):\nMaximum ppm error to use for calibration. Default is 1.0.
\n- min_calib_ppm_error (float, optional):\nMinimum ppm error to use for calibration. Default is -1.0.
\n- calib_sn_threshold (float, optional):\nSignal to noise threshold to use for calibration. Default is 2.0.
\n- do_calibration (bool, optional):\nIf True, perform calibration. Default is True.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.__init__", "kind": "function", "doc": "\n", "signature": "(\tnoise_threshold_method: str = 'log',\tnoise_threshold_methods_implemented: tuple = ('minima', 'signal_noise', 'relative_abundance', 'absolute_abundance', 'log'),\tnoise_threshold_min_std: int = 6,\tnoise_threshold_min_s2n: float = 4,\tnoise_threshold_min_relative_abundance: float = 6,\tnoise_threshold_absolute_abundance: float = 1000000,\tnoise_threshold_log_nsigma: int = 6,\tnoise_threshold_log_nsigma_corr_factor: float = 0.463,\tnoise_threshold_log_nsigma_bins: int = 500,\tnoise_min_mz: float = 50.0,\tnoise_max_mz: float = 1200.0,\tmin_picking_mz: float = 50.0,\tmax_picking_mz: float = 1200.0,\tpicking_point_extrapolate: int = 3,\tcalib_minimize_method: str = 'Powell',\tcalib_pol_order: int = 2,\tmax_calib_ppm_error: float = 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"qualname": "MassSpectrumSetting.noise_threshold_min_std", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "6"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_min_s2n", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_min_s2n", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "4"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_min_relative_abundance", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_threshold_min_relative_abundance", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "6"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_threshold_absolute_abundance", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": 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"MassSpectrumSetting.noise_threshold_log_nsigma_bins", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "500"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_min_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_min_mz", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "50.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.noise_max_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.noise_max_mz", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1200.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.min_picking_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.min_picking_mz", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "50.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.max_picking_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.max_picking_mz", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1200.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.picking_point_extrapolate", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.picking_point_extrapolate", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.calib_minimize_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.calib_minimize_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'Powell'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.calib_pol_order", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.calib_pol_order", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "2"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.max_calib_ppm_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.max_calib_ppm_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.min_calib_ppm_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.min_calib_ppm_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "-1.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.calib_sn_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.calib_sn_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "2.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpectrumSetting.do_calibration", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpectrumSetting.do_calibration", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting", "kind": "class", "doc": "Mass spectrum peak processing settings class
\n\nAttributes
\n\n\n- kendrick_base (Dict, optional):\nDictionary specifying the elements and their counts in the Kendrick base.\nDefaults to {'C': 1, 'H': 2}.
\n- kendrick_rounding_method (str, optional):\nMethod for calculating the nominal Kendrick mass. Valid values are 'floor', 'ceil', or 'round'.\nDefaults to 'floor'.
\n- implemented_kendrick_rounding_methods (tuple):\nTuple of valid rounding methods for calculating the nominal Kendrick mass.\nDefaults to ('floor', 'ceil', 'round').
\n- peak_derivative_threshold (float, optional):\nThreshold for defining derivative crossing. Should be a value between 0 and 1.\nDefaults to 0.0.
\n- peak_min_prominence_percent (float, optional):\nMinimum prominence percentage used for peak detection. Should be a value between 1 and 100.\nDefaults to 0.1.
\n- min_peak_datapoints (float, optional):\nMinimum number of data points used for peak detection. Should be a value between 0 and infinity.\nDefaults to 5.
\n- peak_max_prominence_percent (float, optional):\nMaximum prominence percentage used for baseline detection. Should be a value between 1 and 100.\nDefaults to 0.1.
\n- peak_height_max_percent (float, optional):\nMaximum height percentage used for baseline detection. Should be a value between 1 and 100.\nDefaults to 10.
\n- legacy_resolving_power (bool, optional):\nFlag indicating whether to use the legacy (CoreMS v1) resolving power calculation.\nDefaults to True.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.__init__", "kind": "function", "doc": "\n", "signature": "(\tkendrick_base: Dict = <factory>,\tkendrick_rounding_method: str = 'floor',\timplemented_kendrick_rounding_methods: tuple = ('floor', 'ceil', 'round'),\tpeak_derivative_threshold: float = 0.0,\tpeak_min_prominence_percent: float = 0.1,\tmin_peak_datapoints: float = 5,\tpeak_max_prominence_percent: float = 0.1,\tpeak_height_max_percent: float = 10,\tlegacy_resolving_power: bool = True)"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.kendrick_base", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.kendrick_base", "kind": "variable", "doc": "\n", "annotation": ": Dict"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.kendrick_rounding_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.kendrick_rounding_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'floor'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.implemented_kendrick_rounding_methods", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.implemented_kendrick_rounding_methods", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('floor', 'ceil', 'round')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.peak_derivative_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.peak_derivative_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.peak_min_prominence_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.peak_min_prominence_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.min_peak_datapoints", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.min_peak_datapoints", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.peak_max_prominence_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.peak_max_prominence_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.peak_height_max_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.peak_height_max_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "10"}, {"fullname": "corems.encapsulation.factory.processingSetting.MassSpecPeakSetting.legacy_resolving_power", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MassSpecPeakSetting.legacy_resolving_power", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting", "kind": "class", "doc": "Gas chromatograph processing settings class
\n\nAttributes
\n\n\n- use_deconvolution (bool, optional):\nIf True, use deconvolution. Default is False.
\n- implemented_smooth_method (tuple, optional):\nSmoothing methods that can be implemented. Default is ('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar').
\n- smooth_window (int, optional):\nWindow size for smoothing the ion chromatogram. Default is 5.
\n- smooth_method (str, optional):\nSmoothing method to use. Default is 'savgol'. Other options are 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'.
\n- savgol_pol_order (int, optional):\nPolynomial order for Savitzky-Golay smoothing. Default is 2.
\n- peak_derivative_threshold (float, optional):\nThreshold for defining derivative crossing. Should be a value between 0 and 1.\nDefaults to 0.0005.
\n- peak_height_max_percent (float, optional):\nMaximum height percentage used for baseline detection. Should be a value between 1 and 100.\nDefaults to 10.
\n- peak_max_prominence_percent (float, optional):\nMaximum prominence percentage used for baseline detection. Should be a value between 1 and 100.\nDefaults to 1.
\n- min_peak_datapoints (float, optional):\nMinimum number of data points used for peak detection. Should be a value between 0 and infinity.\nDefaults to 5.
\n- max_peak_width (float, optional):\nMaximum peak width used for peak detection. Should be a value between 0 and infinity.\nDefaults to 0.1.
\n- noise_threshold_method (str, optional):\nMethod for detecting noise threshold. Default is 'manual_relative_abundance'.
\n- noise_threshold_methods_implemented (tuple, optional):\nMethods for detected noise threshold that can be implemented. Default is ('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative').
\n- std_noise_threshold (int, optional):\nDefault is 3.
\n- peak_height_min_percent (float, optional):\n0-100 % used for peak detection. Default is 0.1.
\n- peak_min_prominence_percent (float, optional):\n0-100 % used for peak detection. Default is 0.1.
\n- eic_signal_threshold (float, optional):\n0-100 % used for extracted ion chromatogram peak detection. Default is 0.01.
\n- max_rt_distance (float, optional):\nMaximum distance allowance for hierarchical cluster, in minutes. Default is 0.025.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.__init__", "kind": "function", "doc": "\n", "signature": "(\tuse_deconvolution: bool = False,\timplemented_smooth_method: tuple = ('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar'),\tsmooth_window: int = 5,\tsmooth_method: str = 'savgol',\tsavgol_pol_order: int = 2,\tpeak_derivative_threshold: float = 0.0005,\tpeak_height_max_percent: float = 10,\tpeak_max_prominence_percent: float = 1,\tmin_peak_datapoints: float = 5,\tmax_peak_width: float = 0.1,\tnoise_threshold_method: str = 'manual_relative_abundance',\tnoise_threshold_methods_implemented: tuple = ('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative'),\tstd_noise_threshold: int = 3,\tpeak_height_min_percent: float = 0.1,\tpeak_min_prominence_percent: float = 0.1,\teic_signal_threshold: float = 0.01,\tmax_rt_distance: float = 0.025)"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.use_deconvolution", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.use_deconvolution", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.implemented_smooth_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.implemented_smooth_method", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('savgol', 'hanning', 'blackman', 'bartlett', 'flat', 'boxcar')"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.smooth_window", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.smooth_window", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.smooth_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.smooth_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'savgol'"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.savgol_pol_order", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.savgol_pol_order", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "2"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.peak_derivative_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.peak_derivative_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0005"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.peak_height_max_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.peak_height_max_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "10"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.peak_max_prominence_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.peak_max_prominence_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.min_peak_datapoints", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.min_peak_datapoints", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "5"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.max_peak_width", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.max_peak_width", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.noise_threshold_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.noise_threshold_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'manual_relative_abundance'"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.noise_threshold_methods_implemented", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.noise_threshold_methods_implemented", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative')"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.std_noise_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.std_noise_threshold", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.peak_height_min_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.peak_height_min_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.peak_min_prominence_percent", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.peak_min_prominence_percent", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.eic_signal_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.eic_signal_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.01"}, {"fullname": "corems.encapsulation.factory.processingSetting.GasChromatographSetting.max_rt_distance", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "GasChromatographSetting.max_rt_distance", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.025"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings", "kind": "class", "doc": "Settings for compound search
\n\nAttributes
\n\n\n- url_database (str, optional):\nURL for the database. Default is 'sqlite:///db/pnnl_lowres_gcms_compounds.sqlite'.
\n- ri_search_range (float, optional):\nRetention index search range. Default is 35.
\n- rt_search_range (float, optional):\nRetention time search range, in minutes. Default is 1.0.
\n- correlation_threshold (float, optional):\nThreshold for correlation for spectral similarity. Default is 0.5.
\n- score_threshold (float, optional):\nThreshold for compsite score. Default is 0.0.
\n- ri_spacing (float, optional):\nRetention index spacing. Default is 200.
\n- ri_std (float, optional):\nRetention index standard deviation. Default is 3.
\n- ri_calibration_compound_names (list, optional):\nList of compound names to use for retention index calibration. Default is ['Methyl Caprylate', 'Methyl Caprate', 'Methyl Pelargonate', 'Methyl Laurate', 'Methyl Myristate', 'Methyl Palmitate', 'Methyl Stearate', 'Methyl Eicosanoate', 'Methyl Docosanoate', 'Methyl Linocerate', 'Methyl Hexacosanoate', 'Methyl Octacosanoate', 'Methyl Triacontanoate'].
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.__init__", "kind": "function", "doc": "\n", "signature": "(\turl_database: str = 'postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/lowres',\tri_search_range: float = 35,\trt_search_range: float = 1.0,\tcorrelation_threshold: float = 0.5,\tscore_threshold: float = 0.0,\tri_spacing: float = 200,\tri_std: float = 3,\tri_calibration_compound_names: List = <factory>,\texploratory_mode: bool = False,\tscore_methods: tuple = ('highest_sim_score', 'highest_ss'),\toutput_score_method: str = 'All')"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.url_database", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.url_database", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/lowres'"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.ri_search_range", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.ri_search_range", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "35"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.rt_search_range", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.rt_search_range", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.correlation_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.correlation_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.5"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.score_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.score_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.ri_spacing", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.ri_spacing", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "200"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.ri_std", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.ri_std", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.ri_calibration_compound_names", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.ri_calibration_compound_names", "kind": "variable", "doc": "\n", "annotation": ": List"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.exploratory_mode", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.exploratory_mode", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.score_methods", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.score_methods", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('highest_sim_score', 'highest_ss')"}, {"fullname": "corems.encapsulation.factory.processingSetting.CompoundSearchSettings.output_score_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "CompoundSearchSettings.output_score_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'All'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings", "kind": "class", "doc": "Settings for molecular searching
\n\nThese are used to generate the database entries, do not change.
\n\nAttributes
\n\n\n- usedAtoms (dict, optional):\nDictionary of atoms and ranges. Default is {'C': (1, 90), 'H': (4, 200), 'O': (0, 12), 'N': (0, 0), 'S': (0, 0), 'P': (0, 0), 'Cl': (0, 0)}.
\n- min_mz (float, optional):\nMinimum m/z to use for searching. Default is 50.0.
\n- max_mz (float, optional):\nMaximum m/z to use for searching. Default is 1200.0.
\n- min_dbe (float, optional):\nMinimum double bond equivalent to use for searching. Default is 0.
\n- max_dbe (float, optional):\nMaximum double bond equivalent to use for searching. Default is 50.
\n- use_pah_line_rule (bool, optional):\nIf True, use the PAH line rule. Default is False.
\n- isRadical (bool, optional):\nIf True, search for radical ions. Default is True.
\n- isProtonated (bool, optional):\nIf True, search for protonated ions. Default is True.
\n- min_op_filter (float, optional):\nMinimum oxygen to phosphorous ratio. Default is 2.
\n- min_hc_filter (float, optional):\nMinimum hydrogen to carbon ratio. Default is 0.3.
\n- min_oc_filter (float, optional):\nMinimum oxygen to carbon ratio. Default is 1.2.
\n- max_oc_filter (float, optional):\nMaximum oxygen to carbon ratio. Default is 0.0.
\n- url_database (str, optional):\nURL for the database. Default is None.
\n- db_jobs (int, optional):\nNumber of jobs to use for database queries. Default is 1.
\n- used_atom_valences (dict, optional):\nDictionary of atoms and valences. Default is {'C': 4, '13C': 4, 'H': 1, 'O': 2, '18O': 2, 'N': 3, 'S': 2, '34S': 2, 'P': 3, 'Cl': 1, '37Cl': 1, 'Br': 1, 'Na': 1, 'F': 1, 'K': 0}.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.usedAtoms", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.usedAtoms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.min_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.min_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.max_mz", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.max_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.min_dbe", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.min_dbe", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.max_dbe", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.max_dbe", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.use_pah_line_rule", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.use_pah_line_rule", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.isRadical", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.isRadical", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.isProtonated", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.isProtonated", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.min_op_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.min_op_filter", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.min_hc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.min_hc_filter", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.min_oc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.min_oc_filter", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.max_oc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.max_oc_filter", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.url_database", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.url_database", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.db_jobs", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.db_jobs", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularLookupDictSettings.used_atom_valences", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularLookupDictSettings.used_atom_valences", "kind": "variable", "doc": "\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings", "kind": "class", "doc": "Settings for molecular searching
\n\nAttributes
\n\n\n- use_isotopologue_filter (bool, optional):\nIf True, use isotopologue filter. Default is False.
\n- isotopologue_filter_threshold (float, optional):\nThreshold for isotopologue filter. Default is 33.
\n- isotopologue_filter_atoms (tuple, optional):\nTuple of atoms to use for isotopologue filter. Default is ('Cl', 'Br').
\n- use_runtime_kendrick_filter (bool, optional):\nIf True, use runtime Kendrick filter. Default is False.
\n- use_min_peaks_filter (bool, optional):\nIf True, use minimum peaks filter. Default is True.
\n- min_peaks_per_class (int, optional):\nMinimum number of peaks per class. Default is 15.
\n- url_database (str, optional):\nURL for the database. Default is 'postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp'.
\n- db_jobs (int, optional):\nNumber of jobs to use for database queries. Default is 3.
\n- db_chunk_size (int, optional):\nChunk size to use for database queries. Default is 300.
\n- ion_charge (int, optional):\nIon charge. Default is -1.
\n- min_hc_filter (float, optional):\nMinimum hydrogen to carbon ratio. Default is 0.3.
\n- max_hc_filter (float, optional):\nMaximum hydrogen to carbon ratio. Default is 3.
\n- min_oc_filter (float, optional):\nMinimum oxygen to carbon ratio. Default is 0.0.
\n- max_oc_filter (float, optional):\nMaximum oxygen to carbon ratio. Default is 1.2.
\n- min_op_filter (float, optional):\nMinimum oxygen to phosphorous ratio. Default is 2.
\n- use_pah_line_rule (bool, optional):\nIf True, use the PAH line rule. Default is False.
\n- min_dbe (float, optional):\nMinimum double bond equivalent to use for searching. Default is 0.
\n- max_dbe (float, optional):\nMaximum double bond equivalent to use for searching. Default is 40.
\n- mz_error_score_weight (float, optional):\nWeight for m/z error score to contribute to composite score. Default is 0.6.
\n- isotopologue_score_weight (float, optional):\nWeight for isotopologue score to contribute to composite score. Default is 0.4.
\n- adduct_atoms_neg (tuple, optional):\nTuple of atoms to use in negative polarity. Default is ('Cl', 'Br').
\n- adduct_atoms_pos (tuple, optional):\nTuple of atoms to use in positive polarity. Default is ('Na', 'K').
\n- score_methods (tuple, optional):\nTuple of score method that can be implemented. \nDefault is ('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error').
\n- score_method (str, optional):\nScore method to use. Default is 'prob_score'. Options are 'S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error'.
\n- output_min_score (float, optional):\nMinimum score for output. Default is 0.1.
\n- output_score_method (str, optional):\nScore method to use for output. Default is 'All Candidates'.
\n- output_min_score (float, optional):\nMinimum score for output. Default is 0.1.
\n- isRadical (bool, optional):\nIf True, search for radical ions. Default is False.
\n- isProtonated (bool, optional):\nIf True, search for protonated ions. Default is True.
\n- isAdduct (bool, optional):\nIf True, search for adduct ions. Default is False.
\n- usedAtoms (dict, optional):\nDictionary of atoms and ranges. Default is {'C': (1, 90), 'H': (4, 200), 'O': (0, 12), 'N': (0, 0), 'S': (0, 0), 'P': (0, 0), 'Cl': (0, 0)}.
\n- ionization_type (str, optional):\nIonization type. Default is 'ESI'.
\n- min_ppm_error (float, optional):\nMinimum ppm error. Default is -10.0.
\n- max_ppm_error (float, optional):\nMaximum ppm error. Default is 10.0.
\n- min_abun_error (float, optional):\nMinimum abundance error for isotolopologue search. Default is -100.0.
\n- max_abun_error (float, optional):\nMaximum abundance error for isotolopologue search. Default is 100.0.
\n- mz_error_range (float, optional):\nm/z error range. Default is 1.5.
\n- error_method (str, optional):\nError method. Default is 'None'. Options are 'distance', 'lowest', 'symmetrical','average' 'None'.
\n- mz_error_average (float, optional):\nm/z error average. Default is 0.0.
\n- used_atom_valences (dict, optional):\nDictionary of atoms and valences. Default is {'C': 4, '13C': 4, 'H': 1, 'O': 2, '18O': 2, 'N': 3, 'S': 2, '34S': 2, 'P': 3, 'Cl': 1, '37Cl': 1, 'Br': 1, 'Na': 1, 'F': 1, 'K': 0}.
\n
\n"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.__init__", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.__init__", "kind": "function", "doc": "\n", "signature": "(\tuse_isotopologue_filter: bool = False,\tisotopologue_filter_threshold: float = 33,\tisotopologue_filter_atoms: tuple = ('Cl', 'Br'),\tuse_runtime_kendrick_filter: bool = False,\tuse_min_peaks_filter: bool = True,\tmin_peaks_per_class: int = 15,\turl_database: str = 'postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp',\tdb_jobs: int = 3,\tdb_chunk_size: int = 300,\tion_charge: int = -1,\tmin_hc_filter: float = 0.3,\tmax_hc_filter: float = 3,\tmin_oc_filter: float = 0.0,\tmax_oc_filter: float = 1.2,\tmin_op_filter: float = 2,\tuse_pah_line_rule: bool = False,\tmin_dbe: float = 0,\tmax_dbe: float = 40,\tmz_error_score_weight: float = 0.6,\tisotopologue_score_weight: float = 0.4,\tadduct_atoms_neg: tuple = ('Cl', 'Br'),\tadduct_atoms_pos: tuple = ('Na', 'K'),\tscore_methods: tuple = ('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error'),\tscore_method: str = 'prob_score',\toutput_min_score: float = 0.1,\toutput_score_method: str = 'All Candidates',\tisRadical: bool = False,\tisProtonated: bool = True,\tisAdduct: bool = False,\tusedAtoms: dict = <factory>,\tionization_type: str = 'ESI',\tmin_ppm_error: float = -10.0,\tmax_ppm_error: float = 10.0,\tmin_abun_error: float = -100.0,\tmax_abun_error: float = 100.0,\tmz_error_range: float = 1.5,\terror_method: str = 'None',\tmz_error_average: float = 0.0,\tused_atom_valences: dict = <factory>)"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.use_isotopologue_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.use_isotopologue_filter", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isotopologue_filter_threshold", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isotopologue_filter_threshold", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "33"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isotopologue_filter_atoms", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isotopologue_filter_atoms", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('Cl', 'Br')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.use_runtime_kendrick_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.use_runtime_kendrick_filter", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.use_min_peaks_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.use_min_peaks_filter", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_peaks_per_class", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_peaks_per_class", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "15"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.url_database", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.url_database", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.db_jobs", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.db_jobs", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.db_chunk_size", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.db_chunk_size", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "300"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.ion_charge", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.ion_charge", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "-1"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_hc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_hc_filter", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.3"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.max_hc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.max_hc_filter", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "3"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_oc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_oc_filter", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.max_oc_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.max_oc_filter", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1.2"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_op_filter", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_op_filter", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "2"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.use_pah_line_rule", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.use_pah_line_rule", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_dbe", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_dbe", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.max_dbe", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.max_dbe", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "40"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.mz_error_score_weight", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.mz_error_score_weight", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.6"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isotopologue_score_weight", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isotopologue_score_weight", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.4"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.adduct_atoms_neg", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.adduct_atoms_neg", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('Cl', 'Br')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.adduct_atoms_pos", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.adduct_atoms_pos", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('Na', 'K')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.score_methods", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.score_methods", "kind": "variable", "doc": "\n", "annotation": ": tuple", "default_value": "('S_P_lowest_error', 'N_S_P_lowest_error', 'lowest_error', 'prob_score', 'air_filter_error', 'water_filter_error', 'earth_filter_error')"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.score_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.score_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'prob_score'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.output_min_score", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.output_min_score", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.1"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.output_score_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.output_score_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'All Candidates'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isRadical", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isRadical", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isProtonated", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isProtonated", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.isAdduct", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.isAdduct", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.usedAtoms", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.usedAtoms", "kind": "variable", "doc": "\n", "annotation": ": dict"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.ionization_type", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.ionization_type", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'ESI'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_ppm_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_ppm_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "-10.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.max_ppm_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.max_ppm_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "10.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.min_abun_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.min_abun_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "-100.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.max_abun_error", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.max_abun_error", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "100.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.mz_error_range", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.mz_error_range", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "1.5"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.error_method", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.error_method", "kind": "variable", "doc": "\n", "annotation": ": str", "default_value": "'None'"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.mz_error_average", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.mz_error_average", "kind": "variable", "doc": "\n", "annotation": ": float", "default_value": "0.0"}, {"fullname": "corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings.used_atom_valences", "modulename": "corems.encapsulation.factory.processingSetting", "qualname": "MolecularFormulaSearchSettings.used_atom_valences", "kind": "variable", "doc": "\n", "annotation": ": dict"}, {"fullname": "corems.encapsulation.input", "modulename": "corems.encapsulation.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.input.parameter_from_json", "modulename": "corems.encapsulation.input.parameter_from_json", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_toml_parameters_ms", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_toml_parameters_ms", "kind": "function", "doc": "Load parameters from a toml file and set the parameters in the mass_spec_obj
\n\nParameters
\n\n\n- mass_spec_obj (MassSpectrum):\ncorems MassSpectrum object
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n", "signature": "(mass_spec_obj, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_parameters_ms", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_parameters_ms", "kind": "function", "doc": "Load parameters from a json file and set the parameters in the mass_spec_obj
\n\nParameters
\n\n\n- mass_spec_obj (MassSpectrum):\ncorems MassSpectrum object
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n", "signature": "(mass_spec_obj, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_toml_parameters_gcms", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_toml_parameters_gcms", "kind": "function", "doc": "Load parameters from a toml file and set the parameters in the GCMS object
\n\nParameters
\n\n\n- gcms_obj (GCMSBase):\ncorems GCMSBase object
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n", "signature": "(gcms_obj, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_parameters_gcms", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_parameters_gcms", "kind": "function", "doc": "Load parameters from a json file and set the parameters in the GCMS object
\n\nParameters
\n\n\n- gcms_obj (GCMSBase):\ncorems GCMSBase object
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n", "signature": "(gcms_obj, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_toml_parameters_class", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_toml_parameters_class", "kind": "function", "doc": "Load parameters from a toml file and set the parameters in the instance_parameters_class
\n\nParameters
\n\n\n- parameter_label (str):\nlabel of the parameters in the toml file
\n- instance_parameters_class (object):\ninstance of the parameters class
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n\nReturns
\n\n\n- object: instance of the parameters class
\n
\n", "signature": "(parameter_label, instance_parameters_class, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.input.parameter_from_json.load_and_set_parameters_class", "modulename": "corems.encapsulation.input.parameter_from_json", "qualname": "load_and_set_parameters_class", "kind": "function", "doc": "Load parameters from a json file and set the parameters in the instance_parameters_class
\n\nParameters
\n\n\n- parameter_label (str):\nlabel of the parameters in the json file
\n- instance_parameters_class (object):\ninstance of the parameters class
\n- parameters_path (str, optional):\npath to the parameters file, by default False
\n
\n\nRaises
\n\n\n- FileNotFoundError: if the file is not found
\n
\n\nReturns
\n\n\n- object: instance of the parameters class
\n
\n", "signature": "(parameter_label, instance_parameters_class, parameters_path=False):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output", "modulename": "corems.encapsulation.output", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.output.parameter_to_dict", "modulename": "corems.encapsulation.output.parameter_to_dict", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.output.parameter_to_dict.get_dict_all_default_data", "modulename": "corems.encapsulation.output.parameter_to_dict", "qualname": "get_dict_all_default_data", "kind": "function", "doc": "Return a dictionary with all default parameters for MS and GCMS
\n", "signature": "():", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_dict.get_dict_data_ms", "modulename": "corems.encapsulation.output.parameter_to_dict", "qualname": "get_dict_data_ms", "kind": "function", "doc": "Return a dictionary with all parameters for MS
\n", "signature": "(mass_spec):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_dict.get_dict_ms_default_data", "modulename": "corems.encapsulation.output.parameter_to_dict", "qualname": "get_dict_ms_default_data", "kind": "function", "doc": "Return a dictionary with all default parameters for MS including data input
\n", "signature": "():", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_dict.get_dict_gcms_default_data", "modulename": "corems.encapsulation.output.parameter_to_dict", "qualname": "get_dict_gcms_default_data", "kind": "function", "doc": "Return a dictionary with all default parameters for GCMS
\n", "signature": "():", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_dict.get_dict_data_gcms", "modulename": "corems.encapsulation.output.parameter_to_dict", "qualname": "get_dict_data_gcms", "kind": "function", "doc": "Return a dictionary with all parameters for GCMS
\n", "signature": "(gcms):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json", "modulename": "corems.encapsulation.output.parameter_to_json", "kind": "module", "doc": "\n"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_all_settings_json", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_all_settings_json", "kind": "function", "doc": "Write JSON file into current directory with all the default settings for the CoreMS package.
\n\nParameters:
\n\nfilename : str, optional\n The name of the JSON file to be created. Default is 'SettingsCoreMS.json'.\nfile_path : str or Path, optional\n The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
\n", "signature": "(filename='SettingsCoreMS.json', file_path=None):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_ms_settings_json", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_ms_settings_json", "kind": "function", "doc": "Write JSON file into current directory with all the mass spectrum default settings for the CoreMS package.
\n\nParameters
\n\n\n- filename (str, optional):\nThe name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
\n- file_path (str or Path, optional):\nThe path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
\n
\n", "signature": "(filename='SettingsCoreMS.json', file_path=None):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_gcms_settings_json", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_gcms_settings_json", "kind": "function", "doc": "Write JSON file into current directory containing the default GCMS settings data.
\n\nParameters
\n\n\n- filename (str, optional):\nThe name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
\n- file_path (str or Path-like object, optional):\nThe path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
\n
\n", "signature": "(filename='SettingsCoreMS.json', file_path=None):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_all_settings_toml", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_all_settings_toml", "kind": "function", "doc": "Write TOML file into the specified file path or the current directory with all the default settings for the CoreMS package.
\n\nParameters
\n\n\n- filename (str, optional):\nThe name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
\n- file_path (str or Path, optional):\nThe path where the TOML file will be saved. If not provided, the file will be saved in the current directory.
\n
\n", "signature": "(filename='SettingsCoreMS.toml', file_path=None):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_ms_settings_toml", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_ms_settings_toml", "kind": "function", "doc": "Write TOML file into the current directory with all the mass spectrum default settings for the CoreMS package.
\n\nParameters
\n\n\n- filename (str, optional):\nThe name of the TOML file to be created. Default is 'SettingsCoreMS.toml'.
\n- file_path (str or Path, optional):\nThe path where the TOML file should be saved. If not provided, the file will be saved in the current working directory.
\n
\n", "signature": "(filename='SettingsCoreMS.toml', file_path=None):", "funcdef": "def"}, {"fullname": "corems.encapsulation.output.parameter_to_json.dump_gcms_settings_toml", "modulename": "corems.encapsulation.output.parameter_to_json", "qualname": "dump_gcms_settings_toml", "kind": "function", "doc": "Write TOML file into current directory containing the default GCMS settings data.
\n\nParameters
\n\n\n- filename (str, optional):\nThe name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
\n- file_path (str or Path, optional):\nThe path where the TOML file will be saved. If not provided, the file will be saved in the current working directory.
\n
\n", "signature": "(filename='SettingsCoreMS.toml', file_path=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectra", "modulename": "corems.mass_spectra", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc", "modulename": "corems.mass_spectra.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_Calc", "modulename": "corems.mass_spectra.calc.GC_Calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_Calc.GC_Calculations", "modulename": "corems.mass_spectra.calc.GC_Calc", "qualname": "GC_Calculations", "kind": "class", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_Calc.GC_Calculations.calibrate_ri", "modulename": "corems.mass_spectra.calc.GC_Calc", "qualname": "GC_Calculations.calibrate_ri", "kind": "function", "doc": "\n", "signature": "(self, ref_dict, cal_file_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Calc.GC_Calculations.smooth_tic", "modulename": "corems.mass_spectra.calc.GC_Calc", "qualname": "GC_Calculations.smooth_tic", "kind": "function", "doc": "\n", "signature": "(self, tic):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Calc.GC_Calculations.centroid_detector", "modulename": "corems.mass_spectra.calc.GC_Calc", "qualname": "GC_Calculations.centroid_detector", "kind": "function", "doc": "\n", "signature": "(self, tic, rt):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Calc.GC_Calculations.remove_outliers", "modulename": "corems.mass_spectra.calc.GC_Calc", "qualname": "GC_Calculations.remove_outliers", "kind": "function", "doc": "\n", "signature": "(self, data):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution", "kind": "class", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.run_deconvolution", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.run_deconvolution", "kind": "function", "doc": "\n", "signature": "(self, plot_res=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.centroid_detector", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.centroid_detector", "kind": "function", "doc": "this function has been replaced with sp.peak_picking_first_derivative\nand it not used
\n", "signature": "(self, tic, rt):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.ion_extracted_chroma", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.ion_extracted_chroma", "kind": "function", "doc": "\n", "signature": "(self, mass_spectra_obj):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.hc", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.hc", "kind": "function", "doc": "\n", "signature": "(self, X, Y, max_rt_distance=0.025):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.find_peaks_entity", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.find_peaks_entity", "kind": "function", "doc": "combine eic with mathing rt apexes
\n", "signature": "(self, eic_dict):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.mass_spec_factory", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.mass_spec_factory", "kind": "function", "doc": "\n", "signature": "(self, rt, datadict):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.smooth_signal", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.smooth_signal", "kind": "function", "doc": "\n", "signature": "(self, signal):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.add_gcpeak", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.add_gcpeak", "kind": "function", "doc": "\n", "signature": "(\tself,\tnew_apex_index,\tstart_rt,\tfinal_rt,\tpeak_rt,\tsmoothed_tic,\tdatadict,\tplot_res):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.deconvolution", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.deconvolution", "kind": "function", "doc": "\n", "signature": "(self, peaks_entity_data, plot_res):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution.quadratic_interpolation", "modulename": "corems.mass_spectra.calc.GC_Deconvolution", "qualname": "MassDeconvolution.quadratic_interpolation", "kind": "function", "doc": "\n", "signature": "(self, rt_list, tic_list, apex_index):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.GC_RI_Calibration", "modulename": "corems.mass_spectra.calc.GC_RI_Calibration", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.GC_RI_Calibration.get_rt_ri_pairs", "modulename": "corems.mass_spectra.calc.GC_RI_Calibration", "qualname": "get_rt_ri_pairs", "kind": "function", "doc": "\n", "signature": "(gcms_ref_obj, sql_obj=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LC_Calc", "modulename": "corems.mass_spectra.calc.LC_Calc", "kind": "module", "doc": "Created on Jun 14, 2019
\n\n@author: eber373
\n"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations", "kind": "class", "doc": "classdocs
\n"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations.get_max_eic", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations.get_max_eic", "kind": "function", "doc": "\n", "signature": "(eic_data: dict):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations.smooth_tic", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations.smooth_tic", "kind": "function", "doc": "\n", "signature": "(self, tic):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations.eic_centroid_detector", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations.eic_centroid_detector", "kind": "function", "doc": "\n", "signature": "(self, rt, eic, max_eic):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations.centroid_detector", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations.centroid_detector", "kind": "function", "doc": "\n", "signature": "(self, rt, tic):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LC_Calc.LC_Calculations.find_nearest_scan", "modulename": "corems.mass_spectra.calc.LC_Calc", "qualname": "LC_Calculations.find_nearest_scan", "kind": "function", "doc": "\n", "signature": "(self, rt):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted", "modulename": "corems.mass_spectra.calc.LF_Targeted", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted", "kind": "class", "doc": "\n", "bases": "corems.mass_spectra.calc.GC_Calc.GC_Calculations"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.__init__", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.__init__", "kind": "function", "doc": "\n", "signature": "(ref_file='Unknown', noise_cutoff='Unknown', tolerance='Unknown')"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.tolerance", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.tolerance", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.noise_cutoff", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.noise_cutoff", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.offset_hits", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.offset_hits", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.mz_filtered", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.mz_filtered", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.abund_filtered", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.abund_filtered", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.mz_count", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.mz_count", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.ms_info_get", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.ms_info_get", "kind": "function", "doc": "\n", "signature": "(self, mass_spectra_obj):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.loss_ref_get", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.loss_ref_get", "kind": "function", "doc": "\n", "signature": "(self, file_location, tolerance):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.threshold_filter", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.threshold_filter", "kind": "function", "doc": "\n", "signature": "(self, mz_dict, Intensity, noise_cutoff):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.mz_pair_checker", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.mz_pair_checker", "kind": "function", "doc": "\n", "signature": "(self, chem, lower, upper, mz1, spectrum, Intensity, scan_number):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.findpeakoffset", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.findpeakoffset", "kind": "function", "doc": "\n", "signature": "(self, range_ref, mz_filtered, abund_filtered):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.LF_out", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.LF_out", "kind": "function", "doc": "\n", "signature": "(self, LF_dict, mz_count):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.LF_Targeted.LossFinderTargeted.plot_offset", "modulename": "corems.mass_spectra.calc.LF_Targeted", "qualname": "LossFinderTargeted.plot_offset", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch", "modulename": "corems.mass_spectra.calc.MZSearch", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults", "kind": "class", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults.__init__", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults.__init__", "kind": "function", "doc": "\n", "signature": "(calculated_mz: float, exp_mz: float, error: float, tolerance: float)"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults.calculated_mz", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults.calculated_mz", "kind": "variable", "doc": "\n", "annotation": ": float"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults.exp_mz", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults.exp_mz", "kind": "variable", "doc": "\n", "annotation": ": float"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults.error", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults.error", "kind": "variable", "doc": "\n", "annotation": ": float"}, {"fullname": "corems.mass_spectra.calc.MZSearch.SearchResults.tolerance", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "SearchResults.tolerance", "kind": "variable", "doc": "\n", "annotation": ": float"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch", "kind": "class", "doc": "A class that represents a thread of control.
\n\nThis class can be safely subclassed in a limited fashion. There are two ways\nto specify the activity: by passing a callable object to the constructor, or\nby overriding the run() method in a subclass.
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.__init__", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.__init__", "kind": "function", "doc": "Parameters
\n\n\ncalculated_mzs ([float] calculated m/z):
exp_mzs ([float] experimental m/z):
method (string,):\nppm or ppb
- call run to trigger the m/z search algorithm
\n- or start if using it as thread
\n
\n", "signature": "(\texp_mzs: List[float],\tcalculated_mzs: List[float],\ttolerance,\tmethod='ppm',\taverage_target_mz=True)"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.method", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.method", "kind": "variable", "doc": "method: string,\n ppm or ppb
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.results", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.results", "kind": "variable", "doc": "{calculated_mz: [SearchResults]}\ncontains the results of the search
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.averaged_target_mz", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.averaged_target_mz", "kind": "variable", "doc": "[float]\ncontains the average target m/z to be searched against
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.calculated_mzs", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.calculated_mzs", "kind": "variable", "doc": "[float]\ncontains the mz target to be searched against
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.exp_mzs", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.exp_mzs", "kind": "variable", "doc": "[float]\ncontains the exp mz to be searched against
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.tolerance", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.tolerance", "kind": "variable", "doc": "method: string,\n ppm or ppb
\n"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.colapse_calculated", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.colapse_calculated", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.run", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.run", "kind": "function", "doc": "Method representing the thread's activity.
\n\nYou may override this method in a subclass. The standard run() method\ninvokes the callable object passed to the object's constructor as the\ntarget argument, if any, with sequential and keyword arguments taken\nfrom the args and kwargs arguments, respectively.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.calc_mz_error", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.calc_mz_error", "kind": "function", "doc": "Parameters
\n\n\n", "signature": "(calculated_mz, exp_mz, method='ppm'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.check_ppm_error", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.check_ppm_error", "kind": "function", "doc": "\n", "signature": "(tolerance, error):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.get_nominal_exp", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.get_nominal_exp", "kind": "function", "doc": "\n", "signature": "(self, exp_mzs) -> dict:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.MZSearch.MZSearch.search_mz", "modulename": "corems.mass_spectra.calc.MZSearch", "qualname": "MZSearch.search_mz", "kind": "function", "doc": "\n", "signature": "(self, results, dict_nominal_exp_mz, calculated_mz, offset) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing", "modulename": "corems.mass_spectra.calc.SignalProcessing", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.peak_detector", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "peak_detector", "kind": "function", "doc": "\n", "signature": "(tic, max_tic):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.find_nearest_scan", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "find_nearest_scan", "kind": "function", "doc": "\n", "signature": "(data, nodes):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.peak_picking_first_derivative", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "peak_picking_first_derivative", "kind": "function", "doc": "\n", "signature": "(\tdomain,\tsignal,\tmax_height,\tmax_prominence,\tmax_signal,\tmin_peak_datapoints,\tpeak_derivative_thresould,\tsignal_threshold=0.1,\tcorrect_baseline=True,\tplot_res=False,\tabun_norm=100,\tcheck_abundance=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.find_minima", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "find_minima", "kind": "function", "doc": "\n", "signature": "(index, tic, right=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.derivate", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "derivate", "kind": "function", "doc": "\n", "signature": "(data_array):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.minima_detector", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "minima_detector", "kind": "function", "doc": "\n", "signature": "(tic, max_tic, peak_height_max_percent, peak_max_prominence_percent):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.baseline_detector", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "baseline_detector", "kind": "function", "doc": "\n", "signature": "(\ttic,\trt,\tpeak_height_max_percent,\tpeak_max_prominence_percent,\tdo_interpolation=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.peak_detector_generator", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "peak_detector_generator", "kind": "function", "doc": "\n", "signature": "(\ttic,\tstds,\tmethod,\trt,\tmax_height,\tmin_height,\tmax_prominence,\tmin_datapoints):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.smooth_signal", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "smooth_signal", "kind": "function", "doc": "smooth the data using a window with requested size.
\n\nThis method is based on the convolution of a scaled window with the signal.\nThe signal is prepared by introducing reflected copies of the signal \n(with the window size) in both ends so that transient parts are minimized\nin the begining and end part of the output signal.
\n\noutput:\n the smoothed signal
\n\nsee also:
\n\nnumpy.hanning, numpy.hamming, numpy.bartlett, numpy.blackman, numpy.convolve\nscipy.signal.savgol_filter
\n", "signature": "(x, window_len, window, pol_order, implemented_smooth_method):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.calc.SignalProcessing.second_derivative_threshold", "modulename": "corems.mass_spectra.calc.SignalProcessing", "qualname": "second_derivative_threshold", "kind": "function", "doc": "\n", "signature": "(tic, stds, rt, peak_height_max_percent, peak_max_prominence_percent):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory", "modulename": "corems.mass_spectra.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class", "modulename": "corems.mass_spectra.factory.GC_Class", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase", "kind": "class", "doc": "Base class for GC-MS data processing.
\n\nParameters
\n\n\n- file_location (str, pathlib.Path, or s3path.S3Path):\nPath object containing the file location.
\n- analyzer (str, optional):\nName of the analyzer. Defaults to 'Unknown'.
\n- instrument_label (str, optional):\nLabel of the instrument. Defaults to 'Unknown'.
\n- sample_name (str, optional):\nName of the sample. If not provided, it is derived from the file location.
\n
\n\nAttributes
\n\n\n- file_location (pathlib.Path):\nPath object containing the file location.
\n- sample_name (str):\nName of the sample.
\n- analyzer (str):\nName of the analyzer.
\n- instrument_label (str):\nLabel of the instrument.
\n- gcpeaks (list):\nList of GCPeak objects.
\n- ri_pairs_ref (None):\nReference retention index pairs.
\n- cal_file_path (None):\nCalibration file path.
\n- _parameters (GCMSParameters):\nGC-MS parameters.
\n- _retention_time_list (list):\nList of retention times.
\n- _scans_number_list (list):\nList of scan numbers.
\n- _tic_list (list):\nList of total ion chromatogram values.
\n- _ms (dict):\nDictionary containing all mass spectra.
\n- _processed_tic (list):\nList of processed total ion chromatogram values.
\n
\n\nMethods
\n\n\n- process_chromatogram(plot_res=False). Process the chromatogram.
\n- plot_gc_peaks(ax=None, color='red'). Plot the GC peaks.
\n
\n", "bases": "corems.mass_spectra.calc.GC_Calc.GC_Calculations, corems.mass_spectra.calc.GC_Deconvolution.MassDeconvolution"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.__init__", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.__init__", "kind": "function", "doc": "\n", "signature": "(\tfile_location,\tanalyzer='Unknown',\tinstrument_label='Unknown',\tsample_name=None)"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.file_location", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.analyzer", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.analyzer", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.instrument_label", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.instrument_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.gcpeaks", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.gcpeaks", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.ri_pairs_ref", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.ri_pairs_ref", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.cal_file_path", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.cal_file_path", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.process_chromatogram", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.process_chromatogram", "kind": "function", "doc": "Process the chromatogram.
\n\nThis method processes the chromatogram.
\n\nParameters
\n\n\n- plot_res (bool, optional):\nIf True, plot the results. Defaults to False.
\n
\n", "signature": "(self, plot_res=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.add_mass_spectrum", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.add_mass_spectrum", "kind": "function", "doc": "Add a mass spectrum to the GC-MS object.
\n\nThis method adds a mass spectrum to the GC-MS object.
\n\nParameters
\n\n\n- mass_spec (MassSpectrum):\nMass spectrum to be added.
\n
\n", "signature": "(self, mass_spec):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.set_tic_list_from_data", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.set_tic_list_from_data", "kind": "function", "doc": "Set the total ion chromatogram list from the mass spectra data within the GC-MS data object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.set_retention_time_from_data", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.set_retention_time_from_data", "kind": "function", "doc": "Set the retention time list from the mass spectra data within the GC-MS data object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.set_scans_number_from_data", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.set_scans_number_from_data", "kind": "function", "doc": "Set the scan number list from the mass spectra data within the GC-MS data object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.parameter", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.parameter", "kind": "variable", "doc": "GCMS Parameters
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.molecular_search_settings", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.molecular_search_settings", "kind": "variable", "doc": "Molecular Search Settings
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.chromatogram_settings", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.chromatogram_settings", "kind": "variable", "doc": "Chromatogram Settings
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.scans_number", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.scans_number", "kind": "variable", "doc": "Scans Number
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.retention_time", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.retention_time", "kind": "variable", "doc": "Retention Time
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.processed_tic", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.processed_tic", "kind": "variable", "doc": "Processed Total Ion Current
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.tic", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.tic", "kind": "variable", "doc": "Total Ion Current
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.max_tic", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.max_tic", "kind": "variable", "doc": "Maximum Total Ion Current
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.min_tic", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.min_tic", "kind": "variable", "doc": "Minimum Total Ion Current
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.dynamic_range", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.dynamic_range", "kind": "variable", "doc": "Dynamic Range of the Total Ion Current
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.matched_peaks", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.matched_peaks", "kind": "variable", "doc": "Matched Peaks
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.sorted_gcpeaks", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.sorted_gcpeaks", "kind": "variable", "doc": "Sorted GC Peaks, by retention time
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.unique_metabolites", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.unique_metabolites", "kind": "variable", "doc": "Unique Metabolites
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.metabolites_data", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.metabolites_data", "kind": "variable", "doc": "Metabolites Data
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.no_matched_peaks", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.no_matched_peaks", "kind": "variable", "doc": "Peaks with no Matched Metabolites
\n"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_gc_peaks", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_gc_peaks", "kind": "function", "doc": "Plot the GC peaks.
\n\nThis method plots the GC peaks.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the GC peaks. Defaults to None.
\n- color (str, optional):\nColor of the GC peaks. Defaults to 'red'.
\n
\n", "signature": "(self, ax=None, color='red'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_excel", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_excel", "kind": "function", "doc": "Export the GC-MS data to an Excel file.
\n\nThis method exports the GC-MS data to an Excel file.
\n\nParameters
\n\n\n- out_file_path (str, pathlib.Path, or s3path.S3Path):\nPath object containing the file location.
\n- write_mode (str, optional):\nWrite mode. Defaults to 'ab'.
\n- write_metadata (bool, optional):\nIf True, write the metadata. Defaults to True.
\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n
\n", "signature": "(\tself,\tout_file_path,\twrite_mode='ab',\twrite_metadata=True,\tid_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_csv", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_csv", "kind": "function", "doc": "Export the GC-MS data to a CSV file.
\n\nParameters
\n\n\n- out_file_path (str, pathlib.Path, or s3path.S3Path):\nPath object containing the file location.
\n- separate_output (bool, optional):\nIf True, separate the output. Defaults to False.
\n- write_metadata (bool, optional):\nIf True, write the metadata. Defaults to True.
\n
\n", "signature": "(\tself,\tout_file_path,\tseparate_output=False,\twrite_metadata=True,\tid_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_pandas", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_pandas", "kind": "function", "doc": "Export the GC-MS data to a Pandas dataframe.
\n\nParameters
\n\n\n- out_file_path (str, pathlib.Path, or s3path.S3Path):\nPath object containing the file location.
\n- write_metadata (bool, optional):\nIf True, write the metadata. Defaults to True.
\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n
\n", "signature": "(self, out_file_path, write_metadata=True, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_dataframe", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_dataframe", "kind": "function", "doc": "Export the GC-MS data to a Pandas dataframe.
\n\nParameters
\n\n\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n
\n", "signature": "(self, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.processing_stats", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.processing_stats", "kind": "function", "doc": "Return the processing statistics.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.parameters_json", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.parameters_json", "kind": "function", "doc": "Return the parameters in JSON format.
\n\nParameters
\n\n\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n- output_path (str, optional):\nPath object containing the file location. Defaults to \" \".
\n
\n", "signature": "(self, id_label='corems:', output_path=' '):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_json", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_json", "kind": "function", "doc": "Export the GC-MS data to a JSON file.
\n\nParameters
\n\n\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n
\n", "signature": "(self, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.to_hdf", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.to_hdf", "kind": "function", "doc": "Export the GC-MS data to a HDF file.
\n\nParameters
\n\n\n- id_label (str, optional):\nLabel of the ID. Defaults to 'corems:'.
\n
\n", "signature": "(self, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_chromatogram", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_chromatogram", "kind": "function", "doc": "Plot the chromatogram.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the chromatogram. Defaults to None.
\n- color (str, optional):\nColor of the chromatogram. Defaults to 'blue'.
\n
\n", "signature": "(self, ax=None, color='blue'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_smoothed_chromatogram", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_smoothed_chromatogram", "kind": "function", "doc": "Plot the smoothed chromatogram.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the smoothed chromatogram. Defaults to None.
\n- color (str, optional):\nColor of the smoothed chromatogram. Defaults to 'green'.
\n
\n", "signature": "(self, ax=None, color='green'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_detected_baseline", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_detected_baseline", "kind": "function", "doc": "Plot the detected baseline.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the detected baseline. Defaults to None.
\n- color (str, optional):\nColor of the detected baseline. Defaults to 'blue'.
\n
\n", "signature": "(self, ax=None, color='blue'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_baseline_subtraction", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_baseline_subtraction", "kind": "function", "doc": "Plot the baseline subtraction.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the baseline subtraction. Defaults to None.
\n- color (str, optional):\nColor of the baseline subtraction. Defaults to 'black'.
\n
\n", "signature": "(self, ax=None, color='black'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.peaks_rt_tic", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.peaks_rt_tic", "kind": "function", "doc": "Return the peaks, retention time, and total ion chromatogram.
\n\nParameters
\n\n\n- json_string (bool, optional):\nIf True, return the peaks, retention time, and total ion chromatogram in JSON format. Defaults to False.
\n
\n", "signature": "(self, json_string=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.GC_Class.GCMSBase.plot_processed_chromatogram", "modulename": "corems.mass_spectra.factory.GC_Class", "qualname": "GCMSBase.plot_processed_chromatogram", "kind": "function", "doc": "Plot the processed chromatogram.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nAxes object to plot the processed chromatogram. Defaults to None.
\n- color (str, optional):\nColor of the processed chromatogram. Defaults to 'black'.
\n
\n", "signature": "(self, ax=None, color='black'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class", "modulename": "corems.mass_spectra.factory.LC_Class", "kind": "module", "doc": "Created on Oct 15, 2021
\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase", "kind": "class", "doc": "classdocs
\n", "bases": "collections.abc.Mapping, corems.mass_spectra.calc.LC_Calc.LC_Calculations"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.__init__", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.__init__", "kind": "function", "doc": "Parameters
\n\n ----------\n file_location: text, pathlib.Path(), or s3path.S3Path\n
\n\nPath object from pathlib containing the file location
\n", "signature": "(\tfile_location,\tanalyzer='Unknown',\tinstrument_label='Unknown',\tsample_name=None)"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.file_location", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.analyzer", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.analyzer", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.instrument_label", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.instrument_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.add_mass_spectrum", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.add_mass_spectrum", "kind": "function", "doc": "\n", "signature": "(self, mass_spec):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.set_tic_list_from_data", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.set_tic_list_from_data", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.set_retention_time_from_data", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.set_retention_time_from_data", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.set_scans_number_from_data", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.set_scans_number_from_data", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.scans_number", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.scans_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.retention_time", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.retention_time", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.LCMSBase.tic", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "LCMSBase.tic", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS", "kind": "class", "doc": "classdocs
\n", "bases": "corems.mass_spectra.calc.LC_Calc.LC_Calculations"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.__init__", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.__init__", "kind": "function", "doc": "\n", "signature": "(\tfile_location,\ttarget_mzs: List[float],\tparser,\tanalyzer: str = 'Unknown',\tinstrument_label: str = 'Unknown',\tsample_name: str = None)"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.file_location", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.add_peak", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.add_peak", "kind": "function", "doc": "\n", "signature": "(self, mass_spectrum, peak_scans, eic_data, possible_molform=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.ms1_molecular_search_settings", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.ms1_molecular_search_settings", "kind": "variable", "doc": "\n", "annotation": ": corems.encapsulation.factory.processingSetting.MolecularFormulaSearchSettings"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.chromatogram_settings", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.chromatogram_settings", "kind": "variable", "doc": "\n", "annotation": ": corems.encapsulation.factory.processingSetting.LiquidChromatographSetting"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.parameters", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.parameters", "kind": "variable", "doc": "\n", "annotation": ": corems.encapsulation.factory.parameters.LCMSParameters"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.eic_scans_number", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.eic_scans_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.scans_number", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.scans_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.retention_time", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.retention_time", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.tic", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.tic", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.get_tic", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.get_tic", "kind": "function", "doc": "ms_type: str ('MS', MS2')\nstart_scan: int default -1 will select the lowest available\nend_scan: int default -1 will select the highest available\nreturns:\n chroma: dict\n {\n Scan: [int]\n original thermo scan numberMS\n Time: [floats]\n list of retention times\n TIC: [floats]\n total ion chromatogram\n Apexes: [int]
\n original thermo apex scan number after peak picking
\n }
\n", "signature": "(\tself,\tms_type='MS !d',\tpeak_detection=True,\tsmooth=True,\tplot=False,\tax=None) -> Tuple[corems.mass_spectra.factory.LC_Temp.TIC_Data, matplotlib.axes._axes.Axes]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.get_eics", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.get_eics", "kind": "function", "doc": "ms_type: str ('MS', MS2')\nstart_scan: int default -1 will select the lowest available\nend_scan: int default -1 will select the highest available
\n\nreturns:
\n\nchroma: dict{target_mz: EIC_Data(\n Scans: [int]\n original thermo scan numbers\n Time: [floats]\n list of retention times\n TIC: [floats]\n total ion chromatogram\n Apexes: [int] \n original thermo apex scan number after peak picking \n )\n
\n", "signature": "(\tself,\ttic_data: dict,\tms_type='MS !d',\tpeak_detection=True,\tsmooth=True,\tplot=False,\tax=None,\tlegend=False) -> Tuple[Dict[float, corems.mass_spectra.factory.LC_Temp.EIC_Data], matplotlib.axes._axes.Axes]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Class.DataDependentLCMS.process_ms1", "modulename": "corems.mass_spectra.factory.LC_Class", "qualname": "DataDependentLCMS.process_ms1", "kind": "function", "doc": "\n", "signature": "(self, dict_tarrget_mzs):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.factory.LC_Temp", "modulename": "corems.mass_spectra.factory.LC_Temp", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data", "kind": "class", "doc": "Scans: [int]\n original thermo scan numbers\nTime: [floats]\n list of retention times\nTIC: [floats]\n total ion chromatogram\nApexes: [int]
\n original thermo apex scan number after peak picking
\n"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data.__init__", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data.__init__", "kind": "function", "doc": "\n", "signature": "(\tscans: List[int] = <factory>,\ttime: List[float] = <factory>,\ttic: List[float] = <factory>,\tapexes: List[int] = <factory>)"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data.scans", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data.scans", "kind": "variable", "doc": "\n", "annotation": ": List[int]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data.time", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data.time", "kind": "variable", "doc": "\n", "annotation": ": List[float]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data.tic", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data.tic", "kind": "variable", "doc": "\n", "annotation": ": List[float]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.TIC_Data.apexes", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "TIC_Data.apexes", "kind": "variable", "doc": "\n", "annotation": ": List[int]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data", "kind": "class", "doc": "Scans: [int]\n original thermo scan numbers\nTime: [floats]\n list of retention times\nEIC: [floats]\n extracted ion chromatogram\nApexes: [int]
\n original thermo apex scan number after peak picking
\n"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data.__init__", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data.__init__", "kind": "function", "doc": "\n", "signature": "(\tscans: List[int] = <factory>,\ttime: List[float] = <factory>,\teic: List[float] = <factory>,\tapexes: List[int] = <factory>)"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data.scans", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data.scans", "kind": "variable", "doc": "\n", "annotation": ": List[int]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data.time", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data.time", "kind": "variable", "doc": "\n", "annotation": ": List[float]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data.eic", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data.eic", "kind": "variable", "doc": "\n", "annotation": ": List[float]"}, {"fullname": "corems.mass_spectra.factory.LC_Temp.EIC_Data.apexes", "modulename": "corems.mass_spectra.factory.LC_Temp", "qualname": "EIC_Data.apexes", "kind": "variable", "doc": "\n", "annotation": ": List[int]"}, {"fullname": "corems.mass_spectra.input", "modulename": "corems.mass_spectra.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF", "modulename": "corems.mass_spectra.input.andiNetCDF", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF", "kind": "class", "doc": "A class for reading AndiNetCDF files and extracting mass spectra data.
\n\nParameters
\n\n\n- file_location (str or Path):\nThe location of the AndiNetCDF file.
\n- analyzer (str, optional):\nThe type of analyzer used (default is 'Quadruple').
\n- instrument_label (str, optional):\nThe label of the instrument (default is 'GCMS-Agilent').
\n- auto_process (bool, optional):\nWhether to automatically process the data (default is True).
\n
\n\nAttributes
\n\n\n- file_location (Path):\nThe path to the AndiNetCDF file.
\n- net_cdf_obj (Dataset):\nThe NetCDF dataset object.
\n- ionization_type (str):\nThe ionization type used in the experiment.
\n- experiment_type (str):\nThe type of experiment.
\n- list_scans (range):\nThe range of scan numbers in the dataset.
\n- initial_scan_number (int):\nThe number of the initial scan.
\n- final_scan_number (int):\nThe number of the final scan.
\n- analyzer (str):\nThe type of analyzer used.
\n- instrument_label (str):\nThe label of the instrument.
\n- gcms (GCMSBase):\nThe GCMSBase object for storing mass spectra data.
\n
\n\nMethods
\n\n\n- polarity(). \nGet the polarity of the ionization.
\n- get_mass_spectrum(mz, abun, rp, d_params). \nAdd a mass spectrum to the GCMSBase object.
\n- run(). \nPopulate the GCMSBase object with mass spectra data.
\n- import_mass_spectra(d_params). \nImport mass spectra data from the AndiNetCDF file.
\n- get_gcms_obj(). \nGet the GCMSBase object.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.__init__", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(\tfile_location: str | pathlib.Path,\tanalyzer='Quadruple',\tinstrument_label='GCMS-Agilent',\tauto_process=True)"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.ionization_type", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.ionization_type", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.experiment_type", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.experiment_type", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.list_scans", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.list_scans", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.initial_scan_number", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.initial_scan_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.final_scan_number", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.final_scan_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.analyzer", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.analyzer", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.instrument_label", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.instrument_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.gcms", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.gcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.polarity", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.polarity", "kind": "variable", "doc": "Get the polarity of the ionization.
\n"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.get_mass_spectrum", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.get_mass_spectrum", "kind": "function", "doc": "Add a mass spectrum to the GCMSBase object.
\n\nParameters
\n\n\n- mz (array-like):\nThe m/z values of the mass spectrum.
\n- abun (array-like):\nThe abundance values of the mass spectrum.
\n- rp (array-like):\nThe resolution values of the mass spectrum.
\n- d_params (dict):\nAdditional parameters for the mass spectrum.
\n
\n", "signature": "(self, mz, abun, rp, d_params):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.run", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.run", "kind": "function", "doc": "Populate the GCMSBase object with mass spectra data.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.import_mass_spectra", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.import_mass_spectra", "kind": "function", "doc": "Import mass spectra data from the AndiNetCDF file.
\n\nParameters
\n\n\n- d_params (dict):\nAdditional parameters for the mass spectra.
\n
\n", "signature": "(self, d_params):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.andiNetCDF.ReadAndiNetCDF.get_gcms_obj", "modulename": "corems.mass_spectra.input.andiNetCDF", "qualname": "ReadAndiNetCDF.get_gcms_obj", "kind": "function", "doc": "Get the GCMSBase object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5", "modulename": "corems.mass_spectra.input.boosterHDF5", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra", "kind": "class", "doc": "Class for reading HDF5 files containing booster mass spectra.
\n\nParameters
\n\n\n- file_location (Path or S3Path):\nThe full path to the HDF5 file.
\n- analyzer (str, optional):\nThe type of analyzer used for the mass spectra. Defaults to \"ICR\".
\n- instrument_label (str, optional):\nThe label of the instrument. Defaults to \"21T\".
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectra. Defaults to True.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.__init__", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.__init__", "kind": "function", "doc": "Initialize the ReadHDF_BoosterMassSpectra class.
\n\nParameters
\n\n\n- file_location (Path or S3Path):\nThe full path to the HDF5 file.
\n- analyzer (str, optional):\nThe type of analyzer used for the mass spectra. Defaults to \"ICR\".
\n- instrument_label (str, optional):\nThe label of the instrument. Defaults to \"21T\".
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectra. Defaults to True.
\n
\n", "signature": "(\tfile_location: pathlib.Path | s3path.S3Path,\tanalyzer='ICR',\tinstrument_label='21T',\tauto_process=True)"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.lcms", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.lcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.hdf_obj", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.hdf_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.list_scans", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.list_scans", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.initial_scan_number", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.initial_scan_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.final_scan_number", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.final_scan_number", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.file_location", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.auto_process", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.auto_process", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.analyzer", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.analyzer", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.instrument_label", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.instrument_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.get_polarity", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.get_polarity", "kind": "function", "doc": "Get the polarity of a scan.
\n\nParameters
\n\n\n- file_location (Path or S3Path):\nThe full path to the HDF5 file.
\n- scan (int):\nThe scan number.
\n
\n", "signature": "(self, file_location: pathlib.Path | s3path.S3Path, scan: int):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.get_attr_data", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.get_attr_data", "kind": "function", "doc": "Get the attribute data of a scan.
\n\nParameters
\n\n\n- scan (int):\nThe scan number.
\n- attr_srt (str):\nThe attribute name.
\n
\n", "signature": "(self, scan, attr_srt):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.import_mass_spectra", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.import_mass_spectra", "kind": "function", "doc": "Import the mass spectra from the HDF5 file.
\n\nParameters
\n\n\n- d_params (dict):\nThe parameters for importing the mass spectra.
\n
\n", "signature": "(self, d_params: dict):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.get_mass_spectrum", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.get_mass_spectrum", "kind": "function", "doc": "Get the mass spectrum for a scan.
\n\nParameters
\n\n\n- scan (int):\nThe scan number.
\n- d_params (dict):\nThe parameters for creating the mass spectrum.
\n
\n", "signature": "(self, scan: int, d_params: dict):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.run", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.run", "kind": "function", "doc": "Run the thread to create the LCMS object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.boosterHDF5.ReadHDF_BoosterMassSpectra.get_lcms_obj", "modulename": "corems.mass_spectra.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectra.get_lcms_obj", "kind": "function", "doc": "Get the LCMS object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.brukerSolarix", "modulename": "corems.mass_spectra.input.brukerSolarix", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra", "kind": "class", "doc": "Class for reading Bruker Solarix Transient Mass Spectra.
\n\nParameters
\n\n\n- d_directory_location (str, pathlib.Path, or s3path.S3Path):\nPath object from pathlib containing the file location.
\n- analyzer (str, optional):\nType of analyzer used in the mass spectrometer. Defaults to \"ICR\".
\n- instrument_label (str, optional):\nLabel for the instrument. Defaults to \"15T\".
\n- auto_process (bool, optional):\nFlag indicating whether to automatically process the mass spectra. Defaults to True.
\n- keep_profile (bool, optional):\nFlag indicating whether to keep the profile data in the mass spectra. Defaults to False.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.__init__", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(\td_directory_location: str | pathlib.Path | s3path.S3Path,\tanalyzer='ICR',\tinstrument_label='15T',\tauto_process=True,\tkeep_profile=False)"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.scan_attr", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.scan_attr", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.lcms", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.lcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.auto_process", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.auto_process", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.keep_profile", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.keep_profile", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.get_scan_attr", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.get_scan_attr", "kind": "function", "doc": "Get the scan attributes from the scan.xml file.
\n\nReturns
\n\n\n- dict: Dictionary containing the scan number as key and a tuple of retention time and TIC as value.
\n
\n", "signature": "(self) -> dict:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.import_mass_spectra", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.import_mass_spectra", "kind": "function", "doc": "Import the mass spectra from the scan.xml file.
\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.get_mass_spectrum", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.get_mass_spectrum", "kind": "function", "doc": "Get the mass spectrum for a given scan number.
\n\nParameters
\n\n\n- scan_number (int):\nScan number.
\n
\n", "signature": "(self, scan_number: int):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.run", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.run", "kind": "function", "doc": "Run the import_mass_spectra method.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.brukerSolarix.ReadBruker_SolarixTransientMassSpectra.get_lcms_obj", "modulename": "corems.mass_spectra.input.brukerSolarix", "qualname": "ReadBruker_SolarixTransientMassSpectra.get_lcms_obj", "kind": "function", "doc": "Get the LCMSBase object.
\n\nRaises
\n\n\n- Exception: If the LCMSBase object is empty.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.coremsHDF5", "modulename": "corems.mass_spectra.input.coremsHDF5", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra", "kind": "class", "doc": "Class for reading CoreMS HDF5 mass spectra.
\n\nParameters
\n\n\n- file_location (str):\nThe file location of the CoreMS HDF5 file.
\n
\n\nAttributes
\n\n\n- lcms (LCMSBase):\nThe LCMSBase object for storing mass spectra.
\n- list_scans (list):\nThe list of scan numbers in the HDF5 file.
\n
\n\nMethods
\n\n\n- import_mass_spectra()\nImports the mass spectra from the HDF5 file.
\n- run()\nCreates the LCMS object by importing the mass spectra.
\n- get_lcms_obj()\nReturns the LCMS object.
\n
\n\nRaises
\n\n\n- Exception: If the LCMS object is empty.
\n
\n", "bases": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum, threading.Thread"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.__init__", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(file_location: str)"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.lcms", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.lcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.list_scans", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.list_scans", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.import_mass_spectra", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.import_mass_spectra", "kind": "function", "doc": "Imports the mass spectra from the HDF5 file.
\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.run", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.run", "kind": "function", "doc": "Creates the LCMS object by importing the mass spectra.
\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.coremsHDF5.ReadCoreMSHDF_MassSpectra.get_lcms_obj", "modulename": "corems.mass_spectra.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectra.get_lcms_obj", "kind": "function", "doc": "Returns the LCMS object.
\n\nReturns
\n\n\n- LCMSBase: The LCMS object.
\n
\n\nRaises
\n\n\n- Exception: If the LCMS object is empty.
\n
\n", "signature": "(self) -> corems.mass_spectra.factory.LC_Class.LCMSBase:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.massList", "modulename": "corems.mass_spectra.input.massList", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText", "kind": "class", "doc": "Class for reading CoreMS mass spectra from a text file.
\n\nParameters
\n\n\n- file_location (str, pathlib.Path, or s3path.S3Path):\nPath object from pathlib containing the file location
\n- analyzer (str, optional):\nName of the analyzer, by default 'Unknown'
\n- instrument_label (str, optional):\nLabel of the instrument, by default 'Unknown'
\n
\n\nAttributes
\n\n\n- lcms (LCMSBase):\nLCMSBase object for storing the mass spectra data.
\n
\n\nMethods
\n\n\n- get_scans_filename(). Get the filenames of all the scan files associated with the CoreMS file.
\n- set_filepath_datatype_and_delimiter(file_path_obj). Set the file path, data type, and delimiter based on the file path object.
\n- import_mass_spectra(). Import the mass spectra from the scan files and add them to the LCMSBase object.
\n- run(). Run the import_mass_spectra method to create the LCMSBase object.
\n- get_lcms_obj(). Get the LCMSBase object.
\n
\n", "bases": "corems.mass_spectrum.input.massList.ReadCoremsMasslist, threading.Thread"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.__init__", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(file_location, analyzer='Unknown', instrument_label='Unknown')"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.lcms", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.lcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.get_scans_filename", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.get_scans_filename", "kind": "function", "doc": "\n", "signature": "(self) -> list:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.set_filepath_datatype_and_delimiter", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.set_filepath_datatype_and_delimiter", "kind": "function", "doc": "\n", "signature": "(self, file_path_obj) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.import_mass_spectra", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.import_mass_spectra", "kind": "function", "doc": "\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.run", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.run", "kind": "function", "doc": "Creates the LCMS object and imports mass spectra.
\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.massList.ReadCoremsMassSpectraText.get_lcms_obj", "modulename": "corems.mass_spectra.input.massList", "qualname": "ReadCoremsMassSpectraText.get_lcms_obj", "kind": "function", "doc": "Returns the LCMSBase object associated with the massList.
\n\nIf the LCMSBase object is already initialized, it is returned.\nOtherwise, an exception is raised.
\n\nRaises:\n Exception: If the LCMSBase object is not initialized.
\n", "signature": "(self) -> corems.mass_spectra.factory.LC_Class.LCMSBase:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader", "modulename": "corems.mass_spectra.input.rawFileReader", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass", "kind": "class", "doc": "Class for reading Thermo Raw files and extracting information from them.
\n\nParameters:
\n\nfile_location : str or pathlib.Path or s3path.S3Path\n Thermo Raw file path or S3 path.
\n\nAttributes:
\n\nfile_path : str or pathlib.Path or s3path.S3Path\n The file path of the Thermo Raw file.\nparameters : LCMSParameters\n The LCMS parameters for the Thermo Raw file.\nchromatogram_settings : LiquidChromatographSetting\n The chromatogram settings for the Thermo Raw file.\nscans : list or tuple\n The selected scans for the Thermo Raw file.\nstart_scan : int\n The starting scan number for the Thermo Raw file.\nend_scan : int\n The ending scan number for the Thermo Raw file.
\n\nMethods:
\n\n\n- set_msordertype(scanFilter, mstype: str = 'ms1') -> scanFilter\nConvert the user-passed MS Type string to a Thermo MSOrderType object.
\n- get_creation_time() -> datetime.datetime\nExtract the creation date stamp from the .RAW file and return it as a formatted datetime object.
\n- remove_temp_file()\nRemove the temporary file if the path is from S3Path.
\n- get_polarity_mode(scan_number: int) -> int\nGet the polarity mode for the given scan number.
\n- get_filter_for_scan_num(scan_number: int) -> List[str]\nGet the filter for the given scan number.
\n- check_full_scan(scan_number: int) -> bool\nCheck if the given scan number is a full scan.
\n- get_all_filters() -> Tuple[Dict[int, str], List[str]]\nGet all scan filters for the Thermo Raw file.
\n- get_scan_header(scan: int) -> Dict[str, Any]\nGet the full dictionary of scan header metadata for the given scan number.
\n- get_rt_time_from_trace(trace) -> Tuple[List[float], List[float], List[int]]\nGet the retention time, intensity, and scan number from the given trace.
\n- get_eics(target_mzs: List[float], tic_data: Dict[str, Any], ms_type: str = 'MS !d',\n peak_detection: bool = True, smooth: bool = True, plot: bool = False,\n ax: Optional[matplotlib.axes.Axes] = None, legend: bool = False) -> Tuple[Dict[float, EIC_Data], matplotlib.axes.Axes]\nGet the extracted ion chromatograms (EICs) for the target m/z values.
\n
\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.__init__", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.__init__", "kind": "function", "doc": "file_location: srt pathlib.Path or s3path.S3Path\nThermo Raw file path
\n", "signature": "(file_location)"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.iRawDataPlus", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.iRawDataPlus", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.res", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.res", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.file_path", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.file_path", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.iFileHeader", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.iFileHeader", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.parameters", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.parameters", "kind": "variable", "doc": "Get or set the LCMSParameters object.
\n", "annotation": ": corems.encapsulation.factory.parameters.LCMSParameters"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.chromatogram_settings", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.chromatogram_settings", "kind": "variable", "doc": "Get or set the LiquidChromatographSetting object.
\n", "annotation": ": corems.encapsulation.factory.processingSetting.LiquidChromatographSetting"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.scans", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.scans", "kind": "variable", "doc": "scans : list or tuple\nIf list uses Thermo AverageScansInScanRange for selected scans, ortherwise uses Thermo AverageScans for a scan range
\n", "annotation": ": list | tuple"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.start_scan", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.start_scan", "kind": "variable", "doc": "Get the starting scan number for the Thermo Raw file.
\n", "annotation": ": int"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.end_scan", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.end_scan", "kind": "variable", "doc": "Get the ending scan number for the Thermo Raw file.
\n", "annotation": ": int"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.set_msordertype", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.set_msordertype", "kind": "function", "doc": "Function to convert user passed string MS Type to Thermo MSOrderType object\nLimited to MS1 through MS10.
\n\nParameters:
\n\nscanFilter : Thermo.ScanFilter\n The scan filter object.\nmstype : str, optional\n The MS Type string, by default 'ms1'
\n", "signature": "(self, scanFilter, mstype: str = 'ms1'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_creation_time", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_creation_time", "kind": "function", "doc": "Extract the creation date stamp from the .RAW file\nReturn formatted creation date stamp.
\n", "signature": "(self) -> datetime.datetime:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.remove_temp_file", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.remove_temp_file", "kind": "function", "doc": "if the path is from S3Path data cannot be serialized to io.ByteStream and\na temporary copy is stored at the temp dir\nuse this function only at the end of your execution scrip\nsome LCMS class methods depend on this file
\n", "signature": "(self) -> None:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_polarity_mode", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_polarity_mode", "kind": "function", "doc": "Get the polarity mode for the given scan number.
\n\nParameters:
\n\nscan_number : int\n The scan number.
\n\nRaises:
\n\nException\n If the polarity mode is unknown.
\n", "signature": "(self, scan_number: int) -> int:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_filter_for_scan_num", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_filter_for_scan_num", "kind": "function", "doc": "Returns the closest matching run time that corresponds to scan_number for the current\ncontroller. This function is only supported for MS device controllers.\ne.g. ['FTMS', '-', 'p', 'NSI', 'Full', 'ms', '[200.00-1000.00]']
\n\nParameters:
\n\nscan_number : int\n The scan number.
\n", "signature": "(self, scan_number: int) -> System.Collections.Generic.List[String]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.check_full_scan", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.check_full_scan", "kind": "function", "doc": "\n", "signature": "(self, scan_number: int) -> bool:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_all_filters", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_all_filters", "kind": "function", "doc": "Get all scan filters.\nThis function is only supported for MS device controllers.\ne.g. ['FTMS', '-', 'p', 'NSI', 'Full', 'ms', '[200.00-1000.00]']
\n", "signature": "(self) -> Tuple[Dict[int, str], System.Collections.Generic.List[String]]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_scan_header", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_scan_header", "kind": "function", "doc": "Get full dictionary of scan header meta data, i.e. AGC status, ion injection time, etc.
\n\nParameters:
\n\nscan : int\n The scan number.
\n", "signature": "(self, scan: int) -> Dict[str, Any]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_rt_time_from_trace", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_rt_time_from_trace", "kind": "function", "doc": "trace: ThermoFisher.CommonCore.Data.Business.ChromatogramSignal
\n", "signature": "(\ttrace) -> Tuple[System.Collections.Generic.List[Double], System.Collections.Generic.List[Double], System.Collections.Generic.List[Int32]]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_eics", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_eics", "kind": "function", "doc": "ms_type: str ('MS', MS2')\nstart_scan: int default -1 will select the lowest available\nend_scan: int default -1 will select the highest available
\n\nreturns:
\n\nchroma: dict{target_mz: EIC_Data(\n Scans: [int]\n original thermo scan numbers\n Time: [floats]\n list of retention times\n TIC: [floats]\n total ion chromatogram\n Apexes: [int]\n original thermo apex scan number after peak picking\n )\n
\n", "signature": "(\tself,\ttarget_mzs: System.Collections.Generic.List[Double],\ttic_data: Dict[str, Any],\tms_type='MS !d',\tpeak_detection=True,\tsmooth=True,\tplot=False,\tax: Optional[matplotlib.axes._axes.Axes] = None,\tlegend=False) -> Tuple[Dict[float, corems.mass_spectra.factory.LC_Temp.EIC_Data], matplotlib.axes._axes.Axes]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_tic", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_tic", "kind": "function", "doc": "ms_type: str ('MS', MS2')
\n\nreturns:\n chroma: dict\n {\n Scan: [int]\n original thermo scan numberMS\n Time: [floats]\n list of retention times\n TIC: [floats]\n total ion chromatogram\n Apexes: [int]\n original thermo apex scan number after peak picking\n }
\n", "signature": "(\tself,\tms_type='MS !d',\tpeak_detection=True,\tsmooth=True,\tplot=False,\tax=None) -> Tuple[corems.mass_spectra.factory.LC_Temp.TIC_Data, matplotlib.axes._axes.Axes]:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_average_mass_spectrum", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_average_mass_spectrum", "kind": "function", "doc": "Averages mass spectra over a scan range using Thermo's AverageScansInScanRange method\nor a scan list using Thermo's AverageScans method\nspectrum_mode: str\n centroid or profile mass spectrum\nauto_process: bool\n If true performs peak picking, and noise threshold calculation after creation of mass spectrum object\nms_type: str\n String of form 'ms1' or 'ms2' or 'MS3' etc. Valid up to MS10.\n Internal function converts to Thermo MSOrderType class.
\n", "signature": "(\tself,\tspectrum_mode: str = 'profile',\tauto_process: bool = True,\tppm_tolerance: float = 5.0,\tms_type: str = 'MS1') -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile | corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.set_metadata", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.set_metadata", "kind": "function", "doc": "Collect metadata to be ingested in the mass spectrum object
\n\nscans_list: list[int] or false\nlastScanNumber: int\nfirstScanNumber: int
\n", "signature": "(\tself,\tfirstScanNumber=0,\tlastScanNumber=0,\tscans_list=False,\tlabel='Thermo_Profile'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_centroid_msms_data", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_centroid_msms_data", "kind": "function", "doc": "Deprecated since version 2.0:\nThis function will be removed in CoreMS 2.0. Please use get_average_mass_spectrum() instead for similar functionality.
\n", "signature": "(self, scan):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ThermoBaseClass.get_average_mass_spectrum_by_scanlist", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ThermoBaseClass.get_average_mass_spectrum_by_scanlist", "kind": "function", "doc": "Averages selected scans mass spectra using Thermo's AverageScans method\nscans_list: list[int]\nauto_process: bool\n If true performs peak picking, and noise threshold calculation after creation of mass spectrum object\nReturns:\n MassSpecProfile
\n\nDeprecated since version 2.0.
\n\nThis function will be removed in CoreMS 2.0. Please use get_average_mass_spectrum() instead for similar functionality.
\n", "signature": "(\tself,\tscans_list: System.Collections.Generic.List[Int32],\tauto_process: bool = True,\tppm_tolerance: float = 5.0) -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile:", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader", "kind": "class", "doc": "Collection of methdos to import LC data dependent acquisition from Thermo's raw file\nIntended do create the LCMS object --> ChromaPeaks --> MSobj FullScan --> Dependent MS/MS Obj
\n", "bases": "ThermoBaseClass, corems.mass_spectra.calc.LC_Calc.LC_Calculations"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader.__init__", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader.__init__", "kind": "function", "doc": "target_mzs: list[float] monoisotopic target m/z or None\n Details: None will defalt to depends scans selected m/\nfile_location: str, Path, or S3Path
\n", "signature": "(\tfile_location: str,\tselected_mzs: System.Collections.Generic.List[Double] = None)"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader.lcms", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader.lcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader.selected_mzs", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader.selected_mzs", "kind": "variable", "doc": "\n", "annotation": ": System.Collections.Generic.List[Double]"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader.get_lcms_obj", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader.get_lcms_obj", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportDataDependentThermoMSFileReader.get_precursors_list", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportDataDependentThermoMSFileReader.get_precursors_list", "kind": "function", "doc": "returns a set of unique precursors m/z\nprecision_decimals: int\n change this parameters does not seem to affect the number of dependent scans selected\n needs more investigation
\n", "signature": "(self, precision_decimals=5):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportMassSpectraThermoMSFileReader", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportMassSpectraThermoMSFileReader", "kind": "class", "doc": "Collection of methdos to import Summed/Averaged mass spectrum from Thermo's raw file\nCurrently only for profile mode data\nReturns MassSpecProfile object
\n", "bases": "ThermoBaseClass, corems.mass_spectra.calc.LC_Calc.LC_Calculations"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportMassSpectraThermoMSFileReader.get_icr_transient_times", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportMassSpectraThermoMSFileReader.get_icr_transient_times", "kind": "function", "doc": "Return a list for transient time targets for all scans, or selected scans range\nResolving Power and Transient time targets based on 7T FT-ICR MS system
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportMassSpectraThermoMSFileReader.RawFileReader", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportMassSpectraThermoMSFileReader.RawFileReader", "kind": "class", "doc": "\n"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportMassSpectraThermoMSFileReader.RawFileReader.get_data", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportMassSpectraThermoMSFileReader.RawFileReader.get_data", "kind": "function", "doc": "Retrieve mass spectrometry data for a given scan.
\n\nParameters
\n\n\n- scan (int):\nThe scan number.
\n- d_parameter (dict):\nA dictionary to store additional parameters.
\n- scan_type (str):\nThe type of scan (\"Centroid\" or \"Profile\").
\n
\n", "signature": "(self, scan: int, d_parameter: dict, scan_type: str):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.input.rawFileReader.ImportMassSpectraThermoMSFileReader.get_best_scans_idx", "modulename": "corems.mass_spectra.input.rawFileReader", "qualname": "ImportMassSpectraThermoMSFileReader.get_best_scans_idx", "kind": "function", "doc": "Method to determine the best scan indexes for selective co-addition.
\n\nParameters
\n\n\n- stdevs (int, optional):\nThe number of standard deviations to use as the cutoff for filtering out datapoints. Default is 2.
\n- method (str, optional):\nThe method to calculate the mean or median of the TIC values. Default is \"mean\".
\n- plot (bool, optional):\nWhether to plot the TIC with horizontal lines for the standard deviation cutoffs. Default is False.
\n
\n\nNotes
\n\nThis method calculates the mean (default) or median of the TIC values and sets an upper and lower limit\nbased on a specified number of standard deviations. The scans with TIC values outside of this range are\nconsidered the best scans for selective co-addition.
\n\nEmpirically, using 1-2 standard deviations is enough to filter out the worst datapoints.
\n\nIf plot is True, a matplotlib figure is returned along with the list of scan indexes.
\n\nExamples
\n\n\n
>>> reader = RawFileReader()\n>>> scans = reader.get_best_scans_idx(stdevs=2, method="mean", plot=True)\n
\n
A class to export low resolution GC-MS data.
\n\nThis class provides methods to export low resolution GC-MS data to various formats such as Excel, CSV, HDF5, and Pandas DataFrame.
\n\nParameters:
\n\nout_file_path : str\n The output file path.\ngcms : object\n The low resolution GCMS object.
\n\nAttributes:
\n\noutput_file : Path\n The output file path as a Path object.\ngcms : object\n The low resolution GCMS object.
\n\nMethods:
\n\n\n- get_pandas_df(id_label=\"corems:\"). Get the exported data as a Pandas DataFrame.
\n- get_json(nan=False, id_label=\"corems:\"). Get the exported data as a JSON string.
\n- to_pandas(write_metadata=True, id_label=\"corems:\"). Export the data to a Pandas DataFrame and save it as a pickle file.
\n- to_excel(write_mode='a', write_metadata=True, id_label=\"corems:\"),\nExport the data to an Excel file.
\n- to_csv(separate_output=False, write_mode=\"w\", write_metadata=True, id_label=\"corems:\").\nExport the data to a CSV file.
\n- to_hdf(id_label=\"corems:\").\nExport the data to an HDF5 file.
\n- get_data_stats(gcms).\nGet statistics about the GCMS data.
\n
\n"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.__init__", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.__init__", "kind": "function", "doc": "\n", "signature": "(out_file_path, gcms)"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.output_file", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.output_file", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.gcms", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.gcms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_pandas_df", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_pandas_df", "kind": "function", "doc": "Get the exported data as a Pandas DataFrame.
\n\nParameters:
\n\nid_label : str, optional\n The ID label for the data. Default is \"corems:\".
\n\nReturns:
\n\nDataFrame\n The exported data as a Pandas DataFrame.
\n", "signature": "(self, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_json", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_json", "kind": "function", "doc": "Get the exported data as a JSON string.
\n\nParameters:
\n\nnan : bool, optional\n Whether to include NaN values in the JSON string. Default is False.\nid_label : str, optional\n The ID label for the data. Default is \"corems:\".
\n", "signature": "(self, nan=False, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.to_pandas", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.to_pandas", "kind": "function", "doc": "Export the data to a Pandas DataFrame and save it as a pickle file.
\n\nParameters:
\n\nwrite_metadata : bool, optional\n Whether to write metadata to the output file.\nid_label : str, optional\n The ID label for the data.
\n", "signature": "(self, write_metadata=True, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.to_excel", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.to_excel", "kind": "function", "doc": "Export the data to an Excel file.
\n\nParameters:
\n\nwrite_mode : str, optional\n The write mode for the Excel file. Default is 'a' (append).\nwrite_metadata : bool, optional\n Whether to write metadata to the output file. Default is True.\nid_label : str, optional\n The ID label for the data. Default is \"corems:\".
\n", "signature": "(self, write_mode='a', write_metadata=True, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.to_csv", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.to_csv", "kind": "function", "doc": "Export the data to a CSV file.
\n\nParameters:
\n\nseparate_output : bool, optional\n Whether to separate the output into multiple files. Default is False.\nwrite_mode : str, optional\n The write mode for the CSV file. Default is 'w' (write).\nwrite_metadata : bool, optional\n Whether to write metadata to the output file. Default is True.\nid_label : str, optional\n The ID label for the data. Default is \"corems:\".
\n", "signature": "(\tself,\tseparate_output=False,\twrite_mode='w',\twrite_metadata=True,\tid_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.to_hdf", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.to_hdf", "kind": "function", "doc": "Export the data to an HDF5 file.
\n\nParameters:
\n\nid_label : str, optional\n The ID label for the data. Default is \"corems:\".
\n", "signature": "(self, id_label='corems:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_data_stats", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_data_stats", "kind": "function", "doc": "Get statistics about the GCMS data.
\n\nParameters:
\n\ngcms : object\n The low resolution GCMS object.
\n\nReturns:
\n\ndict\n A dictionary containing the data statistics.
\n", "signature": "(self, gcms):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_calibration_stats", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_calibration_stats", "kind": "function", "doc": "Get statistics about the GC-MS calibration.
\n\nParameters:
\n", "signature": "(self, gcms, id_label):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_blank_stats", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_blank_stats", "kind": "function", "doc": "Get statistics about the GC-MS blank.
\n", "signature": "(self, gcms):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_instrument_metadata", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_instrument_metadata", "kind": "function", "doc": "Get metadata about the GC-MS instrument.
\n", "signature": "(self, gcms):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_data_metadata", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_data_metadata", "kind": "function", "doc": "Get metadata about the GC-MS data.
\n\nParameters:
\n\ngcms : object\n The low resolution GCMS object.\nid_label : str \n The ID label for the data.\noutput_path : str\n The output file path.
\n\nReturns:
\n\ndict\n A dictionary containing the data metadata.
\n", "signature": "(self, gcms, id_label, output_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_parameters_json", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_parameters_json", "kind": "function", "doc": "Get the parameters as a JSON string.
\n\nParameters:
\n\ngcms : GCMS object\n The low resolution GCMS object.\nid_label : str\n The ID label for the data.\noutput_path : str\n The output file path.
\n\nReturns:
\n\nstr\n The parameters as a JSON string.
\n", "signature": "(self, gcms, id_label, output_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.write_settings", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.write_settings", "kind": "function", "doc": "Write the settings to a JSON file.
\n\nParameters:
\n\noutput_path : str\n The output file path.\ngcms : GCMS object\n The low resolution GCMS object.\nid_label : str\n The ID label for the data. Default is \"emsl:\".
\n", "signature": "(self, output_path, gcms, id_label='emsl:'):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.LowResGCMSExport.get_list_dict_data", "modulename": "corems.mass_spectra.output.export", "qualname": "LowResGCMSExport.get_list_dict_data", "kind": "function", "doc": "Get the exported data as a list of dictionaries.
\n\nParameters:
\n\ngcms : object\n The low resolution GCMS object.\ninclude_no_match : bool, optional\n Whether to include no match data. Default is True.\nno_match_inline : bool, optional\n Whether to include no match data inline. Default is False.
\n\nReturns:
\n\nlist\n The exported data as a list of dictionaries.
\n", "signature": "(self, gcms, include_no_match=True, no_match_inline=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport", "kind": "class", "doc": "A class to export high resolution mass spectra data.
\n\nThis class provides methods to export high resolution mass spectra data to various formats such as Excel, CSV, HDF5, and Pandas DataFrame.
\n\nParameters:
\n\nout_file_path : str | Path\n The output file path.\nmass_spectra : object\n The high resolution mass spectra object.\noutput_type : str, optional\n The output type. Default is 'excel'.
\n", "bases": "corems.mass_spectrum.output.export.HighResMassSpecExport"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.__init__", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(out_file_path, mass_spectra, output_type='excel')"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.output_file", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.output_file", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.dir_loc", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.dir_loc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.mass_spectra", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.mass_spectra", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.get_pandas_df", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.get_pandas_df", "kind": "function", "doc": "Get the exported data as a Pandas DataFrame.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.to_pandas", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.to_pandas", "kind": "function", "doc": "Export the data to a Pandas DataFrame and save it as a pickle file.
\n\nParameters:
\n\nwrite_metadata : bool, optional\n Whether to write metadata to the output file. Default is True.
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.to_excel", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.to_excel", "kind": "function", "doc": "Export the data to an Excel file.
\n\nParameters:
\n\nwrite_metadata : bool, optional\n Whether to write metadata to the output file. Default is True.
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.to_csv", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.to_csv", "kind": "function", "doc": "Export the data to a CSV file.
\n\nParameters:
\n\nwrite_metadata : bool, optional\n Whether to write metadata to the output file. Default is True.
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.get_mass_spectra_attrs", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.get_mass_spectra_attrs", "kind": "function", "doc": "Get the mass spectra attributes as a JSON string.
\n\nParameters:
\n\nmass_spectra : object\n The high resolution mass spectra object.
\n\nReturns:
\n\nstr\n The mass spectra attributes as a JSON string.
\n", "signature": "(self, mass_spectra):", "funcdef": "def"}, {"fullname": "corems.mass_spectra.output.export.HighResMassSpectraExport.to_hdf", "modulename": "corems.mass_spectra.output.export", "qualname": "HighResMassSpectraExport.to_hdf", "kind": "function", "doc": "Export the data to an HDF5 file.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum", "modulename": "corems.mass_spectrum", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc", "modulename": "corems.mass_spectrum.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "kind": "module", "doc": "Created on March 23 2023
\n\n@author: Will Kew
\n\nModules for automatic mass internal recalibration
\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration", "kind": "class", "doc": "This class is designed for high resolution (FTICR, Orbitrap) data of complex mixture, e.g. Organic matter
\n\nThe tool first does a broad mass range search for the most commonly expected ion type (i.e. CHO, deprotonated - for negative ESI)\nAnd then the assigned data mass error distribution is searched, with a gaussian fit to the most prominent range. \nThis tool works when the data are of sufficient quality, and not outwith the typical expected range of the mass analyzer\nIt presumes the mean error is out by 0-several ppm, but that the spread of error values is modest (<2ppm)
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nCoreMS mass spectrum object
\n- plot (bool, optional):\nWhether to plot the error distribution. The default is False.
\n- docker (bool, optional):\nWhether to use the docker database. The default is True. If not, it uses a dynamically generated sqlite database.
\n- ppmFWHMprior (float, optional):\nThe FWHM of the prior distribution (ppm). The default is 3.
\n- ppmRangeprior (float, optional):\nThe range of the prior distribution (ppm). The default is 15.
\n
\n\nMethods
\n\n\n- determine_error_boundaries(). Determine the error boundaries for recalibration space.
\n
\n\nNotes
\n\nThis initialisation function creates a copy of the MassSpectrum object to avoid over-writing assignments. \nPossible future task is to make the base class copyable.
\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.__init__", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.__init__", "kind": "function", "doc": "\n", "signature": "(\tmass_spectrum,\tplot: bool = False,\tdocker: bool = True,\tppmFWHMprior: float = 3,\tppmRangeprior: float = 15)"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.mass_spectrum", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.plot", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.plot", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.docker", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.docker", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.ppmFWHMprior", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.ppmFWHMprior", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.ppmRangeprior", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.ppmRangeprior", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.set_uncal_settings", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.set_uncal_settings", "kind": "function", "doc": "Set uncalibrated formula search settings
\n\nThis function serves the uncalibrated data (hence broad error tolerance)\nIt only allows CHO formula in deprotonated ion type- as most common for SRFA ESI negative mode
\n\nThis will not work for positive mode data, or for other ion types, or other expected elemental searches.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.positive_search_settings", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.positive_search_settings", "kind": "function", "doc": "Set the positive mode elemental search settings
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.get_error_range", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.get_error_range", "kind": "function", "doc": "Get the error range from the error distribution
\n\nUsing lmfit and seaborn kdeplot to extract the error range from the error distribution of assigned species.
\n\nParameters
\n\n\n- errors (list):\nlist of the errors of the assigned species (ppm)
\n
\n", "signature": "(self, errors: list):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.AutoRecalibration.HighResRecalibration.determine_error_boundaries", "modulename": "corems.mass_spectrum.calc.AutoRecalibration", "qualname": "HighResRecalibration.determine_error_boundaries", "kind": "function", "doc": "Determine the error boundaries for recalibration space
\n\nThis is the main function in this class\nSets the Molecular Formulas search settings, performs the initial formula search\nConverts the data to a dataframe, and gets the error range\nReturns the error thresholds.
\n\nReturns
\n\n\n- mean_error (float):\nmean mass error of the Gaussian distribution (ppm)
\n- fwhm_error (float):\nfull width half max of the gaussian error distribution (ppm)
\n- ppm_thresh (list):\nrecommended thresholds for the recalibration parameters (ppm)\nConsists of [mean_error-fwhm_error,mean_error+fwhm_error]
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration", "modulename": "corems.mass_spectrum.calc.Calibration", "kind": "module", "doc": "Created on Wed May 13 02:16:09 2020
\n\n@author: Will Kew
\n"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration", "kind": "class", "doc": "MzDomainCalibration class for recalibrating mass spectra
\n\nParameters
\n\n\n- mass_spectrum (CoreMS MassSpectrum Object):\nThe mass spectrum to be calibrated.
\n- ref_masslist (str):\nThe path to a reference mass list.
\n- mzsegment (tuple of floats, optional):\nThe mz range to recalibrate, or None. Used for calibration of specific parts of the mz domain at a time.\nFuture work - allow multiple mzsegments to be passed.
\n
\n\nAttributes
\n\n\n- mass_spectrum (CoreMS MassSpectrum Object):\nThe mass spectrum to be calibrated.
\n- mzsegment (tuple of floats or None):\nThe mz range to recalibrate, or None.
\n- ref_mass_list_path (str or Path):\nThe path to the reference mass list.
\n
\n\nMethods
\n\n\n- run(). \nMain function to run this class.
\n- load_ref_mass_list(). \nLoad reference mass list (Bruker format).
\n- gen_ref_mass_list_from_assigned(min_conf=0.7). \nGenerate reference mass list from assigned masses.
\n- find_calibration_points(df_ref, calib_ppm_error_threshold=(-1, 1), calib_snr_threshold=5). \nFind calibration points in the mass spectrum based on the reference mass list.
\n- robust_calib(param, cal_peaks_mz, cal_refs_mz, order=1). \nRecalibration function.
\n- recalibrate_mass_spectrum(cal_peaks_mz, cal_refs_mz, order=1, diagnostic=False). \nMain recalibration function which uses a robust linear regression.
\n
\n"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.__init__", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.__init__", "kind": "function", "doc": "\n", "signature": "(mass_spectrum, ref_masslist, mzsegment=None)"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.mass_spectrum", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.mzsegment", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.mzsegment", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.ref_mass_list_path", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.ref_mass_list_path", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.load_ref_mass_list", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.load_ref_mass_list", "kind": "function", "doc": "Load reference mass list (Bruker format)
\n\nLoads in a reference mass list from a .ref file\nNote that some versions of Bruker's software produce .ref files with a different format. \nAs such, users may need to manually edit the .ref file in a text editor to ensure it is in the correct format. \nCoreMS includes an example .ref file with the correct format for reference.
\n\nReturns
\n\n\n- df_ref (Pandas DataFrame):\nreference mass list object.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.gen_ref_mass_list_from_assigned", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.gen_ref_mass_list_from_assigned", "kind": "function", "doc": "Generate reference mass list from assigned masses
\n\nThis function will generate a ref mass dataframe object from an assigned corems mass spec obj\nusing assigned masses above a certain minimum confidence threshold.
\n\nThis function needs to be retested and check it is covered in the unit tests.
\n\nParameters
\n\n\n- min_conf (float, optional):\nminimum confidence score. The default is 0.7.
\n
\n\nReturns
\n\n\n- df_ref (Pandas DataFrame):\nreference mass list - based on calculated masses.
\n
\n", "signature": "(self, min_conf: float = 0.7):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.find_calibration_points", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.find_calibration_points", "kind": "function", "doc": "Function to find calibration points in the mass spectrum
\n\nBased on the reference mass list.
\n\nParameters
\n\n\n- df_ref (Pandas DataFrame):\nreference mass list for recalibration.
\n- calib_ppm_error_threshold (tuple of floats, optional):\nppm error for finding calibration masses in the spectrum. The default is -1,1.\nNote: This is based on the calculation of ppm = ((mz_measure - mz_theoretical)/mz_theoretical)*1e6. \n Some software does this the other way around and value signs must be inverted for that to work.
\n- calib_snr_threshold (float, optional):\nsnr threshold for finding calibration masses in the spectrum. The default is 5.
\n
\n\nReturns
\n\n\n- cal_peaks_mz (list of floats):\nmasses of measured ions to use in calibration routine
\n- cal_refs_mz (list of floats):\nreference mz values of found calibration points.
\n
\n", "signature": "(\tself,\tdf_ref,\tcalib_ppm_error_threshold: tuple[float, float] = (-1, 1),\tcalib_snr_threshold: float = 5):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.robust_calib", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.robust_calib", "kind": "function", "doc": "Recalibration function
\n\nComputes the rms of m/z errors to minimize when calibrating.\nThis is adapted from from spike.
\n\nParameters
\n\n\n- param (list of floats):\ngenerated by minimize function from scipy optimize.
\n- cal_peaks_mz (list of floats):\nmasses of measured peaks to use in mass calibration.
\n- cal_peaks_mz (list of floats):\nreference mz values of found calibration points.
\n- order (int, optional):\norder of the recalibration function. 1 = linear, 2 = quadratic. The default is 1.
\n
\n\nReturns
\n\n\n- rmserror (float):\nroot mean square mass error for calibration points.
\n
\n", "signature": "(\tself,\tparam: list[float],\tcal_peaks_mz: list[float],\tcal_refs_mz: list[float],\torder: int = 1):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.recalibrate_mass_spectrum", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.recalibrate_mass_spectrum", "kind": "function", "doc": "Main recalibration function which uses a robust linear regression
\n\nThis function performs the recalibration of the mass spectrum object. \nIt iteratively applies
\n\nParameters
\n\n\n- cal_peaks_mz (list of float):\nmasses of measured peaks to use in mass calibration.
\n- cal_refs_mz (list of float):\nreference mz values of found calibration points.
\n- order (int, optional):\norder of the recalibration function. 1 = linear, 2 = quadratic. The default is 1.
\n
\n\nReturns
\n\n\n- mass_spectrum (CoreMS mass spectrum object):\nCalibrated mass spectrum object
\n
\n\nNotes
\n\nThis function is adapted, in part, from the SPIKE project [1,2] and is based on the robust linear regression method.
\n\nReferences
\n\n\n- Chiron L., Coutouly M-A., Starck J-P., Rolando C., Delsuc M-A. \nSPIKE a Processing Software dedicated to Fourier Spectroscopies \nhttps://arxiv.org/abs/1608.06777 (2016)
\n- SPIKE - https://github.com/spike-project/spike
\n
\n", "signature": "(\tself,\tcal_peaks_mz: list[float],\tcal_refs_mz: list[float],\torder: int = 1,\tdiagnostic: bool = False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.Calibration.MzDomainCalibration.run", "modulename": "corems.mass_spectrum.calc.Calibration", "qualname": "MzDomainCalibration.run", "kind": "function", "doc": "Run the calibration routine
\n\nThis function runs the calibration routine.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration", "kind": "class", "doc": "Frequency Domain Calibration class for mass spectrum.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- selected_mass_peaks (list):\nList of selected mass peaks.
\n- include_isotopologue (bool, optional):\nFlag to include isotopologues, by default False.
\n
\n\nAttributes
\n\n\n- mz_exp (ndarray):\nArray of experimental m/z values.
\n- mz_calc (ndarray):\nArray of calculated m/z values.
\n- freq_exp (ndarray):\nArray of experimental frequencies.
\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- freq_exp_ms (ndarray):\nArray of experimental frequencies for mass spectrum.
\n
\n\nMethods
\n\n\n- recal_mass_spec(mz_domain, Aterm, Bterm, Cterm). \nRecalibrate the mass spectrum with the given parameters.
\n- linear(). \nPerform linear calibration.
\n- quadratic(iteration=False). \nPerform quadratic calibration.
\n- ledford_calibration(iteration=False). \nPerform Ledford calibration.
\n- step_fit(steps=4).
\nPerform step fit calibration. \n
\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.__init__", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.__init__", "kind": "function", "doc": "\n", "signature": "(mass_spectrum, selected_mass_peaks, include_isotopologue=False)"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.selected_mspeaks", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.selected_mspeaks", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.mz_exp", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.mz_exp", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.mz_calc", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.mz_calc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.freq_exp", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.freq_exp", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.mass_spectrum", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.freq_exp_ms", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.freq_exp_ms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.recal_mass_spec", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.recal_mass_spec", "kind": "function", "doc": "Recalibrate the mass spectrum with the given parameters.
\n\nParameters
\n\n\n- mz_domain (ndarray):\nArray of m/z values for recalibration.
\n- Aterm (float):\nAterm parameter for recalibration.
\n- Bterm (float):\nBterm parameter for recalibration.
\n- Cterm (float):\nCterm parameter for recalibration.
\n
\n", "signature": "(self, mz_domain, Aterm, Bterm, Cterm):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.linear", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.linear", "kind": "function", "doc": "Perform linear calibration.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.quadratic", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.quadratic", "kind": "function", "doc": "Perform quadratic calibration.
\n\nParameters
\n\n\n- iteration (bool, optional):\nFlag to perform iterative calibration, by default False.
\n
\n", "signature": "(self, iteration: bool = False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.ledford_calibration", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.ledford_calibration", "kind": "function", "doc": "Perform Ledford calibration.
\n\nParameters
\n\n\n- iteration (bool, optional):\nFlag to perform iterative calibration, by default False.
\n
\n", "signature": "(self, iteration: bool = False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.CalibrationCalc.FreqDomain_Calibration.step_fit", "modulename": "corems.mass_spectrum.calc.CalibrationCalc", "qualname": "FreqDomain_Calibration.step_fit", "kind": "function", "doc": "Perform step fit calibration.
\n\nParameters
\n\n\n- steps (int, optional):\nNumber of steps for step fit calibration, by default 4.
\n
\n", "signature": "(self, steps: int = 4):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping", "kind": "class", "doc": "Class for Kendrick grouping of mass spectra.
\n\nMethods
\n\n\n- mz_odd_even_index_lists(). \nGet odd and even indexes lists.
\n- calc_error(current, test). \nCalculate the error between two values.
\n- populate_kendrick_index_dict_error(list_indexes, sort=True). \nPopulate the Kendrick index dictionary based on error.
\n- populate_kendrick_index_dict_rounding(list_indexes, sort=True). \nPopulate the Kendrick index dictionary based on rounding.
\n- sort_abundance_kendrick_dict(even_kendrick_group_index, odd_kendrick_group_index). \nSort the Kendrick index dictionary based on abundance.
\n- kendrick_groups_indexes(sort=True). \nGet the Kendrick groups indexes dictionary.
\n
\n"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.mz_odd_even_index_lists", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.mz_odd_even_index_lists", "kind": "function", "doc": "Get odd and even indexes lists.
\n\nReturns
\n\n\n- tuple: A tuple containing the lists of even and odd indexes.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.calc_error", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.calc_error", "kind": "function", "doc": "Calculate the error between two values.
\n\nParameters
\n\n\n- current (float):\nThe current value.
\n- test (float):\nThe test value.
\n
\n\nReturns
\n\n\n- float: The calculated error.
\n
\n", "signature": "(self, current: float, test: float):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.populate_kendrick_index_dict_error", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.populate_kendrick_index_dict_error", "kind": "function", "doc": "Populate the Kendrick index dictionary based on error.
\n\nParameters
\n\n\n- list_indexes (list):\nThe list of indexes.
\n- sort (bool, optional):\nWhether to sort the dictionary by abundance (default is True).
\n
\n\nReturns
\n\n\n- dict: The Kendrick index dictionary.
\n
\n", "signature": "(self, list_indexes: list, sort: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.populate_kendrick_index_dict_rounding", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.populate_kendrick_index_dict_rounding", "kind": "function", "doc": "Populate the Kendrick index dictionary based on rounding.
\n\nParameters
\n\n\n- list_indexes (list):\nThe list of indexes.
\n- sort (bool, optional):\nWhether to sort the dictionary by abundance (default is True).
\n
\n\nReturns
\n\n\n- dict: The Kendrick index dictionary.
\n
\n", "signature": "(self, list_indexes: list, sort: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.sort_abundance_kendrick_dict", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.sort_abundance_kendrick_dict", "kind": "function", "doc": "Sort the Kendrick index dictionary based on abundance.
\n\nParameters
\n\n\n- even_kendrick_group_index (dict):\nThe Kendrick index dictionary for even indexes.
\n- odd_kendrick_group_index (dict):\nThe Kendrick index dictionary for odd indexes.
\n
\n\nReturns
\n\n\n- dict: The sorted Kendrick index dictionary.
\n
\n", "signature": "(\tself,\teven_kendrick_group_index: dict,\todd_kendrick_group_index: dict):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping.kendrick_groups_indexes", "modulename": "corems.mass_spectrum.calc.KendrickGroup", "qualname": "KendrickGrouping.kendrick_groups_indexes", "kind": "function", "doc": "Get the Kendrick groups indexes dictionary.
\n\nParameters
\n\n\n- sort (bool, optional):\nWhether to sort the dictionary by abundance (default is True).
\n
\n\nReturns
\n\n\n- dict: The Kendrick groups indexes dictionary.
\n
\n", "signature": "(self, sort: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction", "kind": "class", "doc": "Class for mass error prediction.
\n\nParameters
\n\n\n- mass_spectrum (list):\nList of mass spectrum objects.
\n- mz_overlay (int, optional):\nThe mz overlay value for peak simulation. Default is 10.
\n- rp_increments (int, optional):\nThe resolving power increments for peak simulation. Default is 10000.
\n- base_line_target (float, optional):\nThe target value for the baseline resolution. Default is 0.01.
\n- max_interation (int, optional):\nThe maximum number of iterations for peak simulation. Default is 1000.
\n- interpolation (str, optional):\nThe interpolation method for missing data. Default is 'linear'.
\n
\n\nAttributes
\n\n\n- mass_spectrum_obj (list):\nList of mass spectrum objects.
\n- mz_overlay (int):\nThe mz overlay value for peak simulation.
\n- rp_increments (int):\nThe resolving power increments for peak simulation.
\n- base_line_target (float):\nThe target value for the baseline resolution.
\n- max_interation (int):\nThe maximum number of iterations for peak simulation.
\n- df (DataFrame or None):\nThe calculated error distribution dataframe.
\n- interpolation (str):\nThe interpolation method for missing data.
\n
\n\nMethods
\n\n\n- run().\nRuns the mass error prediction calculation.
\n- get_results().\nReturns the calculated error distribution dataframe.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.__init__", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(\tmass_spectrum,\tmz_overlay=10,\trp_increments=10000,\tbase_line_target: float = 0.01,\tmax_interation=1000,\tinterpolation='linear')"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.mass_spectrum_obj", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.mass_spectrum_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.mz_overlay", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.mz_overlay", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.rp_increments", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.rp_increments", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.base_line_target", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.base_line_target", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.max_interation", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.max_interation", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.df", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.df", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.interpolation", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.interpolation", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.run", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.run", "kind": "function", "doc": "Runs the mass error prediction calculation.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.get_results", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.get_results", "kind": "function", "doc": "Returns the calculated error distribution dataframe.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.calc_error_dist", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.calc_error_dist", "kind": "function", "doc": "Calculate the error distribution.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.sum_data", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.sum_data", "kind": "function", "doc": "Sum the abundances of the simulated peaks.
\n\nParameters
\n\n\n- tuple_mz_abun_list (tuple):\nA tuple containing the mz and abundance lists.
\n
\n\nReturns
\n\n\n- tuple: A tuple containing the summed mz and abundance lists.
\n
\n", "signature": "(self, tuple_mz_abun_list: tuple):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.calc_error", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.calc_error", "kind": "function", "doc": "Calculate the error between two values.
\n\nParameters
\n\n\n- mass_ref (float):\nThe reference value.
\n- mass_sim (float):\nThe simulated value.
\n- factor (float):\nThe factor to multiply the error by.
\n
\n\nReturns
\n\n\n- float: The calculated error.
\n
\n", "signature": "(self, mass_ref, mass_sim, factor):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.find_peak_apex", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.find_peak_apex", "kind": "function", "doc": "Find the peak apex.
\n\nParameters
\n\n\n- mz (array):\nThe mz array.
\n- abund (array):\nThe abundance array.
\n
\n\nReturns
\n\n\n- tuple: A tuple containing the peak apex mass and abundance.
\n
\n", "signature": "(self, mz, abund):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassErrorPrediction.MassErrorPrediction.find_peak_valley", "modulename": "corems.mass_spectrum.calc.MassErrorPrediction", "qualname": "MassErrorPrediction.find_peak_valley", "kind": "function", "doc": "Find the peak valley.
\n\nParameters
\n\n\n- mz (array):\nThe mz array.
\n- abund (array):\nThe abundance array.
\n
\n\nReturns
\n\n\n- tuple: A tuple containing the peak valley mz and abundance.
\n
\n", "signature": "(self, mz, abund):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "qualname": "MassSpecCalc", "kind": "class", "doc": "Class for Mass Spectrum Calculations
\n\nClass including numerical calculations related to mass spectrum class\nInherited PeakPicking and NoiseThresholdCalc ensuring its methods are \navailable to the instantiated mass spectrum class object
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nCoreMS mass spectrum object
\n
\n\nAttributes
\n\n\n- All Attributes are derivative from the MassSpecBase Class
\n
\n\nMethods
\n\n\n- check_mspeaks(). \nCheck if the mspeaks attribute is populated
\n- sort_by_abundance(). \nSort the mspeaks by abundance
\n- percentile_assigned(report_error=False,verbose=True). \nCalculate the percentage of assigned peaks
\n- resolving_power_calc(B, T). \nCalculate the resolving power
\n- number_average_molecular_weight(profile=False). \nCalculate the number average molecular weight
\n- weight_average_molecular_weight(profile=False). \nCalculate the weight average molecular weight
\n
\n", "bases": "corems.mass_spectrum.calc.PeakPicking.PeakPicking, corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc.percentile_assigned", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "qualname": "MassSpecCalc.percentile_assigned", "kind": "function", "doc": "Percentage of peaks which are assigned
\n\nParameters
\n\n\n- report_error (bool, optional):\nReport the error of the assigned peaks. Default is False.
\n- verbose (bool, optional):\nPrint the results. Default is True.
\n
\n", "signature": "(self, report_error: bool = False, verbose: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc.resolving_power_calc", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "qualname": "MassSpecCalc.resolving_power_calc", "kind": "function", "doc": "Calculate the theoretical resolving power
\n\nCalls on the MSPeak object function to calculate the resolving power of a peak, this calcs for all peaks in a spectrum.
\n\nParameters
\n\n\n- T (float):\ntransient time
\n- B (float):\nMagnetic Filed Strength (Tesla)
\n
\n\nReferences
\n\n\n- Marshall et al. (Mass Spectrom Rev. 1998 Jan-Feb;17(1):1-35.)\nDOI: 10.1002/(SICI)1098-2787(1998)17:1<1::AID-MAS1>3.0.CO;2-K
\n
\n", "signature": "(self, B: float, T: float):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc.number_average_molecular_weight", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "qualname": "MassSpecCalc.number_average_molecular_weight", "kind": "function", "doc": "Average molecular weight calculation
\n\nParameters
\n\n\n- profile (bool, optional):\nis data profile or centroid mode. The default is False (e.g. Centroid data)
\n
\n\nReturns
\n\n\n- float: The average molecular weight.
\n
\n", "signature": "(self, profile: bool = False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc.weight_average_molecular_weight", "modulename": "corems.mass_spectrum.calc.MassSpectrumCalc", "qualname": "MassSpecCalc.weight_average_molecular_weight", "kind": "function", "doc": "Weighted Average molecular weight calculation
\n\nReturns
\n\n\n- float: The weight average molecular weight.
\n
\n", "signature": "(self, profile: bool = False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "kind": "module", "doc": "Created on June 2nd 2023
\n\n@author: Will Kew
\n\nModule for mean resolving power filtration\nBased upon the work in:
\n\nKanawati, B, Bader, TM, Wanczek, K-P, Li, Y, Schmitt-Kopplin, P. \nFourier transform (FT)-artifacts and power-function resolution filter in Fourier transform mass spectrometry. \nRapid Commun Mass Spectrom. 2017; 31: 1607- 1615. https://doi.org/10.1002/rcm.7940
\n\nCalculates a m/z normalised resolving power, fits a gaussian distribution to this, and then filters out peaks which are outside of the user defined number of standard deviations
\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter", "kind": "class", "doc": "Class for for mean resolving power filtration.
\n\nThis module implements a mean resolving power filter based on the work described [1]
\n\nThe MeanResolvingPowerFilter class provides methods to calculate the m/z normalized resolving power, fit a Gaussian distribution to it, and filter out peaks that are outside of the user-defined number of standard deviations.
\n\nAttributes
\n\n\nmass_spectrum (object) (The mass spectrum object.):
ndeviations (int) (The number of standard deviations used for filtering.):
plot (bool) (Flag indicating whether to plot the results.):
guess_pars (bool) (Flag indicating whether to guess the parameters for the Gaussian model.):
\n\nMethods
\n\n\n- extract_peaks(): Extracts the peaks from the mass spectrum.
\n- normalise_rps(tmpdf_ms): Normalizes the resolving powers to be independent of m/z.
\n- calculate_distribution(tmpdf_ms): Calculates the distribution of the resolving powers.
\n- create_index_list_to_remove(tmpdf_ms, rps_thresh): Creates an index list of peaks to remove based on the calculated thresholds.
\n- main(): Executes the main filtering process and returns the index list of peaks to remove.
\n
\n\nReferences
\n\n\n- Kanawati, B, Bader, TM, Wanczek, K-P, Li, Y, Schmitt-Kopplin, P. \nFourier transform (FT)-artifacts and power-function resolution filter in Fourier transform mass spectrometry. \nRapid Commun Mass Spectrom. 2017; 31: 1607- 1615. https://doi.org/10.1002/rcm.7940
\n
\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.__init__", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.__init__", "kind": "function", "doc": "\n", "signature": "(\tmass_spectrum,\tndeviations: float = 3,\tplot: bool = False,\tguess_pars: bool = False)"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.mass_spectrum", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.plot", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.plot", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.ndeviations", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.ndeviations", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.guess_pars", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.guess_pars", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.extract_peaks", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.extract_peaks", "kind": "function", "doc": "Extracts the peaks from the mass spectrum.
\n\nReturns
\n\n\n- tmpdf_ms (Pandas DataFrame):\nA DataFrame containing the extracted peaks.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.normalise_rps", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.normalise_rps", "kind": "function", "doc": "Normalizes the resolving powers to be independent of m/z.
\n\nParameters
\n\n\n- tmpdf_ms (Pandas DataFrame):\nA DataFrame containing the extracted peaks.
\n
\n\nReturns
\n\n\n- tmpdf_ms (Pandas DataFrame):\nA DataFrame with the resolving powers normalized.
\n
\n", "signature": "(self, tmpdf_ms):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.calculate_distribution", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.calculate_distribution", "kind": "function", "doc": "Calculates the distribution of the resolving powers.
\n\nParameters
\n\n\n- tmpdf_ms (Pandas DataFrame):\nA DataFrame containing the extracted peaks with normalized resolving powers.
\n
\n\nReturns
\n\n\n- rps_thresh (list):\nA list of the calculated thresholds for filtering.
\n
\n", "signature": "(self, tmpdf_ms):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.create_index_list_to_remove", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.create_index_list_to_remove", "kind": "function", "doc": "Creates an index list of peaks to remove based on the calculated thresholds.
\n\nParameters
\n\n\n- tmpdf_ms (Pandas DataFrame):\nA DataFrame containing the extracted peaks with normalized resolving powers.
\n- rps_thresh (list):\nA list of the calculated thresholds for filtering.
\n
\n\nReturns
\n\n\n- index_to_keep (list):\nA list of indices of peaks to keep.
\n
\n", "signature": "(self, tmpdf_ms, rps_thresh: list):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.MeanResolvingPowerFilter.MeanResolvingPowerFilter.main", "modulename": "corems.mass_spectrum.calc.MeanResolvingPowerFilter", "qualname": "MeanResolvingPowerFilter.main", "kind": "function", "doc": "Executes the main filtering process and returns the index list of peaks to remove.
\n\nReturns
\n\n\n- index_to_remove (list):\nA list of indices of peaks to remove.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc", "kind": "class", "doc": "Class for noise threshold calculation.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- settings (MSParameters):\nThe mass spectrum parameters object.
\n- is_centroid (bool):\nFlag indicating whether the mass spectrum is centroid or profile.
\n- baseline_noise (float):\nThe baseline noise.
\n- baseline_noise_std (float):\nThe baseline noise standard deviation.
\n- max_signal_to_noise (float):\nThe maximum signal to noise.
\n- max_abundance (float):\nThe maximum abundance.
\n- abundance (np.array):\nThe abundance array.
\n- abundance_profile (np.array):\nThe abundance profile array.
\n- mz_exp (np.array):\nThe experimental m/z array.
\n- mz_exp_profile (np.array):\nThe experimental m/z profile array.
\n
\n\nAttributes
\n\n\n\nMethods
\n\n\n- get_noise_threshold(). Get the noise threshold.
\n- cut_mz_domain_noise(). Cut the m/z domain to the noise threshold regions.
\n- get_noise_average(ymincentroid). \nGet the average noise and standard deviation.
\n- get_abundance_minima_centroid(abun_cut)\nGet the abundance minima for centroid data.
\n- run_log_noise_threshold_calc(). \nRun the log noise threshold calculation.
\n- run_noise_threshold_calc(). \nRun the noise threshold calculation.
\n
\n"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.get_noise_threshold", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.get_noise_threshold", "kind": "function", "doc": "Get the noise threshold.
\n\nReturns
\n\n\n- Tuple[Tuple[float, float], Tuple[float, float]]: A tuple containing the m/z and abundance noise thresholds.\n(min_mz, max_mz), (noise_threshold, noise_threshold)
\n
\n", "signature": "(self) -> Tuple[Tuple[float, float], Tuple[float, float]]:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.cut_mz_domain_noise", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.cut_mz_domain_noise", "kind": "function", "doc": "Cut the m/z domain to the noise threshold regions.
\n\nReturns
\n\n\n- Tuple[np.array, np.array]: A tuple containing the m/z and abundance arrays of the truncated spectrum region.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.get_noise_average", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.get_noise_average", "kind": "function", "doc": "Get the average noise and standard deviation.
\n\nParameters
\n\n\n- ymincentroid (np.array):\nThe ymincentroid array.
\n
\n\nReturns
\n\n\n- Tuple[float, float]: A tuple containing the average noise and standard deviation.
\n
\n", "signature": "(self, ymincentroid):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.get_abundance_minima_centroid", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.get_abundance_minima_centroid", "kind": "function", "doc": "Get the abundance minima for centroid data.
\n\nParameters
\n\n\n- abun_cut (np.array):\nThe abundance cut array.
\n
\n\nReturns
\n\n\n- np.array: The abundance minima array.
\n
\n", "signature": "(self, abun_cut):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.run_log_noise_threshold_calc", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.run_log_noise_threshold_calc", "kind": "function", "doc": "Run the log noise threshold calculation.
\n\nReturns
\n\n\n- Tuple[float, float]: A tuple containing the average noise and standard deviation.
\n
\n\nNotes
\n\nMethod for estimating the noise based on decimal log of all the data point
\n\nIdea is that you calculate a histogram of of the log10(abundance) values. \nThe maximum of the histogram == the standard deviation of the noise.
\n\nFor aFT data it is a gaussian distribution of noise - not implemented here!\nFor mFT data it is a Rayleigh distribution, and the value is actually 10^(abu_max)*0.463.
\n\nSee the publication cited above for the derivation of this.
\n\nReferences
\n\n\n- dx.doi.org/10.1021/ac403278t | Anal. Chem. 2014, 86, 3308\u22123316
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc.run_noise_threshold_calc", "modulename": "corems.mass_spectrum.calc.NoiseCalc", "qualname": "NoiseThresholdCalc.run_noise_threshold_calc", "kind": "function", "doc": "Runs noise threshold calculation (not log based method)
\n\nReturns
\n\n\n- Tuple[float, float]: A tuple containing the average noise and standard deviation.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "modulename": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "kind": "module", "doc": "This code is for Bayesian estimation of the noise levels. \nIt is it not implemented or used in the current code base. \nThe packages it uses are not part of the requirements. \nIf you want to use it, you will need to install them manually.
\n"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc_Bayes.BayesNoiseCalc", "modulename": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "qualname": "BayesNoiseCalc", "kind": "class", "doc": "Class for noise threshold calculation.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- settings (MSParameters):\nThe mass spectrum parameters object.
\n- is_centroid (bool):\nFlag indicating whether the mass spectrum is centroid or profile.
\n- baseline_noise (float):\nThe baseline noise.
\n- baseline_noise_std (float):\nThe baseline noise standard deviation.
\n- max_signal_to_noise (float):\nThe maximum signal to noise.
\n- max_abundance (float):\nThe maximum abundance.
\n- abundance (np.array):\nThe abundance array.
\n- abundance_profile (np.array):\nThe abundance profile array.
\n- mz_exp (np.array):\nThe experimental m/z array.
\n- mz_exp_profile (np.array):\nThe experimental m/z profile array.
\n
\n\nAttributes
\n\n\n\nMethods
\n\n\n- get_noise_threshold(). Get the noise threshold.
\n- cut_mz_domain_noise(). Cut the m/z domain to the noise threshold regions.
\n- get_noise_average(ymincentroid). \nGet the average noise and standard deviation.
\n- get_abundance_minima_centroid(abun_cut)\nGet the abundance minima for centroid data.
\n- run_log_noise_threshold_calc(). \nRun the log noise threshold calculation.
\n- run_noise_threshold_calc(). \nRun the noise threshold calculation.
\n
\n", "bases": "corems.mass_spectrum.calc.NoiseCalc.NoiseThresholdCalc"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc_Bayes.BayesNoiseCalc.from_posterior", "modulename": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "qualname": "BayesNoiseCalc.from_posterior", "kind": "function", "doc": "Legacy code for Bayesian efforts - not used.
\n\npymc3 is not installed by default, \n if have plans to use it manual installation of pymc3 \n package before using this method is needed
\n", "signature": "(self, param, samples):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc_Bayes.BayesNoiseCalc.error_model_from_trace", "modulename": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "qualname": "BayesNoiseCalc.error_model_from_trace", "kind": "function", "doc": "Legacy code for Bayesian efforts - not used.
\n\npymc3 is not installed by default, \n if have plans to use it manual installation of pymc3 \n package before using this method is needed
\n", "signature": "(self, trace, ymincentroid):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.NoiseCalc_Bayes.BayesNoiseCalc.simple_model_error_dist", "modulename": "corems.mass_spectrum.calc.NoiseCalc_Bayes", "qualname": "BayesNoiseCalc.simple_model_error_dist", "kind": "function", "doc": "Legacy code for Bayesian efforts - not used.
\n\npymc3 is not installed by default, \n if have plans to use it manual installation of pymc3 \n package before using this method is needed
\n", "signature": "(self, ymincentroid):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking", "modulename": "corems.mass_spectrum.calc.PeakPicking", "kind": "module", "doc": "@author: Yuri E. Corilo\n@date: Jun 27, 2019
\n"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking", "kind": "class", "doc": "Class for peak picking.
\n\nParameters
\n\n\n\nAttributes
\n\n\n\nMethods
\n\n\n- cut_mz_domain_peak_picking().\nCut the m/z domain for peak picking.
\n- extrapolate_axes_for_pp().\nExtrapolate the m/z axis and fill the abundance axis with 0s.
\n- do_peak_picking().\nPerform peak picking.
\n- find_minima(apex_index, abundance, len_abundance, right=True).\nFind the minima of a peak.
\n- calculate_resolving_power(intes, massa, current_index).\nCalculate the resolving power of a peak.
\n- cal_minima(mass, abun).\nCalculate the minima of a peak.
\n- calc_centroid(mass, abund, freq).\nCalculate the centroid of a peak.
\n
\n"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.cut_mz_domain_peak_picking", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.cut_mz_domain_peak_picking", "kind": "function", "doc": "Cut the m/z domain for peak picking.
\n\nReturns
\n\n\n- mz_domain_X_low_cutoff (ndarray):\nThe m/z values within the specified range.
\n- mz_domain_low_Y_cutoff (ndarray):\nThe abundance values within the specified range.
\n- freq_domain_low_Y_cutoff (ndarray or None):\nThe frequency values within the specified range, if available.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.extrapolate_axes_for_pp", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.extrapolate_axes_for_pp", "kind": "function", "doc": "Extrapolate the m/z axis and fill the abundance axis with 0s.
\n\nReturns
\n\n\n- mz (ndarray):\nThe extrapolated m/z axis.
\n- abund (ndarray):\nThe abundance axis with 0s filled.
\n- freq (ndarray or None):\nThe extrapolated frequency axis, if available.
\n
\n\nNotes
\n\nThis function will extrapolate the mz axis by N datapoints, and fill the abundance axis with 0s. \nThis should prevent peak picking issues at the spectrum edge.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.do_peak_picking", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.do_peak_picking", "kind": "function", "doc": "Perform peak picking.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.find_minima", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.find_minima", "kind": "function", "doc": "Find the minima of a peak.
\n\nParameters
\n\n\n- apex_index (int):\nThe index of the peak apex.
\n- abundance (ndarray):\nThe abundance values.
\n- len_abundance (int):\nThe length of the abundance array.
\n- right (bool, optional):\nFlag indicating whether to search for minima to the right of the apex (default is True).
\n
\n\nReturns
\n\n\n- int: The index of the minima.
\n
\n", "signature": "(self, apex_index, abundance, len_abundance, right=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.calculate_resolving_power", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.calculate_resolving_power", "kind": "function", "doc": "Calculate the resolving power of a peak.
\n\nParameters
\n\n\n- intes (ndarray):\nThe intensity values.
\n- massa (ndarray):\nThe mass values.
\n- current_index (int):\nThe index of the current peak.
\n
\n\nReturns
\n\n\n- float: The resolving power of the peak.
\n
\n\nNotes
\n\nThis is a conservative calculation of resolving power,\nthe peak need to be resolved at least at the half-maximum magnitude,\notherwise, the combined full width at half maximum is used to calculate resolving power.
\n", "signature": "(self, intes, massa, current_index):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.cal_minima", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.cal_minima", "kind": "function", "doc": "Calculate the minima of a peak.
\n\nParameters
\n\n\n- mass (ndarray):\nThe mass values.
\n- abun (ndarray):\nThe abundance values.
\n
\n\nReturns
\n\n\n- ndarray or None: The mass values at the minima, if found.
\n
\n", "signature": "(self, mass, abun):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.calc_centroid", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.calc_centroid", "kind": "function", "doc": "Calculate the centroid of a peak.
\n\nParameters
\n\n\n- mass (ndarray):\nThe mass values.
\n- abund (ndarray):\nThe abundance values.
\n- freq (ndarray or None):\nThe frequency values, if available.
\n
\n\nReturns
\n\n\n", "signature": "(self, mass, abund, freq):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.get_threshold", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.get_threshold", "kind": "function", "doc": "Get the intensity threshold for peak picking.
\n\nParameters
\n\n\n- intes (ndarray):\nThe intensity values.
\n
\n\nReturns
\n\n\n- float: The intensity threshold.
\n- float: The factor to multiply the intensity threshold by.
\n
\n", "signature": "(self, intes):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.find_apex_fit_quadratic", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.find_apex_fit_quadratic", "kind": "function", "doc": "Find the apex of a peak.
\n\nParameters
\n\n\n- mass (ndarray):\nThe mass values.
\n- abund (ndarray):\nThe abundance values.
\n- freq (ndarray or None):\nThe frequency values, if available.
\n- current_index (int):\nThe index of the current peak.
\n
\n\nReturns
\n\n\n- float: The m/z value of the peak apex.
\n- float: The frequency value of the peak apex, if available.
\n- float: The abundance value of the peak apex.
\n
\n", "signature": "(self, mass, abund, freq, current_index):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.check_prominence", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.check_prominence", "kind": "function", "doc": "Check the prominence of a peak.
\n\nParameters
\n\n\n- abun (ndarray):\nThe abundance values.
\n- current_index (int):\nThe index of the current peak.
\n- len_abundance (int):\nThe length of the abundance array.
\n- peak_height_diff (function):\nThe function to calculate the peak height difference.
\n
\n\nReturns
\n\n\n- tuple or False: A tuple containing the indexes of the peak, if the prominence is above the threshold.\nOtherwise, False.
\n
\n", "signature": "(self, abun, current_index, len_abundance, peak_height_diff) -> tuple:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.use_the_max", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.use_the_max", "kind": "function", "doc": "Use the max peak height as the centroid
\n\nParameters
\n\n\n- mass (ndarray):\nThe mass values.
\n- abund (ndarray):\nThe abundance values.
\n- current_index (int):\nThe index of the current peak.
\n- len_abundance (int):\nThe length of the abundance array.
\n- peak_height_diff (function):\nThe function to calculate the peak height difference.
\n
\n\nReturns
\n\n\n- float: The m/z value of the peak apex.
\n- float: The abundance value of the peak apex.
\n- tuple or None: A tuple containing the indexes of the peak, if the prominence is above the threshold.\nOtherwise, None.
\n
\n", "signature": "(self, mass, abund, current_index, len_abundance, peak_height_diff):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.calc.PeakPicking.PeakPicking.calc_centroid_legacy", "modulename": "corems.mass_spectrum.calc.PeakPicking", "qualname": "PeakPicking.calc_centroid_legacy", "kind": "function", "doc": "Legacy centroid calculation\nDeprecated - for deletion.
\n", "signature": "(self, mass, abund, freq):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory", "modulename": "corems.mass_spectrum.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.overrides", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "overrides", "kind": "function", "doc": "Checks if the method overrides a method from an interface class.
\n", "signature": "(interface_class):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase", "kind": "class", "doc": "A mass spectrum base class, stores the profile data and instrument settings.
\n\nIteration over a list of MSPeaks classes stored at the _mspeaks attributes.\n_mspeaks is populated under the hood by calling process_mass_spec method.\nIteration is null if _mspeaks is empty.
\n\nParameters
\n\n\n- mz_exp (array_like):\nThe m/z values of the mass spectrum.
\n- abundance (array_like):\nThe abundance values of the mass spectrum.
\n- d_params (dict):\nA dictionary of parameters for the mass spectrum.
\n- **kwargs: Additional keyword arguments.
\n
\n\nAttributes
\n\n\n- mspeaks (list):\nA list of mass peaks.
\n- is_calibrated (bool):\nWhether the mass spectrum is calibrated.
\n- is_centroid (bool):\nWhether the mass spectrum is centroided.
\n- has_frequency (bool):\nWhether the mass spectrum has a frequency domain.
\n- calibration_order (None or int):\nThe order of the mass spectrum's calibration.
\n- calibration_points (None or ndarray):\nThe calibration points of the mass spectrum.
\n- calibration_RMS (None or float):\nThe root mean square of the mass spectrum's calibration.
\n- calibration_segment (None or CalibrationSegment):\nThe calibration segment of the mass spectrum.
\n- _abundance (ndarray):\nThe abundance values of the mass spectrum.
\n- _mz_exp (ndarray):\nThe m/z values of the mass spectrum.
\n- _mspeaks (list):\nA list of mass peaks.
\n- _dict_nominal_masses_indexes (dict):\nA dictionary of nominal masses and their indexes.
\n- _baseline_noise (float):\nThe baseline noise of the mass spectrum.
\n- _baseline_noise_std (float):\nThe standard deviation of the baseline noise of the mass spectrum.
\n- _dynamic_range (float or None):\nThe dynamic range of the mass spectrum.
\n- _transient_settings (None or TransientSettings):\nThe transient settings of the mass spectrum.
\n- _frequency_domain (None or FrequencyDomain):\nThe frequency domain of the mass spectrum.
\n- _mz_cal_profile (None or MzCalibrationProfile):\nThe m/z calibration profile of the mass spectrum.
\n
\n\nMethods
\n\n\n- process_mass_spec(). Main function to process the mass spectrum, \nincluding calculating the noise threshold, peak picking, and resetting the MSpeak indexes.
\n
\n\nSee also: MassSpecCentroid(), MassSpecfromFreq(), MassSpecProfile()
\n", "bases": "corems.mass_spectrum.calc.MassSpectrumCalc.MassSpecCalc, corems.mass_spectrum.calc.KendrickGroup.KendrickGrouping"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.__init__", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.__init__", "kind": "function", "doc": "\n", "signature": "(mz_exp, abundance, d_params, **kwargs)"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mspeaks", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mspeaks", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.is_calibrated", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.is_calibrated", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.is_centroid", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.is_centroid", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.has_frequency", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.has_frequency", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.calibration_order", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.calibration_order", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.calibration_points", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.calibration_points", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.calibration_RMS", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.calibration_RMS", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.calibration_segment", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.calibration_segment", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.set_indexes", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.set_indexes", "kind": "function", "doc": "Set the mass spectrum to iterate over only the selected MSpeaks indexes.
\n\nParameters
\n\n\n- list_indexes (list of int):\nA list of integers representing the indexes of the MSpeaks to iterate over.
\n
\n", "signature": "(self, list_indexes):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.reset_indexes", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.reset_indexes", "kind": "function", "doc": "Reset the mass spectrum to iterate over all MSpeaks objects.
\n\nThis method resets the mass spectrum to its original state, allowing iteration over all MSpeaks objects.\nIt also sets the index of each MSpeak object to its corresponding position in the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.add_mspeak", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.add_mspeak", "kind": "function", "doc": "Add a new MSPeak object to the MassSpectrum object.
\n\nParameters
\n\n\n- ion_charge (int):\nThe ion charge of the MSPeak.
\n- mz_exp (float):\nThe experimental m/z value of the MSPeak.
\n- abundance (float):\nThe abundance of the MSPeak.
\n- resolving_power (float):\nThe resolving power of the MSPeak.
\n- signal_to_noise (float):\nThe signal-to-noise ratio of the MSPeak.
\n- massspec_indexes (list):\nA list of indexes of the MSPeak in the MassSpectrum object.
\n- exp_freq (float, optional):\nThe experimental frequency of the MSPeak. Defaults to None.
\n- ms_parent (MSParent, optional):\nThe MSParent object associated with the MSPeak. Defaults to None.
\n
\n", "signature": "(\tself,\tion_charge,\tmz_exp,\tabundance,\tresolving_power,\tsignal_to_noise,\tmassspec_indexes,\texp_freq=None,\tms_parent=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.reset_cal_therms", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.reset_cal_therms", "kind": "function", "doc": "Reset calibration terms and recalculate the mass-to-charge ratio and abundance.
\n\nParameters
\n\n\n- Aterm (float):\nThe A-term calibration coefficient.
\n- Bterm (float):\nThe B-term calibration coefficient.
\n- C (float):\nThe C-term calibration coefficient.
\n- fas (float, optional):\nThe frequency amplitude scaling factor. Default is 0.
\n
\n", "signature": "(self, Aterm, Bterm, C, fas=0):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.clear_molecular_formulas", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.clear_molecular_formulas", "kind": "function", "doc": "Clear the molecular formulas for all mspeaks in the MassSpectrum.
\n\nReturns
\n\n\n- numpy.ndarray: An array of the cleared molecular formulas for each mspeak in the MassSpectrum.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.process_mass_spec", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.process_mass_spec", "kind": "function", "doc": "Process the mass spectrum.
\n\nParameters
\n\n\n- keep_profile (bool, optional):\nWhether to keep the profile data after processing. Defaults to True.
\n
\n\nNotes
\n\nThis method does the following:
\n\n\n- calculates the noise threshold
\n- does peak picking (creates mspeak_objs)
\n- resets the mspeak_obj indexes
\n
\n", "signature": "(self, keep_profile=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.cal_noise_threshold", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.cal_noise_threshold", "kind": "function", "doc": "Calculate the noise threshold of the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.parameters", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.parameters", "kind": "variable", "doc": "Return the parameters of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.set_parameter_from_json", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.set_parameter_from_json", "kind": "function", "doc": "Set the parameters of the mass spectrum from a JSON file.
\n\nParameters
\n\n\n- parameters_path (str):\nThe path to the JSON file containing the parameters.
\n
\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.set_parameter_from_toml", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.set_parameter_from_toml", "kind": "function", "doc": "\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mspeaks_settings", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mspeaks_settings", "kind": "variable", "doc": "Return the MS peak settings of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.settings", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.settings", "kind": "variable", "doc": "Return the settings of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.molecular_search_settings", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.molecular_search_settings", "kind": "variable", "doc": "Return the molecular search settings of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mz_cal_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mz_cal_profile", "kind": "variable", "doc": "Return the calibrated m/z profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mz_cal", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mz_cal", "kind": "variable", "doc": "Return the calibrated m/z values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mz_exp", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mz_exp", "kind": "variable", "doc": "Return the experimental m/z values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.freq_exp_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.freq_exp_profile", "kind": "variable", "doc": "Return the experimental frequency profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.mz_exp_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.mz_exp_profile", "kind": "variable", "doc": "Return the experimental m/z profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.abundance_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.abundance_profile", "kind": "variable", "doc": "Return the abundance profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.abundance", "kind": "variable", "doc": "Return the abundance values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.freq_exp", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.freq_exp", "kind": "function", "doc": "Return the experimental frequency values of the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.resolving_power", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.resolving_power", "kind": "variable", "doc": "Return the resolving power values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.signal_to_noise", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.signal_to_noise", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.nominal_mz", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.nominal_mz", "kind": "variable", "doc": "Return the nominal m/z values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.get_mz_and_abundance_peaks_tuples", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.get_mz_and_abundance_peaks_tuples", "kind": "function", "doc": "Return a list of tuples containing the m/z and abundance values of the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.kmd", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.kmd", "kind": "variable", "doc": "Return the Kendrick mass defect values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.kendrick_mass", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.kendrick_mass", "kind": "variable", "doc": "Return the Kendrick mass values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.max_mz_exp", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.max_mz_exp", "kind": "variable", "doc": "Return the maximum experimental m/z value of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.min_mz_exp", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.min_mz_exp", "kind": "variable", "doc": "Return the minimum experimental m/z value of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.max_abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.max_abundance", "kind": "variable", "doc": "Return the maximum abundance value of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.max_signal_to_noise", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.max_signal_to_noise", "kind": "variable", "doc": "Return the maximum signal-to-noise ratio of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.most_abundant_mspeak", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.most_abundant_mspeak", "kind": "variable", "doc": "Return the most abundant MSpeak object of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.min_abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.min_abundance", "kind": "variable", "doc": "Return the minimum abundance value of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.dynamic_range", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.dynamic_range", "kind": "variable", "doc": "Return the dynamic range of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.baseline_noise", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.baseline_noise", "kind": "variable", "doc": "Return the baseline noise of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.baseline_noise_std", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.baseline_noise_std", "kind": "variable", "doc": "Return the standard deviation of the baseline noise of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.Aterm", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.Aterm", "kind": "variable", "doc": "Return the A-term calibration coefficient of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.Bterm", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.Bterm", "kind": "variable", "doc": "Return the B-term calibration coefficient of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.Cterm", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.Cterm", "kind": "variable", "doc": "Return the C-term calibration coefficient of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filename", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filename", "kind": "variable", "doc": "Return the filename of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.dir_location", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.dir_location", "kind": "variable", "doc": "Return the directory location of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.sort_by_mz", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.sort_by_mz", "kind": "function", "doc": "Sort the mass spectrum by m/z values.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.sort_by_abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.sort_by_abundance", "kind": "function", "doc": "Sort the mass spectrum by abundance values.
\n", "signature": "(self, reverse=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.tic", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.tic", "kind": "variable", "doc": "Return the total ion current of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.check_mspeaks_warning", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.check_mspeaks_warning", "kind": "function", "doc": "Check if the mass spectrum has MSpeaks objects.
\n\nRaises
\n\n\n- Warning: If the mass spectrum has no MSpeaks objects.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.check_mspeaks", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.check_mspeaks", "kind": "function", "doc": "Check if the mass spectrum has MSpeaks objects.
\n\nRaises
\n\n\n- Exception: If the mass spectrum has no MSpeaks objects.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.remove_assignment_by_index", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.remove_assignment_by_index", "kind": "function", "doc": "Remove the molecular formula assignment of the MSpeaks objects at the specified indexes.
\n\nParameters
\n\n\n- indexes (list of int):\nA list of indexes of the MSpeaks objects to remove the molecular formula assignment from.
\n
\n", "signature": "(self, indexes):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_index", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_index", "kind": "function", "doc": "Filter the mass spectrum by the specified indexes.
\n\nParameters
\n\n\n- list_indexes (list of int):\nA list of indexes of the MSpeaks objects to keep.
\n
\n", "signature": "(self, list_indexes):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_mz", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_mz", "kind": "function", "doc": "Filter the mass spectrum by the specified m/z range.
\n\nParameters
\n\n\n- min_mz (float):\nThe minimum m/z value to keep.
\n- max_mz (float):\nThe maximum m/z value to keep.
\n
\n", "signature": "(self, min_mz, max_mz):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_s2n", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_s2n", "kind": "function", "doc": "Filter the mass spectrum by the specified signal-to-noise ratio range.
\n\nParameters
\n\n\n- min_s2n (float):\nThe minimum signal-to-noise ratio to keep.
\n- max_s2n (float, optional):\nThe maximum signal-to-noise ratio to keep. Defaults to False (no maximum).
\n
\n", "signature": "(self, min_s2n, max_s2n=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_abundance", "kind": "function", "doc": "Filter the mass spectrum by the specified abundance range.
\n\nParameters
\n\n\n- min_abund (float):\nThe minimum abundance to keep.
\n- max_abund (float, optional):\nThe maximum abundance to keep. Defaults to False (no maximum).
\n
\n", "signature": "(self, min_abund, max_abund=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_max_resolving_power", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_max_resolving_power", "kind": "function", "doc": "Filter the mass spectrum by the specified maximum resolving power.
\n\nParameters
\n\n\nB (float):
T (float):
\n", "signature": "(self, B, T):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_mean_resolving_power", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_mean_resolving_power", "kind": "function", "doc": "Filter the mass spectrum by the specified mean resolving power.
\n\nParameters
\n\n\n- ndeviations (float, optional):\nThe number of standard deviations to use for filtering. Defaults to 3.
\n- plot (bool, optional):\nWhether to plot the resolving power distribution. Defaults to False.
\n- guess_pars (bool, optional):\nWhether to guess the parameters for the Gaussian model. Defaults to False.
\n
\n", "signature": "(self, ndeviations=3, plot=False, guess_pars=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_min_resolving_power", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_min_resolving_power", "kind": "function", "doc": "Filter the mass spectrum by the specified minimum resolving power.
\n\nParameters
\n\n\nB (float):
T (float):
\n", "signature": "(self, B, T):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.filter_by_noise_threshold", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.filter_by_noise_threshold", "kind": "function", "doc": "Filter the mass spectrum by the noise threshold.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.find_peaks", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.find_peaks", "kind": "function", "doc": "Find the peaks of the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.change_kendrick_base_all_mspeaks", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.change_kendrick_base_all_mspeaks", "kind": "function", "doc": "Change the Kendrick base of all MSpeaks objects.
\n\nParameters
\n\n\n- kendrick_dict_base (dict):\nA dictionary of the Kendrick base to change to.
\n
\n\nNotes
\n\nExample of kendrick_dict_base parameter: kendrick_dict_base = {\"C\": 1, \"H\": 2} or {\"C\": 1, \"H\": 1, \"O\":1} etc
\n", "signature": "(self, kendrick_dict_base):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.get_nominal_mz_first_last_indexes", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.get_nominal_mz_first_last_indexes", "kind": "function", "doc": "Return the first and last indexes of the MSpeaks objects with the specified nominal mass.
\n\nParameters
\n\n\n- nominal_mass (int):\nThe nominal mass to get the indexes for.
\n
\n\nReturns
\n\n\n- tuple: A tuple containing the first and last indexes of the MSpeaks objects with the specified nominal mass.
\n
\n", "signature": "(self, nominal_mass):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.get_masses_count_by_nominal_mass", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.get_masses_count_by_nominal_mass", "kind": "function", "doc": "Return a dictionary of the nominal masses and their counts.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.datapoints_count_by_nominal_mz", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.datapoints_count_by_nominal_mz", "kind": "function", "doc": "Return a dictionary of the nominal masses and their counts.
\n\nParameters
\n\n\n- mz_overlay (float, optional):\nThe m/z overlay to use for counting. Defaults to 0.1.
\n
\n\nReturns
\n\n\n- dict: A dictionary of the nominal masses and their counts.
\n
\n", "signature": "(self, mz_overlay=0.1):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.get_nominal_mass_indexes", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.get_nominal_mass_indexes", "kind": "function", "doc": "Return the indexes of the MSpeaks objects with the specified nominal mass.
\n\nParameters
\n\n\n- nominal_mass (int):\nThe nominal mass to get the indexes for.
\n- overlay (float, optional):\nThe m/z overlay to use for counting. Defaults to 0.1.
\n
\n\nReturns
\n\n\n- generator: A generator of the indexes of the MSpeaks objects with the specified nominal mass.
\n
\n", "signature": "(self, nominal_mass, overlay=0.1):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.plot_centroid", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.plot_centroid", "kind": "function", "doc": "Plot the centroid data of the mass spectrum.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nThe matplotlib axes to plot on. Defaults to None.
\n- c (str, optional):\nThe color to use for the plot. Defaults to 'g' (green).
\n
\n\nReturns
\n\n\n- matplotlib.axes.Axes: The matplotlib axes containing the plot.
\n
\n\nRaises
\n\n\n- Exception: If no centroid data is found.
\n
\n", "signature": "(self, ax=None, c='g'):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.plot_profile_and_noise_threshold", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.plot_profile_and_noise_threshold", "kind": "function", "doc": "Plot the profile data and noise threshold of the mass spectrum.
\n\nParameters
\n\n\n- ax (matplotlib.axes.Axes, optional):\nThe matplotlib axes to plot on. Defaults to None.
\n- legend (bool, optional):\nWhether to show the legend. Defaults to False.
\n
\n\nReturns
\n\n\n- matplotlib.axes.Axes: The matplotlib axes containing the plot.
\n
\n\nRaises
\n\n\n- Exception: If no noise threshold is found.
\n
\n", "signature": "(self, ax=None, legend=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.plot_mz_domain_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.plot_mz_domain_profile", "kind": "function", "doc": "Plot the m/z domain profile of the mass spectrum.
\n\nParameters
\n\n\n- color (str, optional):\nThe color to use for the plot. Defaults to 'green'.
\n- ax (matplotlib.axes.Axes, optional):\nThe matplotlib axes to plot on. Defaults to None.
\n
\n\nReturns
\n\n\n- matplotlib.axes.Axes: The matplotlib axes containing the plot.
\n
\n", "signature": "(self, color='green', ax=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_excel", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_excel", "kind": "function", "doc": "Export the mass spectrum to an Excel file.
\n\nParameters
\n\n\n- out_file_path (str):\nThe path to the Excel file to export to.
\n- write_metadata (bool, optional):\nWhether to write the metadata to the Excel file. Defaults to True.
\n
\n\nReturns
\n\n\n", "signature": "(self, out_file_path, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_hdf", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_hdf", "kind": "function", "doc": "Export the mass spectrum to an HDF file.
\n\nParameters
\n\n\n- out_file_path (str):\nThe path to the HDF file to export to.
\n
\n\nReturns
\n\n\n", "signature": "(self, out_file_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_csv", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_csv", "kind": "function", "doc": "Export the mass spectrum to a CSV file.
\n\nParameters
\n\n\n- out_file_path (str):\nThe path to the CSV file to export to.
\n- write_metadata (bool, optional):\nWhether to write the metadata to the CSV file. Defaults to True.
\n
\n", "signature": "(self, out_file_path, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_pandas", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_pandas", "kind": "function", "doc": "Export the mass spectrum to a Pandas dataframe with pkl extension.
\n\nParameters
\n\n\n- out_file_path (str):\nThe path to the CSV file to export to.
\n- write_metadata (bool, optional):\nWhether to write the metadata to the CSV file. Defaults to True.
\n
\n", "signature": "(self, out_file_path, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_dataframe", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_dataframe", "kind": "function", "doc": "Return the mass spectrum as a Pandas dataframe.
\n\nReturns
\n\n\n- pandas.DataFrame: The mass spectrum as a Pandas dataframe.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.to_json", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.to_json", "kind": "function", "doc": "Return the mass spectrum as a JSON file.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.parameters_json", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.parameters_json", "kind": "function", "doc": "Return the parameters of the mass spectrum as a JSON string.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecBase.parameters_toml", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecBase.parameters_toml", "kind": "function", "doc": "Return the parameters of the mass spectrum as a TOML string.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecProfile", "kind": "class", "doc": "A mass spectrum class when the entry point is on profile format
\n\nNotes
\n\nStores the profile data and instrument settings. \nIteration over a list of MSPeaks classes stored at the _mspeaks attributes.\n_mspeaks is populated under the hood by calling process_mass_spec method.\nIteration is null if _mspeaks is empty. Many more attributes and methods inherited from MassSpecBase().
\n\nParameters
\n\n\n- data_dict (dict):\nA dictionary containing the profile data.
\n- d_params : dict{'str' (float, int or str}):\ncontains the instrument settings and processing settings
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectrum. Defaults to True.
\n
\n\nAttributes
\n\n_abundance : ndarray\n The abundance values of the mass spectrum.\n_mz_exp : ndarray\n The m/z values of the mass spectrum.\n_mspeaks : list\n A list of mass peaks.
\n\nMethods
\n\n\n- process_mass_spec(). Process the mass spectrum.
\n
\n\nsee also: MassSpecBase(), MassSpecfromFreq(), MassSpecCentroid()
\n", "bases": "MassSpecBase"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile.__init__", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecProfile.__init__", "kind": "function", "doc": "\n", "signature": "(data_dict, d_params, auto_process=True)"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq", "kind": "class", "doc": "A mass spectrum class when data entry is on frequency domain
\n\nNotes
\n\n\n- Transform to m/z based on the settings stored at d_params
\n- Stores the profile data and instrument settings
\n- Iteration over a list of MSPeaks classes stored at the _mspeaks attributes
\n- _mspeaks is populated under the hood by calling process_mass_spec method
\n- iteration is null if _mspeaks is empty
\n
\n\nParameters
\n\n\n- frequency_domain (list(float)):\nall datapoints in frequency domain in Hz
\n- magnitude : frequency_domain (list(float)):\nall datapoints in for magnitude of each frequency datapoint
\n- d_params : dict{'str' (float, int or str}):\ncontains the instrument settings and processing settings
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectrum. Defaults to True.
\n- keep_profile (bool, optional):\nWhether to keep the profile data. Defaults to True.
\n
\n\nAttributes
\n\n\n- has_frequency (bool):\nWhether the mass spectrum has frequency data.
\n- _frequency_domain (list(float)):\nFrequency domain in Hz
\n- label (str):\nstore label (Bruker, Midas Transient, see Labels class ). It across distinct processing points
\n- _abundance (ndarray):\nThe abundance values of the mass spectrum.
\n- _mz_exp (ndarray):\nThe m/z values of the mass spectrum.
\n- _mspeaks (list):\nA list of mass peaks.
\n- See Also (all the attributes of MassSpecBase class):
\n
\n\nMethods
\n\n\n- _set_mz_domain().\ncalculates the m_z based on the setting of d_params
\n- process_mass_spec(). Process the mass spectrum.
\n
\n\nsee also: MassSpecBase(), MassSpecProfile(), MassSpecCentroid()
\n", "bases": "MassSpecBase"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.__init__", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.__init__", "kind": "function", "doc": "\n", "signature": "(\tfrequency_domain,\tmagnitude,\td_params,\tauto_process=True,\tkeep_profile=True)"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.has_frequency", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.has_frequency", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.magnetron_frequency", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.magnetron_frequency", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.magnetron_frequency_sigma", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.magnetron_frequency_sigma", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.transient_settings", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.transient_settings", "kind": "variable", "doc": "Return the transient settings of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq.calc_magnetron_freq", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecfromFreq.calc_magnetron_freq", "kind": "function", "doc": "Calculates the magnetron frequency of the mass spectrum.
\n\nParameters
\n\n\n- max_magnetron_freq (float, optional):\nThe maximum magnetron frequency. Defaults to 50.
\n- magnetron_freq_bins (int, optional):\nThe number of bins to use for the histogram. Defaults to 300.
\n
\n\nReturns
\n\n\n\nNotes
\n\nCalculates the magnetron frequency by examining all the picked peaks and the distances between them in the frequency domain.\nA histogram of those values below the threshold 'max_magnetron_freq' with the 'magnetron_freq_bins' number of bins is calculated.\nA gaussian model is fit to this histogram - the center value of this (statistically probably) the magnetron frequency.\nThis appears to work well or nOmega datasets, but may not work well for 1x datasets or those with very low magnetron peaks.
\n", "signature": "(self, max_magnetron_freq=50, magnetron_freq_bins=300):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid", "kind": "class", "doc": "A mass spectrum class when the entry point is on centroid format
\n\nNotes
\n\n\n- Stores the centroid data and instrument settings
\n- Simulate profile data based on Gaussian or Lorentzian peak shape
\n- Iteration over a list of MSPeaks classes stored at the _mspeaks attributes
\n- _mspeaks is populated under the hood by calling process_mass_spec method
\n- iteration is null if _mspeaks is empty
\n
\n\nParameters
\n\n\n- data_dict : dict {string (numpy array float64 )):\ncontains keys [m/z, Abundance, Resolving Power, S/N]
\n- d_params : dict{'str' (float, int or str}):\ncontains the instrument settings and processing settings
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectrum. Defaults to True.
\n
\n\nAttributes
\n\n\n- label (str):\nstore label (Bruker, Midas Transient, see Labels class)
\n- _baseline_noise (float):\nstore baseline noise
\n- _baseline_noise_std (float):\nstore baseline noise std
\n- _abundance (ndarray):\nThe abundance values of the mass spectrum.
\n- _mz_exp (ndarray):\nThe m/z values of the mass spectrum.
\n- _mspeaks (list):\nA list of mass peaks.
\n
\n\nMethods
\n\n\n- process_mass_spec().\nProcess the mass spectrum. Overriden from MassSpecBase. Populates the _mspeaks list with MSpeaks class using the centroid data.
\n- __simulate_profile__data__().\nSimulate profile data based on Gaussian or Lorentzian peak shape. Needs theoretical resolving power calculation and define peak shape, intended for plotting and inspection purposes only.
\n
\n\nsee also: MassSpecBase(), MassSpecfromFreq(), MassSpecProfile()
\n", "bases": "MassSpecBase"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.__init__", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.__init__", "kind": "function", "doc": "\n", "signature": "(data_dict, d_params, auto_process=True)"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.is_centroid", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.is_centroid", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.data_dict", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.data_dict", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.mz_exp_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.mz_exp_profile", "kind": "variable", "doc": "Return the m/z profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.abundance_profile", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.abundance_profile", "kind": "variable", "doc": "Return the abundance profile of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.tic", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.tic", "kind": "variable", "doc": "Return the total ion current of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid.process_mass_spec", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroid.process_mass_spec", "kind": "function", "doc": "Process the mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes", "kind": "class", "doc": "A mass spectrum class when the entry point is on low resolution centroid format
\n\nNotes
\n\nDoes not store MSPeak Objs, will iterate over mz, abundance pairs instead
\n\nParameters
\n\n\n- data_dict : dict {string (numpy array float64 )):\ncontains keys [m/z, Abundance, Resolving Power, S/N]
\n- d_params : dict{'str' (float, int or str}):\ncontains the instrument settings and processing settings
\n
\n\nAttributes
\n\n\n- _processed_tic (float):\nstore processed total ion current
\n- _abundance (ndarray):\nThe abundance values of the mass spectrum.
\n- _mz_exp (ndarray):\nThe m/z values of the mass spectrum.
\n
\n", "bases": "MassSpecCentroid"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.__init__", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.__init__", "kind": "function", "doc": "\n", "signature": "(data_dict, d_params)"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.mz_exp", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.mz_exp", "kind": "variable", "doc": "Return the m/z values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.abundance", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.abundance", "kind": "variable", "doc": "Return the abundance values of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.processed_tic", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.processed_tic", "kind": "variable", "doc": "Return the processed total ion current of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.tic", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.tic", "kind": "variable", "doc": "Return the total ion current of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.mz_abun_tuples", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.mz_abun_tuples", "kind": "variable", "doc": "Return the m/z and abundance values of the mass spectrum as a list of tuples.
\n"}, {"fullname": "corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroidLowRes.mz_abun_dict", "modulename": "corems.mass_spectrum.factory.MassSpectrumClasses", "qualname": "MassSpecCentroidLowRes.mz_abun_dict", "kind": "variable", "doc": "Return the m/z and abundance values of the mass spectrum as a dictionary.
\n"}, {"fullname": "corems.mass_spectrum.input", "modulename": "corems.mass_spectrum.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass", "modulename": "corems.mass_spectrum.input.baseClass", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass", "kind": "class", "doc": "The MassListBaseClass object reads mass list data types and returns the mass spectrum obj
\n\nParameters
\n\n\n- file_location (Path or S3Path):\nFull data path.
\n- isCentroid (bool, optional):\nDetermines the mass spectrum data structure. If set to True, it assumes centroid mode. If set to False, it assumes profile mode and attempts to peak pick. Default is True.
\n- analyzer (str, optional):\nThe analyzer used for the mass spectrum. Default is 'Unknown'.
\n- instrument_label (str, optional):\nThe label of the instrument used for the mass spectrum. Default is 'Unknown'.
\n- sample_name (str, optional):\nThe name of the sample. Default is None.
\n- header_lines (int, optional):\nThe number of lines to skip in the file, including the column labels line. Default is 0.
\n- isThermoProfile (bool, optional):\nDetermines the number of expected columns in the file. If set to True, only m/z and intensity columns are expected. Signal-to-noise ratio (S/N) and resolving power (RP) will be calculated based on the data. Default is False.
\n- headerless (bool, optional):\nIf True, assumes that there are no headers present in the file (e.g., a .xy file from Bruker) and assumes two columns: m/z and intensity. Default is False.
\n
\n\nAttributes
\n\n\n- parameters (DataInputSetting):\nThe data input settings for the mass spectrum.
\n- data_type (str):\nThe type of data in the file.
\n- delimiter (str):\nThe delimiter used to read text-based files.
\n
\n\nMethods
\n\n\n- set_parameter_from_toml(parameters_path). Sets the data input settings from a TOML file.
\n- set_parameter_from_json(parameters_path). Sets the data input settings from a JSON file.
\n- get_dataframe(). Reads the file and returns the data as a pandas DataFrame.
\n- load_settings(mass_spec_obj, output_parameters). Loads the settings for the mass spectrum.
\n- get_output_parameters(polarity, scan_index=0). Returns the output parameters for the mass spectrum.
\n- clean_data_frame(dataframe). Cleans the data frame by removing columns that are not in the expected columns set.
\n
\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.__init__", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.__init__", "kind": "function", "doc": "\n", "signature": "(\tfile_location: pathlib.Path | s3path.S3Path,\tisCentroid: bool = True,\tanalyzer: str = 'Unknown',\tinstrument_label: str = 'Unknown',\tsample_name: str = None,\theader_lines: int = 0,\tisThermoProfile: bool = False,\theaderless: bool = False)"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.file_location", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.header_lines", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.header_lines", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.isCentroid", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.isCentroid", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.isThermoProfile", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.isThermoProfile", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.headerless", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.headerless", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.analyzer", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.analyzer", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.instrument_label", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.instrument_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.sample_name", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.sample_name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.parameters", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.parameters", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.set_parameter_from_toml", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.set_parameter_from_toml", "kind": "function", "doc": "\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.set_parameter_from_json", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.set_parameter_from_json", "kind": "function", "doc": "\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.data_type", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.data_type", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.delimiter", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.delimiter", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.encoding_detector", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.encoding_detector", "kind": "function", "doc": "Detects the encoding of a file.
\n\nParameters
\n\n\n- file_location (str):\nThe location of the file to be analyzed.
\n
\n\nReturns
\n\n\n- str: The detected encoding of the file.
\n
\n", "signature": "(self, file_location) -> str:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.set_data_type", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.set_data_type", "kind": "function", "doc": "Set the data type and delimiter based on the file extension.
\n\nRaises
\n\n\n- TypeError: If the data type could not be automatically recognized.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.get_dataframe", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.get_dataframe", "kind": "function", "doc": "Get the data as a pandas DataFrame.
\n\nReturns
\n\n\n- pandas.DataFrame: The data as a pandas DataFrame.
\n
\n\nRaises
\n\n\n- TypeError: If the data type is not supported.
\n
\n", "signature": "(self) -> pandas.core.frame.DataFrame:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.load_settings", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.load_settings", "kind": "function", "doc": "TODO loading output parameters from json file is not functional
\n\nLoad settings from a JSON file and apply them to the given mass_spec_obj.
\n\nParameters
\n\n\n- mass_spec_obj (MassSpec):\nThe mass spectrum object to apply the settings to.
\n
\n", "signature": "(self, mass_spec_obj, output_parameters):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.get_output_parameters", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.get_output_parameters", "kind": "function", "doc": "Get the output parameters for the mass spectrum.
\n\nParameters
\n\n\n- polarity (int):\nThe polarity of the mass spectrum +1 or -1.
\n- scan_index (int, optional):\nThe index of the scan. Default is 0.
\n
\n\nReturns
\n\n\n- dict: A dictionary containing the output parameters.
\n
\n", "signature": "(self, polarity: int, scan_index: int = 0) -> dict:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.clean_data_frame", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.clean_data_frame", "kind": "function", "doc": "Clean the input dataframe by removing columns that are not expected.
\n\nParameters
\n\n\n- pandas.DataFrame: The input dataframe to be cleaned.
\n
\n", "signature": "(self, dataframe):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.check_columns", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.check_columns", "kind": "function", "doc": "Check if the given header labels match the expected columns.
\n\nParameters
\n\n\n- header_labels (list):\nThe header labels to be checked.
\n
\n\nRaises
\n\n\n- Exception: If any expected column is not found in the header labels.
\n
\n", "signature": "(self, header_labels: list[str]):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.read_xml_peaks", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.read_xml_peaks", "kind": "function", "doc": "Read peaks from a Bruker .xml file and return a pandas DataFrame.
\n\nParameters
\n\n\n- data (str):\nThe path to the .xml file.
\n
\n\nReturns
\n\n\n- pandas.DataFrame: A DataFrame containing the peak data with columns: 'm/z', 'I', 'Resolving Power', 'Area', 'S/N', 'fwhm'.
\n
\n", "signature": "(self, data: str) -> pandas.core.frame.DataFrame:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.baseClass.MassListBaseClass.get_xml_polarity", "modulename": "corems.mass_spectrum.input.baseClass", "qualname": "MassListBaseClass.get_xml_polarity", "kind": "function", "doc": "Get the polarity from an XML peaklist.
\n\nReturns
\n\n\n- int: The polarity of the XML peaklist. Returns -1 for negative polarity, +1 for positive polarity.
\n
\n\nRaises
\n\n\n- Exception: If the data type is not XML peaklist in Bruker format or if the polarity is unhandled.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5", "modulename": "corems.mass_spectrum.input.boosterHDF5", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum", "kind": "class", "doc": "The ReadHDF_BoosterMassSpectrum class parses the mass spectrum data from an HDF file and generate a mass spectrum object.
\n\nParameters
\n\n\n- file_location (str):\nThe path to the HDF file.
\n- isCentroid (bool, optional):\nSpecifies whether the mass spectrum is centroided or not. Default is False.
\n
\n\nAttributes
\n\n\n- polarity (int):\nThe polarity of the mass spectrum.
\n- h5pydata (h5py.File):\nThe HDF file object.
\n- scans (list):\nThe list of scan names in the HDF file.
\n
\n\nMethods
\n\n\n- get_data_profile(mz, abundance, auto_process). Returns a MassSpecProfile object from the given m/z and abundance arrays.
\n- get_attr_data(scan, attr_srt). Returns the attribute value for the given scan and attribute name.
\n- get_polarity(file_location). Returns the polarity of the mass spectrum.
\n- get_mass_spectrum(auto_process). Returns the mass spectrum as a MassSpecProfile object.
\n- get_output_parameters(). Returns the default output parameters for the mass spectrum.
\n
\n", "bases": "corems.mass_spectrum.input.baseClass.MassListBaseClass"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.__init__", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.__init__", "kind": "function", "doc": "\n", "signature": "(file_location, isCentroid=False)"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.polarity", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.polarity", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.get_data_profile", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.get_data_profile", "kind": "function", "doc": "Returns a MassSpecProfile object from the given m/z and abundance arrays.
\n\nParameters
\n\n\n- mz (array_like):\nThe m/z values.
\n- abundance (array_like):\nThe abundance values.
\n- auto_process (bool):\nSpecifies whether to automatically process the mass spectrum.
\n
\n\nReturns
\n\n\n- MassSpecProfile: The MassSpecProfile object.
\n
\n", "signature": "(\tself,\tmz,\tabundance,\tauto_process) -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.get_attr_data", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.get_attr_data", "kind": "function", "doc": "Returns the attribute value for the given scan and attribute name.
\n\nParameters
\n\n\n- scan (int):\nThe scan index.
\n- attr_srt (str):\nThe attribute name.
\n
\n\nReturns
\n\n\n- object: The attribute value.
\n
\n", "signature": "(self, scan, attr_srt):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.get_polarity", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.get_polarity", "kind": "function", "doc": "Returns the polarity of the mass spectrum.
\n\nParameters
\n\n\n- file_location (str):\nThe path to the HDF file.
\n
\n\nReturns
\n\n\n- int: The polarity of the mass spectrum.
\n
\n", "signature": "(self, file_location: str | s3path.S3Path) -> int:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.get_mass_spectrum", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.get_mass_spectrum", "kind": "function", "doc": "Returns the mass spectrum as a MassSpecProfile object.
\n\nParameters
\n\n\n- auto_process (bool, optional):\nSpecifies whether to automatically process the mass spectrum. Default is True.
\n
\n\nReturns
\n\n\n- MassSpecProfile: The MassSpecProfile object.
\n
\n", "signature": "(\tself,\tauto_process=True) -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecProfile:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.boosterHDF5.ReadHDF_BoosterMassSpectrum.get_output_parameters", "modulename": "corems.mass_spectrum.input.boosterHDF5", "qualname": "ReadHDF_BoosterMassSpectrum.get_output_parameters", "kind": "function", "doc": "Returns the default output parameters for the mass spectrum.
\n\nReturns
\n\n\n- dict: The default output parameters.
\n
\n", "signature": "(self) -> dict:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5", "modulename": "corems.mass_spectrum.input.coremsHDF5", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum", "kind": "class", "doc": "Class for reading mass spectrum data from a CoreMS HDF5 file.
\n\nAttributes
\n\n\n- h5pydata (h5py.File):\nThe HDF5 file object.
\n- scans (list):\nList of scan labels in the HDF5 file.
\n
\n\nParameters
\n\n\n- file_location (str or S3Path):\nThe path to the CoreMS HDF5 file.
\n
\n\nMethods
\n\n\n- load_raw_data(mass_spectrum, scan_index=0) Load raw data into the mass spectrum object.
\n- get_mass_spectrum(scan_number=0, time_index=-1, auto_process=True, load_settings=True, load_raw=True).Get a mass spectrum object.
\n- load_settings(mass_spectrum, scan_index=0, time_index=-1). Load settings into the mass spectrum object.
\n- get_dataframe(scan_index=0, time_index=-1). Get a pandas DataFrame representing the mass spectrum.
\n- get_time_index_to_pull(scan_label, time_index). Get the time index to pull from the HDF5 file.
\n- get_high_level_attr_data(attr_str). Get high-level attribute data from the HDF5 file.
\n- get_scan_group_attr_data(scan_index, time_index, attr_group, attr_srt=None). Get scan group attribute data from the HDF5 file.
\n- get_raw_data_attr_data(scan_index, attr_group, attr_str). Get raw data attribute data from the HDF5 file.
\n- get_output_parameters(polarity, scan_index=0). Get the output parameters for the mass spectrum.
\n
\n", "bases": "corems.mass_spectrum.input.massList.ReadCoremsMasslist"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.__init__", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.__init__", "kind": "function", "doc": "\n", "signature": "(file_location)"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.h5pydata", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.h5pydata", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.scans", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.scans", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.load_raw_data", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.load_raw_data", "kind": "function", "doc": "Load raw data into the mass spectrum object.
\n\nParameters
\n\n\n- mass_spectrum (MassSpecCentroid):\nThe mass spectrum object to load the raw data into.
\n- scan_index (int, optional):\nThe index of the scan to load the raw data from. Default is 0.
\n
\n", "signature": "(self, mass_spectrum, scan_index=0):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_mass_spectrum", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_mass_spectrum", "kind": "function", "doc": "Get a mass spectrum object.
\n\nParameters
\n\n\n- scan_number (int, optional):\nThe index of the scan to retrieve the mass spectrum from. Default is 0.
\n- time_index (int, optional):\nThe index of the time point to retrieve the mass spectrum from. Default is -1.
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectrum. Default is True.
\n- load_settings (bool, optional):\nWhether to load the settings into the mass spectrum object. Default is True.
\n- load_raw (bool, optional):\nWhether to load the raw data into the mass spectrum object. Default is True.
\n
\n\nReturns
\n\n\n- MassSpecCentroid: The mass spectrum object.
\n
\n", "signature": "(\tself,\tscan_number=0,\ttime_index=-1,\tauto_process=True,\tload_settings=True,\tload_raw=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.load_settings", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.load_settings", "kind": "function", "doc": "Load settings into the mass spectrum object.
\n\nParameters
\n\n\n- mass_spectrum (MassSpecCentroid):\nThe mass spectrum object to load the settings into.
\n- scan_index (int, optional):\nThe index of the scan to load the settings from. Default is 0.
\n- time_index (int, optional):\nThe index of the time point to load the settings from. Default is -1.
\n
\n", "signature": "(self, mass_spectrum, scan_index=0, time_index=-1):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_dataframe", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_dataframe", "kind": "function", "doc": "Get a pandas DataFrame representing the mass spectrum.
\n\nParameters
\n\n\n- scan_index (int, optional):\nThe index of the scan to retrieve the DataFrame from. Default is 0.
\n- time_index (int, optional):\nThe index of the time point to retrieve the DataFrame from. Default is -1.
\n
\n\nReturns
\n\n\n- DataFrame: The pandas DataFrame representing the mass spectrum.
\n
\n", "signature": "(self, scan_index=0, time_index=-1):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_time_index_to_pull", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_time_index_to_pull", "kind": "function", "doc": "Get the time index to pull from the HDF5 file.
\n\nParameters
\n\n\n- scan_label (str):\nThe label of the scan.
\n- time_index (int):\nThe index of the time point.
\n
\n\nReturns
\n\n\n- str: The time index to pull.
\n
\n", "signature": "(self, scan_label, time_index):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_high_level_attr_data", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_high_level_attr_data", "kind": "function", "doc": "Get high-level attribute data from the HDF5 file.
\n\nParameters
\n\n\n- attr_str (str):\nThe attribute string.
\n
\n\nReturns
\n\n\n- dict: The attribute data.
\n
\n\nRaises
\n\n\n- KeyError: If the attribute string is not found in the HDF5 file.
\n
\n", "signature": "(self, attr_str):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_scan_group_attr_data", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_scan_group_attr_data", "kind": "function", "doc": "Get scan group attribute data from the HDF5 file.
\n\nParameters
\n\n\n- scan_index (int):\nThe index of the scan.
\n- time_index (int):\nThe index of the time point.
\n- attr_group (str):\nThe attribute group.
\n- attr_srt (str, optional):\nThe attribute string. Default is None.
\n
\n\nReturns
\n\n\n- dict: The attribute data.
\n
\n\nNotes
\n\nThis method retrieves attribute data from the HDF5 file for a specific scan and time point.\nThe attribute data is stored in the specified attribute group.\nIf an attribute string is provided, only the corresponding attribute value is returned.\nIf no attribute string is provided, all attribute data in the group is returned as a dictionary.
\n", "signature": "(self, scan_index, time_index, attr_group, attr_srt=None):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.coremsHDF5.ReadCoreMSHDF_MassSpectrum.get_raw_data_attr_data", "modulename": "corems.mass_spectrum.input.coremsHDF5", "qualname": "ReadCoreMSHDF_MassSpectrum.get_raw_data_attr_data", "kind": "function", "doc": "Get raw data attribute data from the HDF5 file.
\n\nParameters
\n\n\n- scan_index (int):\nThe index of the scan.
\n- attr_group (str):\nThe attribute group.
\n- attr_str (str):\nThe attribute string.
\n
\n\nReturns
\n\n\n- dict: The attribute data.
\n
\n\nRaises
\n\n\n- KeyError: If the attribute string is not found in the attribute group.
\n
\n\nNotes
\n\nThis method retrieves the attribute data associated with a specific scan, attribute group, and attribute string\nfrom the HDF5 file. It returns the attribute data as a dictionary.
\n\nExample usage:
\n\n\n
>>> data = get_raw_data_attr_data(0, "group1", "attribute1")\n>>> print(data)\n{'key1': 'value1', 'key2': 'value2'}\n
\n
Get the output parameters for the mass spectrum.
\n\nParameters
\n\n\n- polarity (str):\nThe polarity of the mass spectrum.
\n- scan_index (int, optional):\nThe index of the scan. Default is 0.
\n
\n\nReturns
\n\n\n- dict: The output parameters.
\n
\n", "signature": "(self, polarity, scan_index=0):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.massList", "modulename": "corems.mass_spectrum.input.massList", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.massList.ReadCoremsMasslist", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadCoremsMasslist", "kind": "class", "doc": "The ReadCoremsMasslist object reads processed mass list data types\nand returns the mass spectrum obj with the molecular formula obj
\n\nOnly available for centroid mass spectrum type: it will ignore the parameter isCentroid \nPlease see MassListBaseClass for more details
\n", "bases": "corems.mass_spectrum.input.baseClass.MassListBaseClass"}, {"fullname": "corems.mass_spectrum.input.massList.ReadCoremsMasslist.get_mass_spectrum", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadCoremsMasslist.get_mass_spectrum", "kind": "function", "doc": "Get the mass spectrum object from the processed mass list data.
\n\nParameters
\n\n\n- loadSettings (bool, optional):\nWhether to load the settings for the mass spectrum. Default is True.
\n
\n\nReturns
\n\n\n- MassSpecCentroid: The mass spectrum object.
\n
\n\nRaises
\n\n\n- ValueError: If the input file is not a valid CoreMS file.
\n
\n", "signature": "(\tself,\tloadSettings: bool = True) -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecCentroid:", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.massList.ReadCoremsMasslist.add_molecular_formula", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadCoremsMasslist.add_molecular_formula", "kind": "function", "doc": "Add molecular formula information to the mass spectrum object.
\n\nParameters
\n\n\n- mass_spec_obj (MassSpecCentroid):\nThe mass spectrum object to add the molecular formula to.
\n- dataframe (pandas.DataFrame):\nThe processed mass list data.
\n
\n", "signature": "(self, mass_spec_obj, dataframe):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.massList.ReadMassList", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadMassList", "kind": "class", "doc": "The ReadMassList object reads unprocessed mass list data types\nand returns the mass spectrum object.
\n\nParameters
\n\n\n- MassListBaseClass (class):\nThe base class for reading mass list data types.
\n
\n\nMethods
\n\n\n- get_mass_spectrum(polarity, scan=0, auto_process=True, loadSettings=True). Reads mass list data types and returns the mass spectrum object.
\n
\n", "bases": "corems.mass_spectrum.input.baseClass.MassListBaseClass"}, {"fullname": "corems.mass_spectrum.input.massList.ReadMassList.get_mass_spectrum", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadMassList.get_mass_spectrum", "kind": "function", "doc": "Reads mass list data types and returns the mass spectrum object.
\n\nParameters
\n\n\n- polarity (int):\nThe polarity of the mass spectrum (+1 or -1).
\n- scan (int, optional):\nThe scan number of the mass spectrum (default is 0).
\n- auto_process (bool, optional):\nFlag indicating whether to automatically process the mass spectrum (default is True).
\n- loadSettings (bool, optional):\nFlag indicating whether to load settings for the mass spectrum (default is True).
\n
\n\nReturns
\n\n\n- mass_spec (MassSpecCentroid or MassSpecProfile):\nThe mass spectrum object.
\n
\n", "signature": "(\tself,\tpolarity: int,\tscan: int = 0,\tauto_process: bool = True,\tloadSettings: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.massList.ReadBrukerXMLList", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadBrukerXMLList", "kind": "class", "doc": "The ReadBrukerXMLList object reads Bruker XML objects\nand returns the mass spectrum object.\nSee MassListBaseClass for details
\n\nParameters
\n\n\n- MassListBaseClass (class):\nThe base class for reading mass list data types and returning the mass spectrum object.
\n
\n\nMethods
\n\n\n- get_mass_spectrum(polarity: bool = None, scan: int = 0, auto_process: bool = True, loadSettings: bool = True). Reads mass list data types and returns the mass spectrum object.
\n
\n", "bases": "corems.mass_spectrum.input.baseClass.MassListBaseClass"}, {"fullname": "corems.mass_spectrum.input.massList.ReadBrukerXMLList.get_mass_spectrum", "modulename": "corems.mass_spectrum.input.massList", "qualname": "ReadBrukerXMLList.get_mass_spectrum", "kind": "function", "doc": "Reads mass list data types and returns the mass spectrum object.
\n\nParameters
\n\n\n- polarity (bool, optional):\nThe polarity of the mass spectrum. Can be +1 or -1. If not provided, it will be determined from the XML file.
\n- scan (int, optional):\nThe scan number of the mass spectrum. Default is 0.
\n- auto_process (bool, optional):\nWhether to automatically process the mass spectrum. Default is True.
\n- loadSettings (bool, optional):\nWhether to load the settings for the mass spectrum. Default is True.
\n
\n\nReturns
\n\n\n- mass_spec (MassSpecCentroid):\nThe mass spectrum object representing the centroided mass spectrum.
\n
\n", "signature": "(\tself,\tpolarity: bool = None,\tscan: int = 0,\tauto_process: bool = True,\tloadSettings: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.numpyArray", "modulename": "corems.mass_spectrum.input.numpyArray", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.input.numpyArray.ms_from_array_profile", "modulename": "corems.mass_spectrum.input.numpyArray", "qualname": "ms_from_array_profile", "kind": "function", "doc": "Create a MassSpecProfile object from an array of m/z values and abundance values.
\n\nParameters
\n\n\n- mz (numpy.ndarray):\nArray of m/z values.
\n- abundance (numpy.ndarray):\nArray of abundance values.
\n- dataname (str):\nName of the data.
\n- polarity (int, optional):\nPolarity of the data. The default is -1.
\n- auto_process (bool, optional):\nFlag to automatically process the data. The default is True.
\n- data_type (str, optional):\nType of the data. The default is Labels.simulated_profile.
\n
\n\nReturns
\n\n\n- MassSpecProfile: The created MassSpecProfile object.
\n
\n", "signature": "(\tmz,\tabundance,\tdataname: str,\tpolarity: int = -1,\tauto_process: bool = True,\tdata_type: str = 'Simulated Profile'):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.numpyArray.ms_from_array_centroid", "modulename": "corems.mass_spectrum.input.numpyArray", "qualname": "ms_from_array_centroid", "kind": "function", "doc": "Create a MassSpecCentroid object from an array of m/z values, abundance values, resolution power, and signal-to-noise ratio.
\n\nParameters
\n\n\n- mz (numpy.ndarray):\nArray of m/z values.
\n- abundance (numpy.ndarray):\nArray of abundance values.
\n- rp (list(float)):\nList of resolving power values.
\n- s2n (list(float)):\nList of signal-to-noise ratio values.
\n- dataname (str):\nName of the data.
\n- polarity (int, optional):\nPolarity of the data. The default is -1.
\n- auto_process (bool, optional):
\n
\n\nReturns
\n\n\n- MassSpecCentroid: The created MassSpecCentroid object.
\n
\n", "signature": "(\tmz,\tabundance,\trp: list[float],\ts2n: list[float],\tdataname: str,\tpolarity: int = -1,\tauto_process: bool = True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.numpyArray.get_output_parameters", "modulename": "corems.mass_spectrum.input.numpyArray", "qualname": "get_output_parameters", "kind": "function", "doc": "Generate the output parameters for creating a MassSpecProfile or MassSpecCentroid object.
\n\nParameters
\n\n\n- polarity (int):\nPolarity of the data.
\n- file_location (str):\nFile location.
\n
\n\nReturns
\n\n\n- dict: Output parameters.
\n
\n", "signature": "(polarity: int, file_location: str):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.input.win_only", "modulename": "corems.mass_spectrum.input.win_only", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output", "modulename": "corems.mass_spectrum.output", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output.export", "modulename": "corems.mass_spectrum.output.export", "kind": "module", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport", "kind": "class", "doc": "A class for exporting high-resolution mass spectra.
\n\nParameters
\n\n\n- out_file_path (str):\nThe output file path.
\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n- output_type (str, optional):\nThe type of output file. Defaults to 'excel'. Can be 'excel', 'csv', 'pandas' or 'hdf5'.
\n
\n\nAttributes
\n\n\n- output_file (Path):\nThe output file path.
\n- output_type (str):\nThe type of output file.
\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n- atoms_order_list (list):\nThe list of assigned atoms in the order specified by Atoms.atoms_order list.
\n- columns_label (list):\nThe column labels in order.
\n
\n\nMethods
\n\n\n- save().\nSave the mass spectrum data to the output file.
\n- run().\nRun the export process.
\n- get_pandas_df().\nReturns the mass spectrum data as a pandas DataFrame.
\n- write_settings(output_path, mass_spectrum).\nWrites the settings of the mass spectrum to a JSON file.
\n- to_pandas(write_metadata=True).\nExports the mass spectrum data to a pandas DataFrame and saves it as a pickle file.
\n- to_excel(write_metadata=True).\nExports the mass spectrum data to an Excel file.
\n- to_csv(write_metadata=True).\nExports the mass spectrum data to a CSV file.
\n- to_json().\nExports the mass spectrum data to a JSON string.
\n- to_hdf().\nExports the mass spectrum data to an HDF5 file.
\n- parameters_to_toml().\nConverts the mass spectrum parameters to a TOML string.
\n- parameters_to_json().\nConverts the mass spectrum parameters to a JSON string.
\n- get_mass_spec_attrs(mass_spectrum).\nReturns the mass spectrum attributes as a dictionary.
\n- get_all_used_atoms_in_order(mass_spectrum).\nReturns the list of assigned atoms in the order specified by Atoms.atoms_order list.
\n- list_dict_to_list(mass_spectrum, is_hdf5=False).\nReturns the mass spectrum data as a list of dictionaries.
\n- get_list_dict_data(mass_spectrum, include_no_match=True, include_isotopologues=True, isotopologue_inline=True, no_match_inline=False, is_hdf5=False).\nReturns the mass spectrum data as a list of dictionaries.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.__init__", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(out_file_path, mass_spectrum, output_type='excel')"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.output_file", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.output_file", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.output_type", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.output_type", "kind": "variable", "doc": "Returns the output type of the mass spectrum.
\n"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.mass_spectrum", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.mass_spectrum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.atoms_order_list", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.atoms_order_list", "kind": "variable", "doc": "\n"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.save", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.save", "kind": "function", "doc": "Save the mass spectrum data to the output file.
\n\nRaises
\n\n\n- ValueError: If the output type is not supported.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.run", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.run", "kind": "function", "doc": "Run the export process.
\n\nThis method is called when the thread starts.\nIt calls the save method to perform the export.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.get_pandas_df", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.get_pandas_df", "kind": "function", "doc": "Returns the mass spectrum data as a pandas DataFrame.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.write_settings", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.write_settings", "kind": "function", "doc": "Writes the settings of the mass spectrum to a JSON file.
\n\nParameters
\n\n\n- output_path (str):\nThe output file path.
\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n
\n", "signature": "(self, output_path, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.to_pandas", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.to_pandas", "kind": "function", "doc": "Exports the mass spectrum data to a pandas DataFrame and saves it as a pickle file.
\n\nParameters
\n\n\n- write_metadata (bool, optional):\nWhether to write the metadata to a JSON file. Defaults to True.
\n
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.to_excel", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.to_excel", "kind": "function", "doc": "Exports the mass spectrum data to an Excel file.
\n\nParameters
\n\n\n- write_metadata (bool, optional):\nWhether to write the metadata to a JSON file. Defaults to True.
\n
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.to_csv", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.to_csv", "kind": "function", "doc": "Exports the mass spectrum data to a CSV file.
\n\nParameters
\n\n\n- write_metadata (bool, optional):\nWhether to write the metadata to a JSON file. Defaults to True.
\n
\n", "signature": "(self, write_metadata=True):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.to_json", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.to_json", "kind": "function", "doc": "Exports the mass spectrum data to a JSON string.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.to_hdf", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.to_hdf", "kind": "function", "doc": "Exports the mass spectrum data to an HDF5 file.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.parameters_to_toml", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.parameters_to_toml", "kind": "function", "doc": "Converts the mass spectrum parameters to a TOML string.
\n\nReturns
\n\n\n- str: The TOML string of the mass spectrum parameters.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.parameters_to_json", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.parameters_to_json", "kind": "function", "doc": "Converts the mass spectrum parameters to a JSON string.
\n\nReturns
\n\n\n- str: The JSON string of the mass spectrum parameters.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.get_mass_spec_attrs", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.get_mass_spec_attrs", "kind": "function", "doc": "Returns the mass spectrum attributes as a dictionary.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n
\n\nReturns
\n\n\n- dict: The mass spectrum attributes.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.get_all_used_atoms_in_order", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.get_all_used_atoms_in_order", "kind": "function", "doc": "Returns the list of assigned atoms in the order specified by Atoms.atoms_order list.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n
\n\nReturns
\n\n\n- list: The list of assigned atoms in the order specified by Atoms.atoms_order list.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.list_dict_to_list", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.list_dict_to_list", "kind": "function", "doc": "Returns the mass spectrum data as a list of dictionaries.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n- is_hdf5 (bool, optional):\nWhether the mass spectrum is being exported to an HDF5 file. Defaults to False.
\n
\n\nReturns
\n\n\n- list: The mass spectrum data as a list of dictionaries.
\n
\n", "signature": "(self, mass_spectrum, is_hdf5=False):", "funcdef": "def"}, {"fullname": "corems.mass_spectrum.output.export.HighResMassSpecExport.get_list_dict_data", "modulename": "corems.mass_spectrum.output.export", "qualname": "HighResMassSpecExport.get_list_dict_data", "kind": "function", "doc": "Returns the mass spectrum data as a list of dictionaries.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum to export.
\n- include_no_match (bool, optional):\nWhether to include unassigned (no match) data. Defaults to True.
\n- include_isotopologues (bool, optional):\nWhether to include isotopologues. Defaults to True.
\n- isotopologue_inline (bool, optional):\nWhether to include isotopologues inline. Defaults to True.
\n- no_match_inline (bool, optional):\nWhether to include unassigned (no match) data inline. Defaults to False.
\n- is_hdf5 (bool, optional):\nWhether the mass spectrum is being exported to an HDF5 file. Defaults to False.
\n
\n\nReturns
\n\n\n- list: The mass spectrum data as a list of dictionaries.
\n
\n", "signature": "(\tself,\tmass_spectrum,\tinclude_no_match=True,\tinclude_isotopologues=True,\tisotopologue_inline=True,\tno_match_inline=False,\tis_hdf5=False):", "funcdef": "def"}, {"fullname": "corems.molecular_formula", "modulename": "corems.molecular_formula", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.calc", "modulename": "corems.molecular_formula.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.calc.MolecularFormulaCalc", "modulename": "corems.molecular_formula.calc.MolecularFormulaCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.calc.MolecularFormulaCalc.MolecularFormulaCalc", "modulename": "corems.molecular_formula.calc.MolecularFormulaCalc", "qualname": "MolecularFormulaCalc", "kind": "class", "doc": "Class of calculations related to molecular formula
\n\nThis class is not intended to be used directly, but rather to be inherited by other classes in the molecular_formula/factory module like MolecularFormula, MolecularFormulaIsotopologue, and LCMSLibRefMolecularFormula
\n\nAttributes
\n\n\n- mz_calc (float):\nThe m/z value of the molecular formula.
\n- neutral_mass (float):\nThe neutral mass of the molecular formula.
\n- ion_charge (int):\nThe ion charge of the molecular formula.
\n- _external_mz (float):\nThe externally provided m/z value of the molecular formula.
\n- _d_molecular_formula (dict):\nThe dictionary representation of the molecular formula.
\n- _mspeak_parent (object):\nThe parent MS peak object associated with the molecular formula.
\n- _assignment_mass_error (float):\nThe mass error of the molecular formula.
\n
\n\nMethods
\n\n\n- _calc_resolving_power_low_pressure(B, T) \nCalculate the resolving power at low pressure.
\n- _calc_resolving_power_high_pressure(B, T)\nCalculate the resolving power at high pressure.
\n- _adduct_mz(adduct_atom, ion_charge)\nGet the m/z value of an adducted ion version of the molecular formula.
\n- _protonated_mz(ion_charge)\nGet the m/z value of a protonated or deprotonated ion version of the molecular formula.
\n- _radical_mz(ion_charge)\nGet the m/z value of a radical ion version of the molecular formula.
\n- _neutral_mass()\nGet the neutral mass of the molecular formula.
\n- _calc_mz()\nGet the m/z value of the molecular formula.
\n- _calc_assignment_mass_error(method='ppm')\nCalculate the mass error of the molecular formula.
\n- _calc_mz_confidence(mean=0)\nCalculate the m/z confidence of the molecular formula.
\n- _calc_isotopologue_confidence()\nCalculate the isotopologue confidence of the molecular formula.
\n- normalize_distance(dist, dist_range)\nNormalize the distance value.
\n- subtract_formula(formula_obj, formated=True)\nSubtract a formula from the current formula object.
\n- _calc_average_mz_score()\nCalculate the average m/z error score of the molecular formula identification, including the isotopologues.
\n
\n"}, {"fullname": "corems.molecular_formula.calc.MolecularFormulaCalc.MolecularFormulaCalc.normalize_distance", "modulename": "corems.molecular_formula.calc.MolecularFormulaCalc", "qualname": "MolecularFormulaCalc.normalize_distance", "kind": "function", "doc": "Normalize the distance value.
\n\nParameters
\n\n\n- dist (float):\nThe distance value to be normalized.
\n- dist_range (list):\nThe range of the distance value.
\n
\n", "signature": "(self, dist, dist_range):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.calc.MolecularFormulaCalc.MolecularFormulaCalc.subtract_formula", "modulename": "corems.molecular_formula.calc.MolecularFormulaCalc", "qualname": "MolecularFormulaCalc.subtract_formula", "kind": "function", "doc": "Subtract a formula from the current formula object
\n\nParameters
\n\n\n- formula_obj (MolecularFormula):\nMolecularFormula object to be subtracted from the current formula object
\n- formated (bool, optional):\nIf True, returns the formula in string format, by default True
\n
\n", "signature": "(self, formula_obj, formated=True):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.calc.MolecularFormulaCalc.MolecularFormulaCalc.dbe_ai", "modulename": "corems.molecular_formula.calc.MolecularFormulaCalc", "qualname": "MolecularFormulaCalc.dbe_ai", "kind": "variable", "doc": "Calculate the double bond equivalent (DBE) of the molecular formula, based on the number of carbons, hydrogens, and oxygens.
\n"}, {"fullname": "corems.molecular_formula.factory", "modulename": "corems.molecular_formula.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase", "kind": "class", "doc": "Base class for representing a molecular formula.
\n\nParameters
\n\n\n- molecular_formula (dict, list, str):\nThe molecular formula.
\n- ion_charge (int):\nThe ion charge.
\n- ion_type (str, optional):\nThe ion type. Defaults to None.
\n- adduct_atom (str, optional):\nThe adduct atom. Defaults to None.
\n- mspeak_parent (_MSPeak, optional):\nThe parent mass spectrum peak object instance. Defaults to None.
\n- external_mz (float, optional):\nThe external m/z value. Defaults to None.
\n
\n\nRaises
\n\n\n- TypeError: If the ion type is not 'DE_OR_PROTONATED', 'RADICAL' or 'ADDUCT'.
\n
\n\nAttributes
\n\n\n- isotopologue_count_percentile (float):\nThe isotopologue count percentile.
\n- O_C (float):\nThe O/C ratio.
\n- H_C (float):\nThe H/C ratio.
\n- dbe (float):\nThe double bond equivalent.
\n- mz_nominal_calc (int):\nThe nominal m/z value.
\n- mz_error (float):\nThe m/z error.
\n- mz_calc (float):\nThe m/z value.
\n- protonated_mz (float):\nThe protonated or deprotonated m/z value.
\n- radical_mz (float):\nThe radical m/z value.
\n- neutral_mass (float):\nThe neutral mass.
\n- ion_type (str):\nThe ion type.
\n- ion_charge (int):\nThe ion charge.
\n- atoms (list):\nThe atoms in the molecular formula.
\n- confidence_score (float):\nThe confidence score of the molecular formula identification.
\n- isotopologue_similarity (float):\nThe isotopologue similarity score of the molecular formula identification.
\n- average_mz_error_score (float):\nThe average m/z error score of the molecular formula identification, including the isotopologues.
\n- mz_error_score (float):\nThe m/z error score of the molecular formula identification.
\n- kmd (float):\nThe Kendrick mass defect (KMD).
\n- kendrick_mass (float):\nThe Kendrick mass.
\n- knm (float):\nThe nominal Kendrick mass.
\n- string (str):\nThe molecular formula string.
\n- string_formated (str):\nThe molecular formula string formated with subscripts and superscripts.
\n- class_label (str):\nThe class label.
\n- class_dict (dict):\nThe class dictionary.
\n
\n\nMethods
\n\n\n- change_kendrick_base(kendrick_dict_base).\nChange the Kendrick base.
\n- isotopologues(min_abundance, current_mono_abundance, dynamic_range).\nCalculate the isotopologues.
\n- atoms_qnt(atom).\nGet the atom quantity.
\n- atoms_symbol(atom).\nGet the atom symbol without the mass number.
\n- to_dict().\nGet the molecular formula as a dictionary.
\n- to_list().\nGet the molecular formula as a list.
\n
\n", "bases": "corems.molecular_formula.calc.MolecularFormulaCalc.MolecularFormulaCalc"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.__init__", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.__init__", "kind": "function", "doc": "\n", "signature": "(\tmolecular_formula,\tion_charge,\tion_type=None,\tadduct_atom=None,\tmspeak_parent=None,\texternal_mz=None)"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.is_isotopologue", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.is_isotopologue", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.expected_isotopologues", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.expected_isotopologues", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.mspeak_mf_isotopologues_indexes", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.mspeak_mf_isotopologues_indexes", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.get", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.get", "kind": "function", "doc": "Get the atom quantity of a specific atom.
\n\nParameters
\n\n\n- atom (str):\nThe atom symbol.
\n
\n\nReturns
\n\n\n- int: The atom quantity.
\n
\n", "signature": "(self, atom):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.split", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.split", "kind": "function", "doc": "Splits the molecular formula string.
\n\nParameters
\n\n\n- delimiters (list):\nThe list of delimiters.
\n- string (str):\nThe molecular formula string.
\n- maxsplit (int, optional):\nThe maximum number of splits. Defaults to 0.
\n
\n\nReturns
\n\n\n- list: The molecular formula list.
\n
\n\nNotes
\n\nDoes not work when formula has atoms with same characters in a row that below to different atoms, i.e. C10H21NNa.
\n", "signature": "(self, delimiters, string, maxsplit=0):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.isotopologue_count_percentile", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.isotopologue_count_percentile", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.O_C", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.O_C", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.H_C", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.H_C", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.dbe", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.dbe", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.mz_nominal_calc", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.mz_nominal_calc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.mz_error", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.mz_error", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.mz_calc", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.mz_calc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.protonated_mz", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.protonated_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.radical_mz", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.radical_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.neutral_mass", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.neutral_mass", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.adduct_mz", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.adduct_mz", "kind": "function", "doc": "Get m/z of an adducted ion version of the molecular formula.
\n\nParameters
\n\n\n- adduct_atom (str):\nThe adduct atom.
\n
\n\nReturns
\n\n\n- float: The m/z value of the adducted ion version of the molecular formula.
\n
\n", "signature": "(self, adduct_atom):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.ion_type", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.ion_type", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.ion_charge", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.ion_charge", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.atoms", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.atoms", "kind": "variable", "doc": "Get the atoms in the molecular formula.
\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.confidence_score", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.confidence_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.isotopologue_similarity", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.isotopologue_similarity", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.average_mz_error_score", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.average_mz_error_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.mz_error_score", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.mz_error_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.kmd", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.kmd", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.kendrick_mass", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.kendrick_mass", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.knm", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.knm", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.change_kendrick_base", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.change_kendrick_base", "kind": "function", "doc": "Change the Kendrick base.
\n\nParameters
\n\n\n- kendrick_dict_base (dict):\nThe Kendrick base dictionary. Ex: {\"C\": 1, \"H\": 2}
\n
\n", "signature": "(self, kendrick_dict_base):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.isotopologues", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.isotopologues", "kind": "function", "doc": "Calculate the isotopologues for a given molecular formula.
\n\nParameters
\n\n\n- min_abundance (float):\nThe minimum abundance.
\n- current_mono_abundance (float):\nThe current monoisotopic abundance.
\n- dynamic_range (float):\nThe dynamic range.
\n
\n\nYields
\n\n\n- MolecularFormulaIsotopologue: The molecular formula isotopologue.
\n
\n\nNotes
\n\nThis calculation ignores the hydrogen isotopes.
\n", "signature": "(self, min_abundance, current_mono_abundance, dynamic_range):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.atoms_qnt", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.atoms_qnt", "kind": "function", "doc": "Get the atom quantity of a specific atom in the molecular formula.
\n", "signature": "(self, atom):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.atoms_symbol", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.atoms_symbol", "kind": "function", "doc": "Get the atom symbol without the mass number.
\n", "signature": "(self, atom):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.string", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.string", "kind": "variable", "doc": "Returns the molecular formula as a string.
\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.string_formated", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.string_formated", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.to_dict", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.to_dict", "kind": "function", "doc": "Returns the molecular formula as a dictionary.
\n\nReturns
\n\n\n- dict: The molecular formula as a dictionary.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.to_list", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.to_list", "kind": "function", "doc": "Returns the molecular formula as a list.
\n\nReturns
\n\n\n- list: The molecular formula as a list.
\n
\n\nRaises
\n\n\n- Exception: If the molecular formula identification was not performed yet.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.class_label", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.class_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaBase.class_dict", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaBase.class_dict", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue", "kind": "class", "doc": "Class for representing a molecular formula isotopologue.
\n\nParameters
\n\n\n- _d_molecular_formula (dict):\nThe molecular formula as a dictionary.
\n- prob_ratio (float):\nThe probability ratio.
\n- mono_abundance (float):\nThe monoisotopic abundance.
\n- ion_charge (int):\nThe ion charge.
\n- mspeak_parent (object, optional):\nThe parent mass spectrum peak object instance. Defaults to None.
\n
\n\nAttributes
\n\n\n- prob_ratio (float):\nThe probability ratio.
\n- abundance_calc (float):\nThe calculated abundance.
\n- area_error (float):\nThe area error.
\n- abundance_error (float):\nThe abundance error.
\n- is_isotopologue (bool):\nThe isotopologue flag. Defaults to True.
\n- mspeak_index_mono_isotopic (int):\nThe index of the monoisotopic peak in the mass spectrum peak list. Defaults to None.
\n- mono_isotopic_formula_index (int):\nThe index of the monoisotopic formula in the molecular formula list. Defaults to None.
\n
\n", "bases": "MolecularFormulaBase"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.__init__", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.__init__", "kind": "function", "doc": "\n", "signature": "(\t_d_molecular_formula,\tprob_ratio,\tmono_abundance,\tion_charge,\tmspeak_parent=None)"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.prob_ratio", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.prob_ratio", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.abundance_calc", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.abundance_calc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.is_isotopologue", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.is_isotopologue", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.mspeak_index_mono_isotopic", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.mspeak_index_mono_isotopic", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.mono_isotopic_formula_index", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.mono_isotopic_formula_index", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.area_error", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.area_error", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormulaIsotopologue.abundance_error", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormulaIsotopologue.abundance_error", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "LCMSLibRefMolecularFormula", "kind": "class", "doc": "Class for representing a molecular formula associated with a molecule in a LCMS library reference.
\n\nParameters
\n\n\n- molecular_formula (dict, list, str):\nThe molecular formula.
\n- ion_charge (int):\nThe ion charge.
\n- ion_type (str, optional):\nThe ion type. Defaults to None.
\n- adduct_atom (str, optional):\nThe adduct atom. Defaults to None.
\n- mspeak_parent (object, optional):\nThe parent mass spectrum peak object instance. Defaults to None.
\n- name (str, optional):\nThe name of the reference molecule. Defaults to None.
\n- kegg_id (str, optional):\nThe KEGG ID of the reference molecule. Defaults to None.
\n- cas (str, optional):\nThe CAS number of the reference molecule. Defaults to None.
\n
\n", "bases": "MolecularFormulaBase"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula.__init__", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "LCMSLibRefMolecularFormula.__init__", "kind": "function", "doc": "\n", "signature": "(\tmolecular_formula,\tion_charge,\tion_type=None,\tadduct_atom=None,\tmspeak_parent=None,\tname=None,\tkegg_id=None,\tcas=None)"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula.name", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "LCMSLibRefMolecularFormula.name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula.kegg_id", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "LCMSLibRefMolecularFormula.kegg_id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula.cas", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "LCMSLibRefMolecularFormula.cas", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormula", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormula", "kind": "class", "doc": "General class for representing a molecular formula.
\n\nParameters
\n\n\n- molecular_formula (dict, list, str):\nThe molecular formula.
\n- ion_charge (int):\nThe ion charge.
\n- ion_type (str, optional):\nThe ion type. Defaults to None.
\n- adduct_atom (str, optional):\nThe adduct atom. Defaults to None.
\n- mspeak_parent (object, optional):\nThe parent mass spectrum peak object instance. Defaults to None.
\n- external_mz (float, optional):\nThe external m/z value. Defaults to False.
\n
\n", "bases": "MolecularFormulaBase"}, {"fullname": "corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormula.__init__", "modulename": "corems.molecular_formula.factory.MolecularFormulaFactory", "qualname": "MolecularFormula.__init__", "kind": "function", "doc": "\n", "signature": "(\tmolecular_formula,\tion_charge,\tion_type=None,\tadduct_atom=None,\tmspeak_parent=None,\texternal_mz=False)"}, {"fullname": "corems.molecular_formula.input", "modulename": "corems.molecular_formula.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref", "modulename": "corems.molecular_formula.input.masslist_ref", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy", "kind": "class", "doc": "Proxy class for MolecularFormulaLink to be used in the molecular formula ref file import
\n\nParameters
\n\n\n- molecular_formula (MolecularFormula | LCMSLibRefMolecularFormula):\ncorems MolecularFormula or LCMSLibRefMolecularFormula object
\n- mz (float):\ntarget m/z
\n
\n\nAttributes
\n\n\n- C (int):\nnumber of carbon atoms
\n- H (int):\nnumber of hydrogen atoms
\n- H_C (float):\nratio of hydrogen to carbon atoms
\n- class_label (str):\nmolecular formula class label
\n- mz_calc (float):\ncalculated m/z
\n- dbe (int):\ndouble bond equivalent
\n- formula_dict (dict):\nmolecular formula dictionary
\n
\n\nMethods
\n\n\n- to_dict(). \nreturn molecular formula dictionary
\n
\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.__init__", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.__init__", "kind": "function", "doc": "\n", "signature": "(molecular_formula, mz)"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.C", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.C", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.H", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.H", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.H_C", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.H_C", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.class_label", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.class_label", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.mz_calc", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.mz_calc", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.dbe", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.dbe", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.formula_dict", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.formula_dict", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.MolecularFormulaLinkProxy.to_dict", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "MolecularFormulaLinkProxy.to_dict", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef", "kind": "class", "doc": "Import Mass List from Reference File
\n\nParameters
\n\n\n- ref_file_location (str):\npath to the reference file
\n
\n\nAttributes
\n\n\n- ref_file_location (str):\npath to the reference file
\n
\n\nMethods
\n\n\n- molecular_formula_ref(mz, molecular_formula). \nReturn MolecularFormulaLinkProxy object
\n- from_lcms_lib_file(ion_charge, ion_types).\nReturn Dict[standard_name, Dict[m/z, List[MolecularFormula]]] from LCMS library reference file
\n- from_bruker_ref_file().\nReturn List[MolecularFormula] from Bruker reference file
\n- from_corems_ref_file(delimiter).\nReturn List[MolecularFormula] from CoreMS reference file
\n- split(delimiters, string, maxsplit).\nSplits a string using a list of delimiters.
\n- mformula_s_to_dict(s_mformulatring, iontype).\nConverts a molecular formula string to a dict
\n
\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.__init__", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.__init__", "kind": "function", "doc": "\n", "signature": "(ref_file_location)"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.ref_file_location", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.ref_file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.molecular_formula_ref", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.molecular_formula_ref", "kind": "function", "doc": "Instantiate a MolecularFormulaLinkProxy object
\n\nParameters
\n\n\n- mz (float):\ntarget m/z
\n- molecular_formula (MolecularFormula | LCMSLibRefMolecularFormula):\ncorems MolecularFormula or LCMSLibRefMolecularFormula object
\n
\n\nReturns
\n\n\n- MolecularFormulaLinkProxy: MolecularFormulaLinkProxy object
\n
\n", "signature": "(self, mz, molecular_formula):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.from_lcms_lib_file", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.from_lcms_lib_file", "kind": "function", "doc": "Create a dictionary of LCMSLibRefMolecularFormula objects from LCMS library reference file
\n\nParameters
\n\n\n- ion_charge (float):\nion charge
\n- ion_types (List[str]):\nlist of ion types
\n
\n\nReturns
\n\n\n- Dict: Dict[standard_name, Dict[m/z, List[MolecularFormula]]] from LCMS library reference file. m/z is the target m/z; standard_name is the name of the molecular standard mix; MolecularFormula is the corems molecular formula class
\n
\n", "signature": "(\tself,\tion_charge: float,\tion_types: List[str]) -> Dict[str, Dict[float, List[corems.molecular_formula.factory.MolecularFormulaFactory.LCMSLibRefMolecularFormula]]]:", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.from_bruker_ref_file", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.from_bruker_ref_file", "kind": "function", "doc": "Create a list of MolecularFormula objects from Bruker reference file
\n\nReturns
\n\n\n- List[MolecularFormula]: List of MolecularFormula objects from Bruker reference file
\n
\n", "signature": "(\tself) -> List[corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormula]:", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.from_corems_ref_file", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.from_corems_ref_file", "kind": "function", "doc": "Create a list of MolecularFormula objects from CoreMS reference file
\n\nNot being used
\n\nParameters
\n\n\n- delimiter (str):\ndelimiter used in the reference file
\n
\n\nReturns
\n\n\n- List[MolecularFormula]: List of MolecularFormula objects from CoreMS reference file
\n
\n", "signature": "(self, delimiter='\\t'):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.split", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.split", "kind": "function", "doc": "Splits a string using a list of delimiters.
\n\nDoes not work when formula has atoms with same characters, i.e - C10H21NNa
\n\nParameters
\n\n\n- delimiters (list):\nlist of delimiters
\n- string (str):\nstring to be split
\n- maxsplit (int, optional):\nmaximum number of splits. Default is 0
\n
\n\nReturns
\n\n\n- list: list of strings obtained after splitting the string
\n- list: list of counts obtained after splitting the string
\n
\n", "signature": "(self, delimiters, string, maxsplit=0):", "funcdef": "def"}, {"fullname": "corems.molecular_formula.input.masslist_ref.ImportMassListRef.mformula_s_to_dict", "modulename": "corems.molecular_formula.input.masslist_ref", "qualname": "ImportMassListRef.mformula_s_to_dict", "kind": "function", "doc": "Converts a molecular formula string to a dict
\n\nParameters
\n\n\n- s_mformulatring (str):\nmolecular formula string, i.e. 'C10H21NNa'
\n- iontype (str, optional):\nion type. Default is 'unknown'
\n
\n\nReturns
\n\n\n- dict: molecular formula dictionary
\n
\n\nNotes
\n\nDoes not work if the atomic mass number is passed i.e. 37Cl, 81Br, convention follow the light isotope labeling 35Cl is Cl, 12C is C, etc.\nIf you need to use heavy isotopes please use another reference file format that separate the formula string by a blank space and parse it using the function corems_ref_file
\n\nRaises
\n\n\n- TypeError: Atom does not exist in Atoms.atoms_order list
\n- Exception: Empty molecular formula
\n
\n", "signature": "(self, s_mformulatring, iontype='unknown'):", "funcdef": "def"}, {"fullname": "corems.molecular_id", "modulename": "corems.molecular_id", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc", "modulename": "corems.molecular_id.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.ClusterFilter", "modulename": "corems.molecular_id.calc.ClusterFilter", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter", "kind": "class", "doc": "Class for filtering and clustering mass spectra data using various algorithms.
\n\nAttributes
\n\n\n- mass_spectrum (MassSpectrum):\nMass spectrum object.
\n- ms_peaks (list):\nList of mass peaks.
\n- ms_peak_indexes (list):\nList of peak indexes.
\n- min_samples (int):\nMinimum number of samples in a cluster.
\n- eps (float):\nThe maximum distance between two samples for one to be considered as in the neighborhood of the other.
\n- bandwidth (float):\nBandwidth used in MeanShift algorithm.
\n- quantile (float):\nQuantile used in estimate_bandwidth function.
\n- n_samples (int):\nNumber of samples used in estimate_bandwidth function.
\n- bin_seeding (bool):\nIf true, initial kernel locations are not locations of all points, but rather the location of the discretized version of points, where points are binned onto a grid whose coarseness corresponds to the bandwidth. Setting this option to True will speed up the algorithm because fewer seeds will be initialized.
\n- min_peaks_per_class (int):\nMinimum number of peaks per class.
\n
\n\nMethods
\n\n\n- get_mass_error_matrix_data(ms_peaks).\nGet the mass error matrix data from a list of mass peaks.
\n- get_kendrick_matrix_data(mass_spectrum).\nGet the Kendrick matrix data from a mass spectrum.
\n- filter_kendrick(mass_spectrum).\nFilter the mass spectrum data using the Kendrick algorithm.
\n- filter_kendrick_by_index(ms_peak_indexes, mass_spectrum_obj).\nFilter the mass spectrum data using the Kendrick algorithm based on a list of peak indexes.
\n- remove_assignment_by_mass_error(mass_spectrum).\nRemove assignments from the mass spectrum based on mass error.
\n
\n"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter.get_mass_error_matrix_data", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter.get_mass_error_matrix_data", "kind": "function", "doc": "Get the mass error matrix data from a list of mass peaks.
\n\nParameters
\n\n\n- ms_peaks (list):\nList of mass peaks.
\n
\n\nReturns
\n\n\n- matrix_data (ndarray):\nMatrix data containing mass and error values.
\n- list_indexes_mass_spec (list):\nList of indexes of mass peaks in the original mass spectrum.
\n
\n", "signature": "(self, ms_peaks):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter.get_kendrick_matrix_data", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter.get_kendrick_matrix_data", "kind": "function", "doc": "Get the Kendrick matrix data from a mass spectrum.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nMass spectrum object.
\n
\n\nReturns
\n\n\n- matrix_data (ndarray):\nMatrix data containing Kendrick mass and Kendrick mass defect values.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter.filter_kendrick", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter.filter_kendrick", "kind": "function", "doc": "Filter the mass spectrum data using the Kendrick algorithm.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nMass spectrum object.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter.filter_kendrick_by_index", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter.filter_kendrick_by_index", "kind": "function", "doc": "Filter the mass spectrum data using the Kendrick algorithm based on a list of peak indexes.
\n\nParameters
\n\n\n- ms_peak_indexes (list):\nList of peak indexes.
\n- mass_spectrum_obj (MassSpectrum):\nMass spectrum object.
\n
\n\nReturns
\n\n\n- noise_idx (list):\nList of indexes of noise points in the mass spectrum.
\n
\n", "signature": "(self, ms_peak_indexes, mass_spectrum_obj):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.ClusterFilter.ClusteringFilter.remove_assignment_by_mass_error", "modulename": "corems.molecular_id.calc.ClusterFilter", "qualname": "ClusteringFilter.remove_assignment_by_mass_error", "kind": "function", "doc": "Remove assignments from the mass spectrum based on mass error.
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nMass spectrum object.
\n
\n", "signature": "(self, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.KendrickGroup", "modulename": "corems.molecular_id.calc.KendrickGroup", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.MolecularFilter", "modulename": "corems.molecular_id.calc.MolecularFilter", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.MolecularFilter.MolecularFormulaSearchFilters", "modulename": "corems.molecular_id.calc.MolecularFilter", "qualname": "MolecularFormulaSearchFilters", "kind": "class", "doc": "Class containing static methods for filtering molecular formulas in a mass spectrum.
\n\nMethods
\n\n\n- filter_kendrick(ms_peak_indexes, mass_spectrum_obj).
\nApply Kendrick filter to the mass spectrum. \n- check_min_peaks(ms_peak_indexes, mass_spectrum_obj).
\nCheck if the number of peaks per class meets the minimum requirement. \n- filter_isotopologue(ms_peak_indexes, mass_spectrum_obj).
\nApply isotopologue filter to the mass spectrum. \n
\n"}, {"fullname": "corems.molecular_id.calc.MolecularFilter.MolecularFormulaSearchFilters.filter_kendrick", "modulename": "corems.molecular_id.calc.MolecularFilter", "qualname": "MolecularFormulaSearchFilters.filter_kendrick", "kind": "function", "doc": "Apply Kendrick filter to the mass spectrum.
\n\nParameters
\n\n\n- ms_peak_indexes (list):\nList of peak indexes and their associated molecular formula objects.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n
\n\nReturns
\n\n\n- filtered_ms_peak_indexes (list):\nList of peak indexes and their associated molecular formula objects after applying the Kendrick filter.
\n
\n", "signature": "(ms_peak_indexes, mass_spectrum_obj):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.MolecularFilter.MolecularFormulaSearchFilters.check_min_peaks", "modulename": "corems.molecular_id.calc.MolecularFilter", "qualname": "MolecularFormulaSearchFilters.check_min_peaks", "kind": "function", "doc": "Check if the number of peaks per class meets the minimum requirement.
\n\nParameters
\n\n\n- ms_peak_indexes (list):\nList of peak indexes and their associated molecular formula objects.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n
\n", "signature": "(ms_peak_indexes, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.MolecularFilter.MolecularFormulaSearchFilters.filter_isotopologue", "modulename": "corems.molecular_id.calc.MolecularFilter", "qualname": "MolecularFormulaSearchFilters.filter_isotopologue", "kind": "function", "doc": "Apply isotopologue filter to the mass spectrum.
\n\nParameters
\n\n\n- ms_peak_indexes (list):\nList of peak indexes and their associated molecular formula objects.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n
\n\nReturns
\n\n\n- filtered_ms_peak_indexes (list):\nList of peak indexes and their associated molecular formula objects after applying the isotopologue filter.
\n
\n", "signature": "(ms_peak_indexes, mass_spectrum):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.methods_name", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "methods_name", "kind": "variable", "doc": "\n", "default_value": "{'chebyshev_distance': 'Chebyshev Distance', 'squared_euclidean_distance': 'Squared Euclidean Distance', 'fidelity_similarity': 'Fidelity Similarity', 'matusita_distance': 'Matusita Distance', 'squared_chord_distance': 'Squared-chord Distance', 'harmonic_mean_similarity': 'Harmonic mean Distance', 'Pearson_chi_squared_distance': 'Pearson Chi Squared Distance', 'Neyman_chi_squared_distance': 'Neyman Chi Squared Distance', 'probabilistic_symmetric_chi_squared_distance': 'Probabilistic symmetric X2 Distance', 'topsoe_distance': 'Topsoe Distance', 'chernoff_distance': 'Chernoff Distance', 'ruzicka_distance': 'Ruzicka Distance', 'roberts_distance': 'Roberts Distance', 'motyka_distance': 'Motyka Distance', 'canberra_distance': 'Canberra Distance', 'canberra_metric': 'Canberra Metric', 'kulczynski_1_distance': 'Kulczynski 1 Distance', 'lorentzian_distance': 'Lorentzian Distance', 'clark_distance': 'Clark Distance', 'hellinger_distance': 'Hellinger Distance', 'whittaker_index_of_association_distance': 'Whittaker index of association Distance', 'spectral_contrast_angle_distance': 'Spectral Contrast Angle', 'wave_hedges_distance': 'Wave Hedges Distance', 'dice_similarity': 'Dice Similarity', 'inner_product_distance': 'Inner Product Distance', 'divergence_distance': 'Divergence Distance', 'jensen_difference_distance': 'Jensen Differences Distance', 'kumar_johnson_distance': 'Kumar Johnson Distance', 'avg_l_distance': 'Avg (L1, L8) Distance', 'vicis_wave_hadges_distance': 'Vicis Wave Hadges Distance', 'vicis_symmetric_chi_squared_1_distance': 'Vicis-Symmetric X2 1 Distance', 'vicis_symmetric_chi_squared_2_distance': 'Vicis-Symmetric X2 2 Distance', 'vicis_symmetric_chi_squared_3_distance': 'Vicis-Symmetric X2 3 Distance', 'max_symmetric_chi_squared_distance': 'Max Symmetric Chi Squared Distance', 'min_symmetric_chi_squared_distance': 'Min Symmetric Chi Squared Distance', 'additive_sym_chi_sq': 'Additive Symmetric Chi Squared', 'bhattacharya_distance': 'Battacharya Distance', 'generalized_ochiai_index': 'Generalized Ochiai Index', 'gower_distance': 'Gower Distance', 'impr_sqrt_cosine_sim': 'Improved Square Root Cosine Similarity', 'intersection_sim': 'Intersection Similarity', 'j_divergence': 'J Divergence', 'jensen_shannon_index': 'Jensen Shannon Index', 'k_divergence': 'K Divergence', 'VW6': 'VW6', 'VW5': 'VW5', 'VW4': 'VW4', 'VW3': 'VW3', 'VW2': 'VW2', 'VW1': 'VW1', 'taneja_divergence': 'Taneja Divergence', 'symmetric_chi_squared_distance': 'Symmetric Chi Squared Distance', 'squared_chi_squared_distance': 'Squared Chi Squared Distance', 'square_root_cosine_correlation': 'Square Root Cosine Correlation', 'sorensen_distance': 'Sorensen Distance', 'Minokowski_3': 'Minokowski 3 Distance', 'Minokowski_4': 'Minokowski 4 Distance', 'kumarjohnson_divergence': 'Kumar Johnson Divergence', 'kumarhassebrook_similarity': 'Kumar Hassebrook Similarity', 'kullbackleibler_divergence': 'Kullback Leibler Divergence', 'soergel_distance': 'Soergel Distance'}"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.methods_scale", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "methods_scale", "kind": "variable", "doc": "\n", "default_value": "{'entropy': [0, 1.3862943611198906], 'weighted_entropy': [0, 1.3862943611198906], 'absolute_value': [0, 2], 'avg_l': [0, 1.5], 'bhattacharya_1': [0, 2.4674011002723395], 'bhattacharya_2': [0, inf], 'canberra': [0, inf], 'clark': [0, inf], 'divergence': [0, inf], 'euclidean': [0, 1.4142135623730951], 'hellinger': [0, inf], 'improved_similarity': [0, inf], 'lorentzian': [0, inf], 'manhattan': [0, 2], 'matusita': [0, 1.4142135623730951], 'mean_character': [0, 2], 'motyka': [-0.5, 0], 'ms_for_id': [-inf, 0], 'ms_for_id_v1': [0, inf], 'pearson_correlation': [-1, 1], 'penrose_shape': [0, 1.4142135623730951], 'penrose_size': [0, inf], 'probabilistic_symmetric_chi_squared': [0, 1], 'similarity_index': [0, inf], 'squared_chord': [0, 2], 'squared_euclidean': [0, 2], 'symmetric_chi_squared': [0, 0.7071067811865476], 'topsoe': [0, 1.4142135623730951], 'vicis_symmetric_chi_squared_3': [0, 2], 'wave_hedges': [0, inf], 'whittaker_index_of_association': [0, inf]}"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity", "kind": "class", "doc": "Class containing methods for calculating spectral similarity between two mass spectra.
\n\nParameters
\n\n\n- ms_mz_abun_dict (dict):\nDictionary of mass to abundance values for the experimental mass spectrum.
\n- ref_obj (dict):\nDictionary of mass to abundance values for the reference mass spectrum.
\n- norm_func (function):\nFunction to normalize the abundance values.
\n
\n\nAttributes
\n\n\n- normalize_func (function):\nFunction to normalize the abundance values.
\n- ms_mz_abun_dict (dict):\nDictionary of mass to abundance values for the experimental mass spectrum.
\n- ref_obj (dict):\nDictionary of mass to abundance values for the reference mass spectrum.
\n- exp_abun (list):\nList of abundance values for the experimental mass spectrum.
\n- exp_mz (list):\nList of mass values for the experimental mass spectrum.
\n- ref_mz (list):\nList of mass values for the reference mass spectrum.
\n- ref_abun (list):\nList of abundance values for the reference mass spectrum.
\n- ref_mz_abun_dict (dict):\nDictionary of mass to abundance values for the reference mass spectrum.
\n- df (DataFrame):\nDataFrame containing the experimental and reference mass spectrum data.
\n- zero_filled_u_l (tuple):\nTuple containing the experimental and reference mass spectrum data after zero filling and normalization.
\n- common_mz_values (list):\nList of common mass values between the experimental and reference mass spectra.
\n- n_x_y (int):\nNumber of common mass values between the experimental and reference mass spectra.
\n
\n\nMethods
\n\n\n- nan_fill(df, fill_with=0).\nFill missing mass values with a given value.
\n- normalize(x, y, norm_func=sum).\nNormalize the abundance values.
\n- weighted_cosine_correlation(a=0.5, b=1.3, nanfill=1e-10).\nCalculate the weighted cosine correlation between the experimental and reference mass spectra.
\n- cosine_correlation().\nCalculate the cosine correlation between the experimental and reference mass spectra.
\n- stein_scott().\nCalculate the Stein-Scott similarity between the experimental and reference mass spectra.
\n- pearson_correlation().\nCalculate the Pearson correlation between the experimental and reference mass spectra.
\n- spearman_correlation().\nCalculate the Spearman correlation between the experimental and reference mass spectra.
\n
\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.__init__", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.__init__", "kind": "function", "doc": "\n", "signature": "(ms_mz_abun_dict, ref_obj, norm_func=<built-in function sum>)"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.normalize_func", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.normalize_func", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.ms_mz_abun_dict", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.ms_mz_abun_dict", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.ref_obj", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.ref_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.exp_abun", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.exp_abun", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.exp_mz", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.exp_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.ref_mz", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.ref_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.ref_abun", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.ref_abun", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.ref_mz_abun_dict", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.ref_mz_abun_dict", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.df", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.df", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.zero_filled_u_l", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.zero_filled_u_l", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.common_mz_values", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.common_mz_values", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.n_x_y", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.n_x_y", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.nan_fill", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.nan_fill", "kind": "function", "doc": "Fill missing mass values with a given value.
\n\nParameters
\n\n\n- df (DataFrame):\nDataFrame containing the experimental and reference mass spectrum data.
\n- fill_with (float):\nValue to fill missing mass values with.
\n
\n\nReturns
\n\n\n- x (list):\nList of abundance values for the experimental mass spectrum.
\n- y (list):\nList of abundance values for the reference mass spectrum.
\n
\n", "signature": "(self, df, fill_with=0):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.normalize", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.normalize", "kind": "function", "doc": "Normalize the abundance values.
\n\nParameters
\n\n\n- x (list):\nList of abundance values for the experimental mass spectrum.
\n- y (list):\nList of abundance values for the reference mass spectrum.
\n- norm_func (function):\nFunction to normalize the abundance values.\nDefault is sum
\n
\n\nReturns
\n\n\n- u_l (tuple):\nTuple containing the experimental and reference mass spectrum data after zero filling and normalization.
\n
\n", "signature": "(self, x, y, norm_func=<built-in function sum>):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.weighted_cosine_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.weighted_cosine_correlation", "kind": "function", "doc": "Calculate the weighted cosine correlation between the experimental and reference mass spectra.
\n\nParameters
\n\n\n- a (float):\nWeighting factor for the abundance values.\nDefault is 0.5
\n- b (float):\nWeighting factor for the mass values.\nDefault is 1.3
\n- nanfill (float):\nValue to fill missing mass values with.\nDefault is 1e-10
\n
\n\nReturns
\n\n\n- correlation (float):\nWeighted cosine correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self, a=0.5, b=1.3, nanfill=1e-10):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.cosine_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.cosine_correlation", "kind": "function", "doc": "Calculate the cosine correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nCosine correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.stein_scott", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.stein_scott", "kind": "function", "doc": "Calculate the Stein-Scott similarity between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- s_ss_x_y (float):\nStein-Scott similarity between the experimental and reference mass spectra.
\n- s_ss_x_y_nist (float):\nStein-Scott similarity between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.pearson_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.pearson_correlation", "kind": "function", "doc": "Calculate the Pearson correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nPearson correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.spearman_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.spearman_correlation", "kind": "function", "doc": "Calculate the Spearman correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- coorelation (float):\nSpearman correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.kendall_tau", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.kendall_tau", "kind": "function", "doc": "Calculate the Kendall's tau correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nKendall's tau correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.dft_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.dft_correlation", "kind": "function", "doc": "Calculate the DFT correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nDFT correlation between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.dwt_correlation", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.dwt_correlation", "kind": "function", "doc": "Calculate the DWT correlation between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nDWT correlation between the experimental and reference mass spectra.
\n
\n\nNotes
\n\nThis function requires the PyWavelets library to be installed. \n This is not a default requirement as this function is not widely used.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.euclidean_distance", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.euclidean_distance", "kind": "function", "doc": "Calculate the Euclidean distance between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nEuclidean distance between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.manhattan_distance", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.manhattan_distance", "kind": "function", "doc": "Calculate the Manhattan distance between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nManhattan distance between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.jaccard_distance", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.jaccard_distance", "kind": "function", "doc": "Calculate the Jaccard distance between the experimental and reference mass spectra.
\n\nReturns
\n\n\n- correlation (float):\nJaccard distance between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.SpectralSimilarity.SpectralSimilarity.extra_distances", "modulename": "corems.molecular_id.calc.SpectralSimilarity", "qualname": "SpectralSimilarity.extra_distances", "kind": "function", "doc": "Function to calculate distances using additional metrics defined in math_distance.py
\n\nCurrently, calculates all distances.
\n\nReturns
\n\n\n- dict_res (dict):\nDictionary containing the distances between the experimental and reference mass spectra.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance", "modulename": "corems.molecular_id.calc.math_distance", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.calc.math_distance.entropy_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "entropy_distance", "kind": "function", "doc": "Calculate entropy distance between two vectors
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Entropy distance between v and y
\n
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.weighted_entropy_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "weighted_entropy_distance", "kind": "function", "doc": "Calculate weighted entropy distance between two vectors
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Weighted entropy distance between v and y
\n
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.chebyshev_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "chebyshev_distance", "kind": "function", "doc": "Chebyshev distance
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Chebyshev distance between v and y
\n
\n\nNotes
\n\n$$\\underset{i}{\\max}{(|v_{i}\\ -\\ y_{i}|)}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.squared_euclidean_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "squared_euclidean_distance", "kind": "function", "doc": "Squared Euclidean distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Squared Euclidean distance between v and y
\n
\n\nNotes
\n\n$$\\sum(v_{i}-y_{i})^2$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.fidelity_similarity", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "fidelity_similarity", "kind": "function", "doc": "Fidelity similarity:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Fidelity similarity between v and y
\n
\n\nNotes
\n\n$$\\sum\\sqrt{v_{i}y_{i}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.matusita_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "matusita_distance", "kind": "function", "doc": "Matusita distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Matusita distance between v and y
\n
\n\nNotes
\n\n$$\\sqrt{\\sum(\\sqrt{v_{i}}-\\sqrt{y_{i}})^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.squared_chord_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "squared_chord_distance", "kind": "function", "doc": "Squared-chord distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Squared-chord distance between v and y
\n
\n\nNotes
\n\n$$\\sum(\\sqrt{v_{i}}-\\sqrt{y_{i}})^2$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.bhattacharya_1_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "bhattacharya_1_distance", "kind": "function", "doc": "Bhattacharya 1 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Bhattacharya 1 distance between v and y
\n
\n\nNotes
\n\n$$(\\arccos{(\\sum\\sqrt{v_{i}y_{i}})})^2$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.bhattacharya_2_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "bhattacharya_2_distance", "kind": "function", "doc": "Bhattacharya 2 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Bhattacharya 2 distance between v and y
\n
\n\nNotes
\n\n$$-\\ln{(\\sum\\sqrt{v_{i}y_{i}})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.harmonic_mean_similarity", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "harmonic_mean_similarity", "kind": "function", "doc": "Harmonic mean similarity:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Harmonic mean similarity between v and y
\n
\n\nNotes
\n\n$$#1-2\\sum(\\frac{v_{i}y_{i}}{v_{i}+y_{i}})\n2\\sum(\\frac{v_{i}y_{i}}{v_{i}+y_{i}})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.chernoff_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "chernoff_distance", "kind": "function", "doc": "Chernoff distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Chernoff distance between v and y
\n
\n\nNotes
\n\n$$\\max{(-ln\\sum(v_{i}^ty_{i}^{1-t})^{1-t})},\\ t=0.1,\\ 0\\le\\ t<1$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.ruzicka_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "ruzicka_distance", "kind": "function", "doc": "Ruzicka distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Ruzicka distance between v and y
\n
\n\nNotes
\n\n$$\\frac{\\sum{|v_{i}-y_{i}|}}{\\sum{\\max(v_{i},y_{i})}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.roberts_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "roberts_distance", "kind": "function", "doc": "Roberts distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Roberts distance between v and y
\n
\n\nNotes
\n\n$$1-\\sum\\frac{(v_{i}+y_{i})\\frac{\\min{(v_{i},y_{i})}}{\\max{(v_{i},y_{i})}}}{\\sum(v_{i}+y_{i})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.intersection_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "intersection_distance", "kind": "function", "doc": "Intersection distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Intersection distance between v and y
\n
\n\nNotes
\n\n$$1-\\frac{\\sum\\min{(v_{i},y_{i})}}{\\min(\\sum{v_{i},\\sum{y_{i})}}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.motyka_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "motyka_distance", "kind": "function", "doc": "Motyka distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Motyka distance between v and y
\n
\n\nNotes
\n\n$$-\\frac{\\sum\\min{(y_{i},v_{i})}}{\\sum(y_{i}+v_{i})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.canberra_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "canberra_distance", "kind": "function", "doc": "Canberra distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Canberra distance between v and y
\n
\n\nNotes
\n\n$$#\\sum\\frac{|v_{i}-y_{i}|}{|v_{i}|+|y_{i}|}\n\\sum_{i}\\frac{|y_{i} - v_{i}|}{y_{i} + v_{i}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.canberra_metric", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "canberra_metric", "kind": "function", "doc": "Canberra Metric
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Canberra metric between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{\\sum_{i}I(v_{i}\\neq 0)}\\sum_{i}\\frac{|y_{i}-v_{i}|}{(y_{i}+v_{i})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.kulczynski_1_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "kulczynski_1_distance", "kind": "function", "doc": "Kulczynski 1 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Kulczynski 1 distance between v and y
\n
\n\nNotes
\n\n$$\\frac{\\sum{|v_i}-y_i|}{\\sum m\\ i\\ n\\ (v_i,y_i)}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.baroni_urbani_buser_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "baroni_urbani_buser_distance", "kind": "function", "doc": "Baroni-Urbani-Buser distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Baroni-Urbani-Buser distance between v and y
\n
\n\nNotes
\n\n$$1-\\frac{\\sum\\min{(v_i,y_i)}+\\sqrt{\\sum\\min{(v_i,y_i)}\\sum(\\max{(v)}-\\max{(v_i,y_i)})}}{\\sum{\\max{(v_i,y_i)}+\\sqrt{\\sum{\\min{(v_i,y_i)}\\sum(\\max{(v)}-\\max{(v_i,y_i)})}}}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.penrose_size_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "penrose_size_distance", "kind": "function", "doc": "Penrose size distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Penrose size distance between v and y
\n
\n\nNotes
\n\n$$\\sqrt N\\sum{|y_i-v_i|}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.mean_character_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "mean_character_distance", "kind": "function", "doc": "Mean character distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Mean character distance between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{N}\\sum{|y_i-v_i|}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.lorentzian_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "lorentzian_distance", "kind": "function", "doc": "Lorentzian distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Lorentzian distance between v and y
\n
\n\nNotes
\n\n$$\\sum{\\ln(1+|v_i-y_i|)}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.penrose_shape_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "penrose_shape_distance", "kind": "function", "doc": "Penrose shape distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Penrose shape distance between v and y
\n
\n\nNotes
\n\n$$\\sqrt{\\sum((v_i-\\bar{v})-(y_i-\\bar{y}))^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.clark_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "clark_distance", "kind": "function", "doc": "Clark distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Clark distance between v and y
\n
\n\nNotes
\n\n$$#(\\frac{1}{N}\\sum(\\frac{v_i-y_i}{|v_i|+|y_i|})^2)^\\frac{1}{2}\n\\sqrt{\\sum(\\frac{|v_i-y_i|}{v_i+y_i})^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.hellinger_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "hellinger_distance", "kind": "function", "doc": "Hellinger distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Hellinger distance between v and y
\n
\n\nNotes
\n\n$$#\\sqrt{2\\sum(\\sqrt{\\frac{v_i}{\\bar{v}}}-\\sqrt{\\frac{y_i}{\\bar{y}}})^2}\n\\sqrt{2\\sum(\\sqrt{v_i}-\\sqrt{y_i})^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.whittaker_index_of_association_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "whittaker_index_of_association_distance", "kind": "function", "doc": "Whittaker index of association distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Whittaker index of association distance between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{2}\\sum|\\frac{v_i}{\\bar{v}}-\\frac{y_i}{\\bar{y}}|$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.similarity_index_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "similarity_index_distance", "kind": "function", "doc": "Similarity Index Distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Similarity Index Distance between v and y
\n
\n\nNotes
\n\n$$\\sqrt{\\frac{\\sum{\\frac{v_i-y_i}{y_i}}^2}{N}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.improved_similarity_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "improved_similarity_distance", "kind": "function", "doc": "Improved Similarity Index:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Improved Similarity Index between v and y
\n
\n\nNotes
\n\n$$\\sqrt{\\frac{1}{N}\\sum{\\frac{y_i-v_i}{y_i+v_i}}^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.absolute_value_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "absolute_value_distance", "kind": "function", "doc": "Absolute Value Distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Absolute Value Distance between v and y
\n
\n\nNotes
\n\n$$\\frac { \\sum(|y_i-v_i|)}{\\sum v_i}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.spectral_contrast_angle_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "spectral_contrast_angle_distance", "kind": "function", "doc": "Spectral Contrast Angle:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Spectral Contrast Angle between v and y
\n
\n\nNotes
\n\n$$1 - \\frac{\\sum{y_iv_i}}{\\sqrt{\\sum y_i^2\\sum v_i^2}}\n\\arccos(\\frac{\\sum_{P}y_{p}^* v_{p}^}{\\sqrt{\\sum_{P}y_{p}^{2} \\sum_{P}v_{p}^{*2}}})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.wave_hedges_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "wave_hedges_distance", "kind": "function", "doc": "Wave Hedges distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Wave Hedges distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{|v_i-y_i|}{\\max{(v_i,y_i)}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.dice_similarity", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "dice_similarity", "kind": "function", "doc": "Dice similarity:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Dice similarity between v and y
\n
\n\nNotes
\n\n$$\\frac{\\sum(v_i-y_i)^2}{\\sum v_i^2+\\sum y_i^2}\n\\frac{2 * \\sum_{i}v_{i}y_{i}}{\\sum_{i}y_{i}^2 + \\sum_{i}v_{i}^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.inner_product_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "inner_product_distance", "kind": "function", "doc": "Inner Product distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Inner product distance between v and y
\n
\n\nNotes
\n\n$$1-\\sum{v_iy_i}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.divergence_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "divergence_distance", "kind": "function", "doc": "Divergence distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Divergence distance between v and y
\n
\n\nNotes
\n\n$$2\\sum\\frac{(v_i-y_i)^2}{(v_i+y_i)^2}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.jensen_difference_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "jensen_difference_distance", "kind": "function", "doc": "Jensen difference:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Jensen difference distance between v and y
\n
\n\nNotes
\n\n$$\\sum[\\frac{1}{2}(v_i\\ln{v_i}+y_i\\ln{y_i})-(\\frac{v_i+y_i}{2})\\ln{(\\frac{v_i+y_i}{2})}]$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.kumar_johnson_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "kumar_johnson_distance", "kind": "function", "doc": "Kumar-Johnson distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Kumar Johnson distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{(v_i^2-y_i^2)^2}{2(v_iy_i)^\\frac{3}{2}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.avg_l_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "avg_l_distance", "kind": "function", "doc": "Avg (L1, L\u221e) distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Average L distance between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{2}(\\sum|v_i-y_i|+\\underset{i}{\\max}{|v_i-y_i|})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.vicis_wave_hadges_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "vicis_wave_hadges_distance", "kind": "function", "doc": "Vicis-Wave Hadges distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Vicis Wave Hadges distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{|v_i-y_i|}{\\min{(v_i,\\ y_i)}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.vicis_symmetric_chi_squared_1_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "vicis_symmetric_chi_squared_1_distance", "kind": "function", "doc": "Vicis-Symmetric \u03c72 1 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Vici Symmetric \u03c72 1 distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{(v_i-y_i)^2}{\\min{(v_i,y_i)^2}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.vicis_symmetric_chi_squared_2_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "vicis_symmetric_chi_squared_2_distance", "kind": "function", "doc": "Vicis-Symmetric \u03c72 2 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Vicis Symmetric \u03c72 2 distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{(v_i-y_i)^2}{\\min{(v_i,y_i)}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.vicis_symmetric_chi_squared_3_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "vicis_symmetric_chi_squared_3_distance", "kind": "function", "doc": "Vicis-Symmetric \u03c72 3 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Vici Symmetric \u03c72 3 distance between v and y
\n
\n\nNotes
\n\n$$\\sum\\frac{(v_i-y_i)^2}{\\max{(v_i,y_i)}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.max_symmetric_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "max_symmetric_chi_squared_distance", "kind": "function", "doc": "Max-Symmetric \u03c72 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Max-Symmetric \u03c72 distance between v and y
\n
\n\nNotes
\n\n$$\\max{(\\sum\\frac{(v_i-y_i)^2}{v_i},\\sum\\frac{(v_i-y_i)^2}{y_i})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.min_symmetric_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "min_symmetric_chi_squared_distance", "kind": "function", "doc": "Min-Symmetric \u03c72 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Min-Symmetric \u03c72 distance between v and y
\n
\n\nNotes
\n\n$$\\min{(\\sum\\frac{(v_i-y_i)^2}{v_i},\\sum\\frac{(v_i-y_i)^2}{y_i})}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.additive_sym_chi_sq", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "additive_sym_chi_sq", "kind": "function", "doc": "Additive Symmetric \u03c72 distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Additive Symmetric \u03c72 distance between v and y
\n
\n\nNotes
\n\n$$\\sum_{i}\\frac{(y_{i} - v_{i})^2(y_{i}+v_{i})}{y_{i}v_{i}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.bhattacharya_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "bhattacharya_distance", "kind": "function", "doc": "Bhattacharya Distance:
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Bhattcharya distance between v and y
\n
\n\nNotes
\n\n$$-ln(\\sum_{i}\\sqrt{y_{i}v_{i}})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.generalized_ochiai_index", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "generalized_ochiai_index", "kind": "function", "doc": "Generalized Ochiai Index
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Generalized Ochiai Index between v and y
\n
\n\nNotes
\n\n$$1 - \\frac{\\sum_{i}min(y_{i}, v_{i})}{\\sqrt{\\sum_{i}y_{i} \\sum_{i}v_{i}}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.gower_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "gower_distance", "kind": "function", "doc": "Gower Distance
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Gower distance between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{N}\\sum_{i}|y_{i} - v_{i}|$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.impr_sqrt_cosine_sim", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "impr_sqrt_cosine_sim", "kind": "function", "doc": "Improved Square Root Cosine Similarity
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Improved Square Root Cosine Similarity between v and y
\n
\n\nNotes
\n\n$$\\frac{\\sum_{i}\\sqrt{y_{i}v_{i}}}{\\sum_{i}\\sqrt{y_{i}}\\sum_{i}\\sqrt{v_{i}}}$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.intersection_sim", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "intersection_sim", "kind": "function", "doc": "Intersection Similarity
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Intersection Similarity between v and y
\n
\n\nNotes
\n\n$$\\sum_{i}min(y_{i}, v_{i})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.j_divergence", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "j_divergence", "kind": "function", "doc": "J Divergence
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: J Divergence between v and y
\n
\n\nNotes
\n\n$$\\sum_{i}(y_{i} - v_{i}) ln(\\frac{y_{i}}{v_{i}})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.jensen_shannon_index", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "jensen_shannon_index", "kind": "function", "doc": "Jensen-Shannon Index
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Jensen Shannon Index between v and y
\n
\n\nNotes
\n\n$$\\frac{1}{2}[\\sum_{i}y_{i}ln(\\frac{2y_{i}}{y_{i} + v_{i}}) + \\sum_{i}v_{i}ln(\\frac{2v_{i}}{y_{i}+v_{i}})]$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.k_divergence", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "k_divergence", "kind": "function", "doc": "K-Divergence
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: K-Divergence between v and y
\n
\n\nNotes
\n\n$$\\sum_{i}y_{i}ln(\\frac{2y_{i}}{y_{i} + v_{i}})$$
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.topsoe_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "topsoe_distance", "kind": "function", "doc": "Topsoe distance
\n\nParameters
\n\n\n- v (array_like):\nVector 1
\n- y (array_like):\nVector 2
\n
\n\nReturns
\n\n\n- float: Topsoe distance between v and y
\n- Notes
\n- -----
\n
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.probabilistic_symmetric_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "probabilistic_symmetric_chi_squared_distance", "kind": "function", "doc": "Fixed\n\"I commented out the previous one; please review\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW6", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW6", "kind": "function", "doc": "\"appears to be the same as max_symmetric_chi_squared_distance\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW5", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW5", "kind": "function", "doc": "\"appears to be the same as max_symmetric_chi_squared_distance\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW4", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW4", "kind": "function", "doc": "\"Tecnically the Symmetric chi2 eq63\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW3", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW3", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW2", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW2", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.VW1", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "VW1", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.taneja_divergence", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "taneja_divergence", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.symmetric_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "symmetric_chi_squared_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.squared_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "squared_chi_squared_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.square_root_cosine_correlation", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "square_root_cosine_correlation", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.sorensen_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "sorensen_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.Pearson_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "Pearson_chi_squared_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.Neyman_chi_squared_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "Neyman_chi_squared_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.Minokowski_3", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "Minokowski_3", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.Minokowski_4", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "Minokowski_4", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.kumarjohnson_divergence", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "kumarjohnson_divergence", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.kumarhassebrook_similarity", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "kumarhassebrook_similarity", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.kullbackleibler_divergence", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "kullbackleibler_divergence", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.calc.math_distance.soergel_distance", "modulename": "corems.molecular_id.calc.math_distance", "qualname": "soergel_distance", "kind": "function", "doc": "\"New\"
\n", "signature": "(v, y):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory", "modulename": "corems.molecular_id.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL", "modulename": "corems.molecular_id.factory.EI_SQL", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Base", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Base", "kind": "class", "doc": "The base class of the class hierarchy.
\n\nWhen called, it accepts no arguments and returns a new featureless\ninstance that has no instance attributes and cannot be given any.
\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Base.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Base.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Base.registry", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Base.registry", "kind": "variable", "doc": "\n", "default_value": "<sqlalchemy.orm.decl_api.registry object>"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Base.metadata", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Base.metadata", "kind": "variable", "doc": "\n", "default_value": "MetaData()"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar", "kind": "class", "doc": "This class is used to store the metadata of the compounds in the database
\n\nAttributes
\n\n\n- id (int):\nThe id of the compound.
\n- cas (str):\nThe CAS number of the compound.
\n- inchikey (str):\nThe InChiKey of the compound.
\n- inchi (str):\nThe InChi of the compound.
\n- chebi (str):\nThe ChEBI ID of the compound.
\n- smiles (str):\nThe SMILES of the compound.
\n- kegg (str):\nThe KEGG ID of the compound.
\n- iupac_name (str):\nThe IUPAC name of the compound.
\n- traditional_name (str):\nThe traditional name of the compound.
\n- common_name (str):\nThe common name of the compound.
\n- data_id (int):\nThe id of the compound in the molecularData table.
\n- data (LowResolutionEICompound):\nThe compound object.
\n
\n", "bases": "sqlalchemy.orm.decl_api.Base"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.cas", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.cas", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.inchikey", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.inchikey", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.inchi", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.inchi", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.chebi", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.chebi", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.smiles", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.smiles", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.kegg", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.kegg", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.iupac_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.iupac_name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.traditional_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.traditional_name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.common_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.common_name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.data_id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.data_id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.Metadatar.data", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "Metadatar.data", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound", "kind": "class", "doc": "This class is used to store the molecular and spectral data of the compounds in the low res EI database
\n\nAttributes
\n\n\n- id (int):\nThe id of the compound.
\n- name (str):\nThe name of the compound.
\n- classify (str):\nThe classification of the compound.
\n- formula (str):\nThe formula of the compound.
\n- ri (float):\nThe retention index of the compound.
\n- retention_time (float):\nThe retention time of the compound.
\n- source (str):\nThe source of the compound.
\n- casno (str):\nThe CAS number of the compound.
\n- comment (str):\nThe comment of the compound.
\n- source_temp_c (float):\nThe source temperature of the spectra.
\n- ev (float):\nThe electron volts of the spectra.
\n- peaks_count (int):\nThe number of peaks in the spectra.
\n- mz (numpy.ndarray):\nThe m/z values of the spectra.
\n- abundance (numpy.ndarray):\nThe abundance values of the spectra.
\n- metadatar (Metadatar):\nThe metadata object.
\n
\n", "bases": "sqlalchemy.orm.decl_api.Base"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.__init__", "kind": "function", "doc": "\n", "signature": "(dict_data)"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.classify", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.classify", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.formula", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.formula", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.ri", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.ri", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.retention_time", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.retention_time", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.derivativenum", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.derivativenum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.derivatization", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.derivatization", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.source", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.source", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.casno", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.casno", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.comment", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.comment", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.source_temp_c", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.source_temp_c", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.ev", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.ev", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.peaks_count", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.peaks_count", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.mz", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.abundance", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.abundance", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResolutionEICompound.metadatar", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResolutionEICompound.metadatar", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata", "kind": "class", "doc": "Dataclass for the Metabolite Metadata
\n\nAttributes
\n\n\n- id (int):\nThe id of the compound.
\n- cas (str):\nThe CAS number of the compound.
\n- inchikey (str):\nThe InChiKey of the compound.
\n- inchi (str):\nThe InChi of the compound.
\n- chebi (str):\nThe ChEBI ID of the compound.
\n- smiles (str):\nThe SMILES of the compound.
\n- kegg (str):\nThe KEGG ID of the compound.
\n- iupac_name (str):\nThe IUPAC name of the compound.
\n- traditional_name (str):\nThe traditional name of the compound.
\n- common_name (str):\nThe common name of the compound.
\n- data_id (int):\nThe id of the compound in the molecularData table.
\n
\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.__init__", "kind": "function", "doc": "\n", "signature": "(\tid: int,\tcas: str,\tinchikey: str,\tinchi: str,\tchebi: str,\tsmiles: str,\tkegg: str,\tdata_id: int,\tiupac_name: str,\ttraditional_name: str,\tcommon_name: str)"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.id", "kind": "variable", "doc": "\n", "annotation": ": int"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.cas", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.cas", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.inchikey", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.inchikey", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.inchi", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.inchi", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.chebi", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.chebi", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.smiles", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.smiles", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.kegg", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.kegg", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.data_id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.data_id", "kind": "variable", "doc": "\n", "annotation": ": int"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.iupac_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.iupac_name", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.traditional_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.traditional_name", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.MetaboliteMetadata.common_name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "MetaboliteMetadata.common_name", "kind": "variable", "doc": "\n", "annotation": ": str"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef", "kind": "class", "doc": "Dataclass for the Low Resolution Compound Reference
\n\nThis class is used to store the molecular and spectral data of the compounds in the low res EI database
\n\nParameters
\n\n\n- compounds_dict (dict):\nA dictionary representing the compound.
\n
\n\nAttributes
\n\n\n- id (int):\nThe id of the compound.
\n- name (str):\nThe name of the compound.
\n- ri (str):\nThe retention index of the compound.
\n- retention_time (str):\nThe retention time of the compound.
\n- casno (str):\nThe CAS number of the compound.
\n- comment (str):\nThe comment of the compound.
\n- peaks_count (int):\nThe number of peaks in the spectra.
\n- classify (str):\nThe classification of the compound.
\n- derivativenum (str):\nThe derivative number of the compound.
\n- derivatization (str):\nThe derivatization applied to the compound.
\n- mz (numpy.ndarray):\nThe m/z values of the spectra.
\n- abundance (numpy.ndarray):\nThe abundance values of the spectra.
\n- source_temp_c (float):\nThe source temperature of the spectra.
\n- ev (float):\nThe electron volts of the spectra.
\n- formula (str):\nThe formula of the compound.
\n- source (str):\nThe source of the spectra data.
\n- classify (str):\nThe classification of the compound.
\n- metadata (MetaboliteMetadata):\nThe metadata object.
\n- similarity_score (float):\nThe similarity score of the compound.
\n- ri_score (float):\nThe RI score of the compound.
\n- spectral_similarity_score (float):\nThe spectral similarity score of the compound.
\n- spectral_similarity_scores (dict):\nThe spectral similarity scores of the compound.
\n
\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.__init__", "kind": "function", "doc": "\n", "signature": "(compounds_dict)"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.id", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.name", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.ri", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.ri", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.retention_time", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.retention_time", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.casno", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.casno", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.comment", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.comment", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.peaks_count", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.peaks_count", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.classify", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.classify", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.derivativenum", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.derivativenum", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.derivatization", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.derivatization", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.mz", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.abundance", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.abundance", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.source_temp_c", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.source_temp_c", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.ev", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.ev", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.formula", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.formula", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.source", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.source", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.similarity_score", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.similarity_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.ri_score", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.ri_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.spectral_similarity_score", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.spectral_similarity_score", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.LowResCompoundRef.spectral_similarity_scores", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "LowResCompoundRef.spectral_similarity_scores", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite", "kind": "class", "doc": "A class for interacting with a SQLite database for low-resolution EI compounds.
\n\nParameters
\n\n\n- url (str, optional):\nThe URL of the SQLite database. Default is 'sqlite://'.
\n
\n\nAttributes
\n\n\n- engine (sqlalchemy.engine.Engine):\nThe SQLAlchemy engine for connecting to the database.
\n- session (sqlalchemy.orm.Session):\nThe SQLAlchemy session for executing database operations.
\n
\n\nMethods
\n\n\n- __init__(self, url='sqlite://').\nInitializes the EI_LowRes_SQLite object.
\n- __exit__(self, exc_type, exc_val, exc_tb).\nCloses the database connection.
\n- init_engine(self, url).\nInitializes the SQLAlchemy engine.
\n- __enter__(self).\nReturns the EI_LowRes_SQLite object.
\n- add_compound_list(self, data_dict_list).\nAdds a list of compounds to the database.
\n- add_compound(self, data_dict).\nAdds a single compound to the database.
\n- commit(self).\nCommits the changes to the database.
\n- row_to_dict(self, row).\nConverts a database row to a dictionary.
\n- get_all(self).\nRetrieves all compounds from the database.
\n- query_min_max_rt(self, min_max_rt).\nQueries compounds based on retention time range.
\n- query_min_max_ri(self, min_max_ri).\nQueries compounds based on RI range.
\n- query_names_and_rt(self, min_max_rt, compound_names).\nQueries compounds based on compound names and retention time range.
\n- query_min_max_ri_and_rt(self, min_max_ri, min_max_rt).\nQueries compounds based on RI range and retention time range.
\n- delete_compound(self, compound).\nDeletes a compound from the database.
\n- purge(self).\nDeletes all compounds from the database table.
\n- clear_data(self).\nClears all tables in the database.
\n
\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.__init__", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.__init__", "kind": "function", "doc": "\n", "signature": "(url='sqlite://')"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.engine", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.engine", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.session", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.session", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.init_engine", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.init_engine", "kind": "function", "doc": "Initializes the SQLAlchemy engine.
\n\nParameters
\n\n\n- url (str):\nThe URL of the SQLite database.
\n
\n\nReturns
\n\n\n- sqlalchemy.engine.Engine: The SQLAlchemy engine for connecting to the database.
\n
\n", "signature": "(self, url):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.add_compound_list", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.add_compound_list", "kind": "function", "doc": "Adds a list of compounds to the database.
\n\nParameters
\n\n\n- data_dict_list (list of dict):\nA list of dictionaries representing the compounds.
\n
\n", "signature": "(self, data_dict_list):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.add_compound", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.add_compound", "kind": "function", "doc": "Adds a single compound to the database.
\n\nParameters
\n\n\n- data_dict (dict):\nA dictionary representing the compound.
\n
\n", "signature": "(self, data_dict):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.commit", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.commit", "kind": "function", "doc": "Commits the changes to the database.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.row_to_dict", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.row_to_dict", "kind": "function", "doc": "Converts a database row to a dictionary.
\n\nParameters
\n\n\n- row (sqlalchemy.engine.row.Row):\nA row from the database.
\n
\n\nReturns
\n\n\n- dict: A dictionary representing the compound.
\n
\n", "signature": "(self, row):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.get_all", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.get_all", "kind": "function", "doc": "Retrieves all compounds from the database.
\n\nReturns
\n\n\n- list: A list of dictionaries representing the compounds.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.query_min_max_rt", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.query_min_max_rt", "kind": "function", "doc": "Queries compounds based on retention time range.
\n\nParameters
\n\n\n- min_max_rt (tuple):\nA tuple containing the minimum and maximum retention time values.
\n
\n\nReturns
\n\n\n- list: A list of dictionaries representing the compounds.
\n
\n", "signature": "(self, min_max_rt):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.query_min_max_ri", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.query_min_max_ri", "kind": "function", "doc": "Queries compounds based on RI range.
\n\nParameters
\n\n\n- min_max_ri (tuple):\nA tuple containing the minimum and maximum RI values.
\n
\n", "signature": "(self, min_max_ri):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.query_names_and_rt", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.query_names_and_rt", "kind": "function", "doc": "Queries compounds based on compound names and retention time range.
\n\nParameters
\n\n\n- min_max_rt (tuple):\nA tuple containing the minimum and maximum retention time values.
\n- compound_names (list):\nA list of compound names.
\n
\n\nReturns
\n\n\n- list: A list of dictionaries representing the compounds.
\n
\n", "signature": "(self, min_max_rt, compound_names):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.query_min_max_ri_and_rt", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.query_min_max_ri_and_rt", "kind": "function", "doc": "Queries compounds based on RI range and retention time range.
\n\nParameters
\n\n\n- min_max_ri (tuple):\nA tuple containing the minimum and maximum RI values.
\n- min_max_rt (tuple):\nA tuple containing the minimum and maximum retention time values.
\n
\n\nReturns
\n\n\n- list: A list of dictionaries representing the compounds.
\n
\n", "signature": "(self, min_max_ri, min_max_rt):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.delete_compound", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.delete_compound", "kind": "function", "doc": "Deletes a compound from the database.
\n\nParameters
\n\n\n- compound (LowResolutionEICompound):\nA compound object.
\n
\n", "signature": "(self, compound):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.purge", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.purge", "kind": "function", "doc": "Deletes all compounds from the database table.
\n\nNotes
\n\nCareful, this will delete the entire database table.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.EI_SQL.EI_LowRes_SQLite.clear_data", "modulename": "corems.molecular_id.factory.EI_SQL", "qualname": "EI_LowRes_SQLite.clear_data", "kind": "function", "doc": "Clears all tables in the database.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.profiled", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "profiled", "kind": "function", "doc": "A context manager for profiling.
\n", "signature": "():", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.insert_database_worker", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "insert_database_worker", "kind": "function", "doc": "Inserts data into the database.
\n", "signature": "(args):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations", "kind": "class", "doc": "A class for generating molecular formula combinations.
\n\nParameters
\n\n\n- molecular_search_settings (object):\nAn object containing user-defined settings.
\n
\n\nAttributes
\n\n\n- sql_db (MolForm_SQL):\nThe SQLite database object.
\n- len_existing_classes (int):\nThe number of existing classes in the SQLite database.
\n- odd_ch_id (list):\nA list of odd carbon and hydrogen atom IDs.
\n- odd_ch_dict (list):\nA list of odd carbon and hydrogen atom dictionaries.
\n- odd_ch_mass (list):\nA list of odd carbon and hydrogen atom masses.
\n- odd_ch_dbe (list):\nA list of odd carbon and hydrogen atom double bond equivalents.
\n- even_ch_id (list):\nA list of even carbon and hydrogen atom IDs.
\n- even_ch_dict (list):\nA list of even carbon and hydrogen atom dictionaries.
\n- even_ch_mass (list):\nA list of even carbon and hydrogen atom masses.
\n- even_ch_dbe (list):\nA list of even carbon and hydrogen atom double bond equivalents.
\n
\n\nMethods
\n\n\n- cProfile_worker(args)
\nA cProfile worker for the get_mol_formulas function. \n- check_database_get_class_list(molecular_search_settings)
\nChecks if the database has all the classes, if not create the missing classes. \n- get_carbonsHydrogens(settings, odd_even)
\nRetrieves carbon and hydrogen atoms from the molecular lookup table based on user-defined settings. \n- add_carbonsHydrogens(settings, existing_classes_objs)
\nAdds carbon and hydrogen atoms to the molecular lookup table based on user-defined settings. \n- runworker(molecular_search_settings)
\nRuns the molecular formula lookup table worker. \n- get_classes_in_order(molecular_search_settings)
\nGets the classes in order. \n- sort_classes(atoms_in_order, combination_dict)
\nSorts the classes in order. \n- get_fixed_initial_number_of_hydrogen(min_h, odd_even)
\nGets the fixed initial number of hydrogen atoms. \n- calc_mz(datadict, class_mass=0)
\nCalculates the mass-to-charge ratio (m/z) of a molecular formula. \n- calc_dbe_class(datadict)
\nCalculates the double bond equivalent (DBE) of a molecular formula. \n- populate_combinations(classe_tuple, settings)
\nPopulates the combinations. \n- get_or_add(SomeClass, kw)
\nGets or adds a class. \n- get_mol_formulas(odd_even_tag, classe_tuple, settings)
\nGets the molecular formulas. \n- get_h_odd_or_even(class_dict)
\nGets the hydrogen odd or even. \n- get_total_halogen_atoms(class_dict)
\nGets the total number of halogen atoms. \n- get_total_hetero_valence(class_dict)\nGets the total valence of heteroatoms other than N, F, Cl, and Br
\n
\n"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.__init__", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.__init__", "kind": "function", "doc": "\n", "signature": "(sql_db=None)"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.cProfile_worker", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.cProfile_worker", "kind": "function", "doc": "cProfile worker for the get_mol_formulas function
\n", "signature": "(self, args):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.check_database_get_class_list", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.check_database_get_class_list", "kind": "function", "doc": "check if the database has all the classes, if not create the missing classes
\n\nParameters
\n\n\n- molecular_search_settings (object):\nAn object containing user-defined settings.
\n
\n\nReturns
\n\n\n- list: list of tuples with the class name and the class dictionary
\n
\n", "signature": "(self, molecular_search_settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_carbonsHydrogens", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_carbonsHydrogens", "kind": "function", "doc": "Retrieve carbon and hydrogen atoms from the molecular lookup table based on user-defined settings.
\n\nParameters
\n\n\n- settings (object):\nAn object containing user-defined settings.
\n- odd_even (str):\nA string indicating whether to retrieve even or odd hydrogen atoms.
\n
\n\nReturns
\n\n\n- list: A list of CarbonHydrogen objects that satisfy the specified conditions.
\n
\n", "signature": "(self, settings, odd_even):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.add_carbonsHydrogens", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.add_carbonsHydrogens", "kind": "function", "doc": "Add carbon and hydrogen atoms to the molecular lookup table based on user-defined settings.
\n\nParameters
\n\n\n- settings (object):\nAn object containing user-defined settings.
\n- existing_classes_objs (list):\nA list of HeteroAtoms objects.
\n
\n", "signature": "(self, settings, existing_classes_objs):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.runworker", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.runworker", "kind": "function", "doc": "Run the molecular formula lookup table worker.
\n\nParameters
\n\n\n- molecular_search_settings (object):\nAn object containing user-defined settings.
\n
\n\nReturns
\n\n\n- list: A list of tuples with the class name and the class dictionary.
\n
\n", "signature": "(*args, **kw):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_classes_in_order", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_classes_in_order", "kind": "function", "doc": "Get the classes in order
\n\nParameters
\n\n\n- molecular_search_settings (object):\nAn object containing user-defined settings.
\n
\n\nReturns
\n\n\n- dict: A dictionary of classes in order.\nstructure is ('HC', {'HC': 1})
\n
\n", "signature": "(self, molecular_search_settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.sort_classes", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.sort_classes", "kind": "function", "doc": "Sort the classes in order
\n\nParameters
\n\n\n- atoms_in_order (list):\nA list of atoms in order.
\n- combination_dict (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- dict: A dictionary of classes in order.
\n
\n", "signature": "(atoms_in_order, combination_dict) -> Dict[str, Dict[str, int]]:", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_fixed_initial_number_of_hydrogen", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_fixed_initial_number_of_hydrogen", "kind": "function", "doc": "Get the fixed initial number of hydrogen atoms
\n\nParameters
\n\n\n- min_h (int):\nThe minimum number of hydrogen atoms.
\n- odd_even (str):\nA string indicating whether to retrieve even or odd hydrogen atoms.
\n
\n", "signature": "(min_h, odd_even):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.calc_mz", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.calc_mz", "kind": "function", "doc": "Calculate the mass-to-charge ratio (m/z) of a molecular formula.
\n\nParameters
\n\n\n- datadict (dict):\nA dictionary of classes.
\n- class_mass (int):\nThe mass of the class.
\n
\n\nReturns
\n\n\n- float: The mass-to-charge ratio (m/z) of a molecular formula.
\n
\n", "signature": "(self, datadict, class_mass=0):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.calc_dbe_class", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.calc_dbe_class", "kind": "function", "doc": "Calculate the double bond equivalent (DBE) of a molecular formula.
\n\nParameters
\n\n\n- datadict (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- float: The double bond equivalent (DBE) of a molecular formula.
\n
\n", "signature": "(self, datadict):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.populate_combinations", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.populate_combinations", "kind": "function", "doc": "Populate the combinations
\n\nParameters
\n\n\n- classe_tuple (tuple):\nA tuple containing the class name, the class dictionary, and the class ID.
\n- settings (object):\nAn object containing user-defined settings.
\n
\n\nReturns
\n\n\n- list: A list of molecular formula data dictionaries.
\n
\n", "signature": "(self, classe_tuple, settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_or_add", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_or_add", "kind": "function", "doc": "Get or add a class
\n\nParameters
\n\n\n- SomeClass (object):\nA class object.
\n- kw (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- object: A class object.
\n
\n", "signature": "(self, SomeClass, kw):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_mol_formulas", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_mol_formulas", "kind": "function", "doc": "Get the molecular formulas
\n\nParameters
\n\n\n\nReturns
\n\n\n- list: A list of molecular formula data dictionaries.
\n
\n", "signature": "(self, odd_even_tag, classe_tuple, settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_h_odd_or_even", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_h_odd_or_even", "kind": "function", "doc": "Get the hydrogen odd or even
\n\nParameters
\n\n\n- class_dict (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- str: A string indicating whether to retrieve even or odd hydrogen atoms.
\n
\n", "signature": "(self, class_dict):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_total_heteroatoms", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_total_heteroatoms", "kind": "function", "doc": "Get the total number of heteroatoms other than N, F, Cl, Br
\n\nParameters
\n\n\n- class_dict (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- int: The total number of heteroatoms.
\n
\n", "signature": "(class_dict):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_total_hetero_valence", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_total_hetero_valence", "kind": "function", "doc": "Get the total valence of heteroatoms other than N, F, Cl, Br
\n\nParameters
\n\n\n- class_dict (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- int: The total heteroatom valence.
\n
\n", "signature": "(class_dict):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.MolecularLookupTable.MolecularCombinations.get_total_halogen_atoms", "modulename": "corems.molecular_id.factory.MolecularLookupTable", "qualname": "MolecularCombinations.get_total_halogen_atoms", "kind": "function", "doc": "Get the total number of halogen atoms
\n\nParameters
\n\n\n- class_dict (dict):\nA dictionary of classes.
\n
\n\nReturns
\n\n\n- int: The total number of halogen atoms.
\n
\n", "signature": "(class_dict):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification", "modulename": "corems.molecular_id.factory.classification", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.flatten_list", "modulename": "corems.molecular_id.factory.classification", "qualname": "flatten_list", "kind": "function", "doc": "\n", "signature": "(l):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification", "kind": "class", "doc": "Class for grouping mass spectrum data by heteroatom classes (Nn, Oo, Ss, NnOo, NnSs, etc..)
\n\nParameters
\n\n\n- mass_spectrum (MassSpectrum):\nThe mass spectrum object.
\n- choose_molecular_formula (bool, optional):\nIf True, the molecular formula with the highest abundance is chosen. If False, all molecular formulas are considered. Default is True.
\n
\n\nRaises
\n\n\n- Exception: If no molecular formula is associated with any mspeak objects.
\n
\n\nAttributes
\n\n\n- _ms_grouped_class (dict):\nA dictionary of classes and a list of ms_peak objects.
\n- choose_mf (bool):\nIf True, the molecular formula with the highest abundance is chosen. If False, all molecular formulas are considered.
\n- total_peaks (int):\nThe total number of peaks.
\n- sum_abundance (float):\nThe sum of the abundance of all peaks.
\n- min_max_mz (tuple):\nThe minimum and maximum mz values.
\n- min_max_abundance (tuple):\nThe minimum and maximum abundance values.
\n- min_ppm_error (float):\nThe minimum ppm error.
\n- max_ppm_error (float):\nThe maximum ppm error.
\n- all_identified_atoms (list):\nA list of all identified atoms.
\n
\n\nMethods
\n\n\n- __len__().\nReturns the number of classes.
\n- __getitem__(classe)
\nReturns the molecular formula list for specified class. \n- __iter__().\nReturns an iterator over the keys of the dictionary.
\n- get_classes(threshold_perc=1, isotopologue=True).\nReturns a list of classes with abundance percentile above threshold.
\n- molecular_formula_string(classe).\nReturns a list of molecular formula string for specified class.
\n- molecular_formula(classe).\nReturns a list of molecular formula for specified class.
\n- carbon_number(classe).\nReturns a list of carbon number for specified class.
\n- atom_count(atom, classe).\nReturns a list of atom count for specified class.
\n- dbe(classe).\nReturns a list of DBE for specified class.
\n- atoms_ratio(classe, numerator, denominator).\nReturns a list of atoms ratio for specified class.
\n- mz_exp(classe).\nReturns a list of experimental mz for specified class.
\n- abundance(classe).\nReturns a list of abundance for specified class.
\n- mz_error(classe).\nReturns a list of mz error for specified class.
\n- mz_calc(classe).\nReturns a list of calculated mz for specified class.
\n- peaks_count_percentile(classe).\nReturns the peaks count percentile of a specific class.
\n- abundance_count_percentile(classe).\nReturns the abundance percentile of a specific class.
\n- mz_exp_assigned().\nReturns a list of experimental mz for all assigned classes.
\n- abundance_assigned().\nReturns a list of abundance for all classes.
\n- mz_exp_all().\nReturns a list of mz for all classes.
\n
\n", "bases": "collections.abc.Mapping"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.__init__", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.__init__", "kind": "function", "doc": "\n", "signature": "(mass_spectrum, choose_molecular_formula=True)"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.choose_mf", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.choose_mf", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.total_peaks", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.total_peaks", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.sum_abundance", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.sum_abundance", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.min_max_mz", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.min_max_mz", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.min_max_abundance", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.min_max_abundance", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.min_ppm_error", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.min_ppm_error", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.max_ppm_error", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.max_ppm_error", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.all_identified_atoms", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.all_identified_atoms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.get_classes", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.get_classes", "kind": "function", "doc": "Return a list of classes with abundance percentile above threshold
\n", "signature": "(self, threshold_perc=1, isotopologue=True):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.molecular_formula_string", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.molecular_formula_string", "kind": "function", "doc": "Return a list of molecular formula string for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.molecular_formula", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.molecular_formula", "kind": "function", "doc": "Return a list of molecular formula for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.carbon_number", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.carbon_number", "kind": "function", "doc": "Return a list of carbon number for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.atom_count", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.atom_count", "kind": "function", "doc": "Return a list of atom count for specified class
\n", "signature": "(self, atom, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.dbe", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.dbe", "kind": "function", "doc": "Return a list of DBE for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.atoms_ratio", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.atoms_ratio", "kind": "function", "doc": "Return a list of atoms ratio for specified class
\n", "signature": "(self, classe, numerator, denominator):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_exp", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_exp", "kind": "function", "doc": "Return a list of experimental mz for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.abundance", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.abundance", "kind": "function", "doc": "Return a list of abundance for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_error", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_error", "kind": "function", "doc": "Return a list of mz error for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_calc", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_calc", "kind": "function", "doc": "Return a list of calculated mz for specified class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.peaks_count_percentile", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.peaks_count_percentile", "kind": "function", "doc": "Return the peaks count percentile of a specific class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.abundance_count_percentile", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.abundance_count_percentile", "kind": "function", "doc": "Return the abundance percentile of a specific class
\n", "signature": "(self, classe):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_exp_assigned", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_exp_assigned", "kind": "function", "doc": "Return a list of experimental mz for all assigned classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.abundance_assigned", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.abundance_assigned", "kind": "function", "doc": "Return a list of abundance for all classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_exp_all", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_exp_all", "kind": "function", "doc": "Return a list of mz for all classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.mz_error_all", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.mz_error_all", "kind": "function", "doc": "Return a list of mz error for all classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.carbon_number_all", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.carbon_number_all", "kind": "function", "doc": "Return a list of carbon number for all classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.dbe_all", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.dbe_all", "kind": "function", "doc": "Return a list of DBE for all classes
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.atoms_ratio_all", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.atoms_ratio_all", "kind": "function", "doc": "Return a list of atoms ratio for all classes
\n", "signature": "(self, numerator, denominator):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.to_dataframe", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.to_dataframe", "kind": "function", "doc": "Return a pandas dataframe with all the data from the class
\n\nParameters
\n\n\n- include_isotopologue (bool, optional):\nInclude isotopologues, by default False
\n- abundance_perc_threshold (int, optional):\nAbundance percentile threshold, by default 5
\n- include_unassigned (bool, optional):\nInclude unassigned peaks, by default False
\n
\n\nReturns
\n\n\n- DataFrame: Pandas dataframe with all the data from the class
\n
\n", "signature": "(\tself,\tinclude_isotopologue=False,\tabundance_perc_threshold=5,\tinclude_unassigned=False):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_ms_assigned_unassigned", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_ms_assigned_unassigned", "kind": "function", "doc": "Plot stick mass spectrum of all classes
\n\nParameters
\n\n\n- assigned_color (str, optional):\nMatplotlib color for the assigned peaks, by default \"b\"
\n- unassigned_color (str, optional):\nMatplotlib color for the unassigned peaks, by default \"r\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n
\n", "signature": "(self, assigned_color='b', unassigned_color='r'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_mz_error", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_mz_error", "kind": "function", "doc": "Plot mz error scatter plot of all classes
\n\nParameters
\n\n\n- color (str, optional):\nMatplotlib color, by default \"g\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n
\n", "signature": "(self, color='g'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_mz_error_class", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_mz_error_class", "kind": "function", "doc": "Plot mz error scatter plot of a specific class
\n\nParameters
\n\n\n- classe (str):\nClass name
\n- color (str, optional):\nMatplotlib color, by default \"g\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n
\n", "signature": "(self, classe, color='g'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_ms_class", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_ms_class", "kind": "function", "doc": "Plot stick mass spectrum of a specific class
\n\nParameters
\n\n\n- classe (str):\nClass name
\n- color (str, optional):\nMatplotlib color, by default \"g\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n
\n", "signature": "(self, classe, color='g'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_van_krevelen", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_van_krevelen", "kind": "function", "doc": "Plot Van Krevelen Diagram
\n\nParameters
\n\n\n- classe (str):\nClass name
\n- max_hc (float, optional):\nMax H/C ratio, by default 2.5
\n- max_oc (float, optional):\nMax O/C ratio, by default 2
\n- ticks_number (int, optional):\nNumber of ticks, by default 5
\n- color (str, optional):\nMatplotlib color, by default \"viridis\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n- abun_perc (float):\nClass percentile of the relative abundance
\n
\n", "signature": "(self, classe, max_hc=2.5, max_oc=2, ticks_number=5, color='viridis'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.classification.HeteroatomsClassification.plot_dbe_vs_carbon_number", "modulename": "corems.molecular_id.factory.classification", "qualname": "HeteroatomsClassification.plot_dbe_vs_carbon_number", "kind": "function", "doc": "Plot DBE vs Carbon Number
\n\nParameters
\n\n\n- classe (str):\nClass name
\n- max_c (int, optional):\nMax Carbon Number, by default 50
\n- max_dbe (int, optional):\nMax DBE, by default 40
\n- dbe_incr (int, optional):\nDBE increment, by default 5
\n- c_incr (int, optional):\nCarbon Number increment, by default 10
\n- color (str, optional):\nMatplotlib color, by default \"viridis\"
\n
\n\nReturns
\n\n\n- ax (matplotlib.axes):\nMatplotlib axes object
\n- abun_perc (float):\nClass percentile of the relative abundance
\n
\n", "signature": "(\tself,\tclasse,\tmax_c=50,\tmax_dbe=40,\tdbe_incr=5,\tc_incr=10,\tcolor='viridis'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL", "modulename": "corems.molecular_id.factory.molecularSQL", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.Base", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "Base", "kind": "class", "doc": "The base class of the class hierarchy.
\n\nWhen called, it accepts no arguments and returns a new featureless\ninstance that has no instance attributes and cannot be given any.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.Base.__init__", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "Base.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.molecularSQL.Base.registry", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "Base.registry", "kind": "variable", "doc": "\n", "default_value": "<sqlalchemy.orm.decl_api.registry object>"}, {"fullname": "corems.molecular_id.factory.molecularSQL.Base.metadata", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "Base.metadata", "kind": "variable", "doc": "\n", "default_value": "MetaData()"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms", "kind": "class", "doc": "HeteroAtoms class for the heteroAtoms table in the SQLite database.
\n\nAttributes
\n\n\n- id (int):\nThe primary key for the table.
\n- name (str):\nThe name of the heteroAtoms class.
\n- halogensCount (int):\nThe number of halogens in the heteroAtoms class.
\n- carbonHydrogen (relationship):\nThe relationship to the carbonHydrogen table.
\n
\n\nMethods
\n\n\n- __repr__()\nReturns the string representation of the object.
\n- to_dict()\nReturns the heteroAtoms class as a dictionary.
\n- halogens_count()\nReturns the number of halogens as a float.
\n
\n", "bases": "sqlalchemy.orm.decl_api.Base"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.__init__", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.id", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.name", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.name", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.halogensCount", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.halogensCount", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.carbonHydrogen", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.carbonHydrogen", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.halogens_count", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.halogens_count", "kind": "variable", "doc": "Returns the number of halogens as a float.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.HeteroAtoms.to_dict", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "HeteroAtoms.to_dict", "kind": "function", "doc": "Returns the heteroAtoms class as a dictionary.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen", "kind": "class", "doc": "CarbonHydrogen class for the carbonHydrogen table in the SQLite database.
\n\nAttributes
\n\n\n- id (int):\nThe primary key for the table.
\n- C (int):\nThe number of carbon atoms.
\n- H (int):\nThe number of hydrogen atoms.
\n- heteroAtoms (relationship):\nThe relationship to the heteroAtoms table.
\n
\n\nMethods
\n\n\n- __repr__()\nReturns the string representation of the object.
\n- mass()\nReturns the mass of the carbonHydrogen class as a float.
\n- c()\nReturns the number of carbon atoms as a float.
\n- h()\nReturns the number of hydrogen atoms as a float.
\n- dbe()\nReturns the double bond equivalent as a float.
\n
\n", "bases": "sqlalchemy.orm.decl_api.Base"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.__init__", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.id", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.C", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.C", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.H", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.H", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.heteroAtoms", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.heteroAtoms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.mass", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.mass", "kind": "variable", "doc": "Returns the mass of the carbonHydrogen class as a float.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.c", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.c", "kind": "variable", "doc": "Returns the number of carbon atoms as a float.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.h", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.h", "kind": "variable", "doc": "Returns the number of hydrogen atoms as a float.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.CarbonHydrogen.dbe", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "CarbonHydrogen.dbe", "kind": "variable", "doc": "Returns the double bond equivalent as a float.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink", "kind": "class", "doc": "MolecularFormulaLink class for the molecularformula table in the SQLite database.
\n\nAttributes
\n\n\n- heteroAtoms_id (int):\nThe foreign key for the heteroAtoms table.
\n- carbonHydrogen_id (int):\nThe foreign key for the carbonHydrogen table.
\n- mass (float):\nThe mass of the molecular formula.
\n- DBE (float):\nThe double bond equivalent of the molecular formula.
\n- carbonHydrogen (relationship):\nThe relationship to the carbonHydrogen table.
\n- heteroAtoms (relationship):\nThe relationship to the heteroAtoms table.
\n- C (association_proxy):\nThe association proxy for the carbonHydrogen table.
\n- H (association_proxy):\nThe association proxy for the carbonHydrogen table.
\n- classe (association_proxy):\nThe association proxy for the heteroAtoms table.
\n
\n\nMethods
\n\n\n- __repr__()\nReturns the string representation of the object.
\n- to_dict()\nReturns the molecular formula as a dictionary.
\n- formula_string()\nReturns the molecular formula as a string.
\n- classe_string()\nReturns the heteroAtoms class as a string.
\n- _adduct_mz(ion_charge, adduct_atom)\nReturns the m/z of the adduct ion as a float.
\n- _protonated_mz(ion_charge)\nReturns the m/z of the protonated ion as a float.
\n- _radical_mz(ion_charge)\nReturns the m/z of the radical ion as a float.
\n
\n", "bases": "sqlalchemy.orm.decl_api.Base"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.__init__", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.__init__", "kind": "function", "doc": "A simple constructor that allows initialization from kwargs.
\n\nSets attributes on the constructed instance using the names and\nvalues in kwargs.
\n\nOnly keys that are present as\nattributes of the instance's class are allowed. These could be,\nfor example, any mapped columns or relationships.
\n", "signature": "(**kwargs)"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.heteroAtoms_id", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.heteroAtoms_id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.carbonHydrogen_id", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.carbonHydrogen_id", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.mass", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.mass", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.DBE", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.DBE", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.carbonHydrogen", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.carbonHydrogen", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.heteroAtoms", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.heteroAtoms", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.C", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.C", "kind": "variable", "doc": "A descriptor that presents a read/write view of an object attribute.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.H", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.H", "kind": "variable", "doc": "A descriptor that presents a read/write view of an object attribute.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.classe", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.classe", "kind": "variable", "doc": "A descriptor that presents a read/write view of an object attribute.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.to_dict", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.to_dict", "kind": "function", "doc": "Returns the molecular formula as a dictionary.
\n\nReturns
\n\n\n- dict: The molecular formula as a dictionary.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.formula_string", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.formula_string", "kind": "variable", "doc": "Returns the molecular formula as a string.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolecularFormulaLink.classe_string", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolecularFormulaLink.classe_string", "kind": "variable", "doc": "Returns the heteroAtoms class as a string.
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL", "kind": "class", "doc": "MolForm_SQL class for the SQLite database.
\n\nAttributes
\n\n\n- engine (sqlalchemy.engine.base.Engine):\nThe SQLAlchemy engine.
\n- session (sqlalchemy.orm.session.Session):\nThe SQLAlchemy session.
\n- type (str):\nThe type of database.
\n- chunks_count (int):\nThe number of chunks to use when querying the database.
\n
\n\nMethods
\n\n\n- __init__(url=None, echo=False)\nInitializes the database.
\n- __exit__(exc_type, exc_val, exc_tb)\nCloses the database.
\n- initiate_database(url, database_name)\nCreates the database.
\n- commit()\nCommits the session.
\n- init_engine(url)\nInitializes the SQLAlchemy engine.
\n__enter__()
get_dict_by_classes(classes, ion_type, nominal_mzs, ion_charge, molecular_search_settings, adducts=None)\nReturns a dictionary of molecular formulas.
- check_entry(classe, ion_type, molecular_search_settings)\nChecks if a molecular formula is in the database.
\n- get_all_classes()\nReturns a list of all classes in the database.
\n- get_all()\nReturns a list of all molecular formulas in the database.
\n- delete_entry(row)\nDeletes a molecular formula from the database.
\n- purge(cls)\nDeletes all molecular formulas from the database.
\n- clear_data()\nClears the database.
\n- close(commit=True)\nCloses the database.
\n- add_engine_pidguard(engine)\nAdds multiprocessing guards.
\n
\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.__init__", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.__init__", "kind": "function", "doc": "\n", "signature": "(url=None, echo=False)"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.engine", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.engine", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.session", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.session", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.initiate_database", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.initiate_database", "kind": "function", "doc": "Creates the database.
\n\nParameters
\n\n\n- url (str):\nThe URL for the database.
\n- database_name (str):\nThe name of the database.
\n
\n", "signature": "(self, url, database_name):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.commit", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.commit", "kind": "function", "doc": "Commits the session.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.init_engine", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.init_engine", "kind": "function", "doc": "Initializes the SQLAlchemy engine.
\n\nParameters
\n\n\n- url (str):\nThe URL for the database.
\n
\n\nReturns
\n\n\n- sqlalchemy.engine.base.Engine: The SQLAlchemy engine.
\n
\n", "signature": "(self, url):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.get_dict_by_classes", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.get_dict_by_classes", "kind": "function", "doc": "Returns a dictionary of molecular formulas.
\n\nParameters
\n\n\n- classes (list):\nThe list of classes.
\n- ion_type (str):\nThe ion type.
\n- nominal_mzs (list):\nThe list of nominal m/z values.
\n- ion_charge (int):\nThe ion charge.
\n- molecular_search_settings (MolecularFormulaSearchSettings):\nThe molecular formula search settings.
\n- adducts (list, optional):\nThe list of adducts. Default is None.
\n
\n\nReturns
\n\n\n- dict: The dictionary of molecular formulas.
\n
\n\nNotes
\n\nKnown issue, when using SQLite:\nif the number of classes and nominal_m/zs are higher than 999 the query will fail\nSolution: use postgres or split query
\n", "signature": "(\tself,\tclasses,\tion_type,\tnominal_mzs,\tion_charge,\tmolecular_search_settings,\tadducts=None):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.check_entry", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.check_entry", "kind": "function", "doc": "Checks if a molecular formula is in the database.
\n\nParameters
\n\n\n- classe (str):\nThe class of the molecular formula.
\n- ion_type (str):\nThe ion type.
\n- molecular_search_settings (MolecularFormulaSearchSettings):\nThe molecular formula search settings.
\n
\n\nReturns
\n\n\n- sqlalchemy.orm.query.Query: The query.
\n
\n", "signature": "(self, classe, ion_type, molecular_search_settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.get_all_classes", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.get_all_classes", "kind": "function", "doc": "Returns a list of all classes in the database.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.get_all", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.get_all", "kind": "function", "doc": "Returns a list of all molecular formulas in the database.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.delete_entry", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.delete_entry", "kind": "function", "doc": "Deletes a molecular formula from the database.
\n", "signature": "(self, row):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.purge", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.purge", "kind": "function", "doc": "Deletes all molecular formulas from the database.
\n\nNotes
\n\nCareful, this will delete the entire database table
\n", "signature": "(self, cls):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.clear_data", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.clear_data", "kind": "function", "doc": "Clears the database.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.close", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.close", "kind": "function", "doc": "Closes the database.
\n\nParameters
\n\n\n- commit (bool, optional):\nWhether to commit the session. Default is True.
\n
\n", "signature": "(self, commit=True):", "funcdef": "def"}, {"fullname": "corems.molecular_id.factory.molecularSQL.MolForm_SQL.add_engine_pidguard", "modulename": "corems.molecular_id.factory.molecularSQL", "qualname": "MolForm_SQL.add_engine_pidguard", "kind": "function", "doc": "Adds multiprocessing guards.
\n\nForces a connection to be reconnected if it is detected\nas having been shared to a sub-process.
\n\nParameters
\n\n\n- engine (sqlalchemy.engine.base.Engine):\nThe SQLAlchemy engine.
\n
\n", "signature": "(self, engine):", "funcdef": "def"}, {"fullname": "corems.molecular_id.input", "modulename": "corems.molecular_id.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.input.nistMSI", "modulename": "corems.molecular_id.input.nistMSI", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI", "kind": "class", "doc": "A class for reading NIST MSI files and storing the data in a SQLite database.
\n\nParameters
\n\n\n- file_path (str):\nThe path to the NIST MSI file.
\n- url (str, optional):\nThe URL for the SQLite database. Default is 'sqlite://'.
\n
\n\nRaises
\n\n\n- FileExistsError: If the specified file does not exist.
\n
\n\nAttributes
\n\n\n- file_path (str):\nThe path to the NIST MSI file.
\n- url (str):\nThe URL for the SQLite database.
\n- sqlLite_obj (EI_LowRes_SQLite):\nThe SQLite object for storing the compound data.
\n
\n\nMethods
\n\n\n- run().\nRuns the thread and initializes the SQLite object.
\n- get_sqlLite_obj().\nReturns the SQLite object.
\n- get_compound_data_dict_list().\nParses the NIST MSI file and returns a list of compound data dictionaries.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.__init__", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(file_path, url='sqlite://')"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.file_path", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.file_path", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.url", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.url", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.run", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.run", "kind": "function", "doc": "Runs the thread and initializes the SQLite object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.get_sqlLite_obj", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.get_sqlLite_obj", "kind": "function", "doc": "Returns the SQLite object.
\n\nReturns
\n\n\n- EI_LowRes_SQLite: The SQLite object for storing the compound data.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.input.nistMSI.ReadNistMSI.get_compound_data_dict_list", "modulename": "corems.molecular_id.input.nistMSI", "qualname": "ReadNistMSI.get_compound_data_dict_list", "kind": "function", "doc": "Parses the NIST MSI file and returns a list of compound data dictionaries.
\n\nReturns
\n\n\n- list: A list of compound data dictionaries.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search", "modulename": "corems.molecular_id.search", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.search.compoundSearch", "modulename": "corems.molecular_id.search.compoundSearch", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch", "kind": "class", "doc": "A class representing a low-resolution mass spectral match.
\n\nParameters
\n\n\n- gcms_obj (object):\nThe GC-MS object.
\n- sql_obj (object, optional):\nThe SQL object for database operations. Default is None.
\n- calibration (bool, optional):\nFlag indicating if the match is for calibration. Default is False.
\n
\n\nAttributes
\n\n\n- gcms_obj (object):\nThe GC-MS object.
\n- sql_obj (object):\nThe SQL object for database operations.
\n- calibration (bool):\nFlag indicating if the match is for calibration.
\n
\n\nMethods
\n\n\n- metabolite_detector_score(gc_peak, ref_obj, spectral_simi).\nCalculates the spectral similarity scores and the similarity score for a given GC peak and reference object.
\n- run().\nRuns the low-resolution mass spectral match.
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch.__init__", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(gcms_obj, sql_obj=None, calibration=False)"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch.gcms_obj", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch.gcms_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch.calibration", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch.calibration", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch.metabolite_detector_score", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch.metabolite_detector_score", "kind": "function", "doc": "Calculates the spectral similarity scores and the similarity score for a given GC peak and reference object.
\n\nParameters
\n\n\n- gc_peak (object):\nThe GC peak object.
\n- ref_obj (object):\nThe reference object.
\n- spectral_simi (object):\nThe spectral similarity object.
\n
\n\nReturns
\n\n\n- tuple: A tuple containing the spectral similarity scores, RI score, and similarity score.
\n
\n", "signature": "(self, gc_peak, ref_obj, spectral_simi):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.compoundSearch.LowResMassSpectralMatch.run", "modulename": "corems.molecular_id.search.compoundSearch", "qualname": "LowResMassSpectralMatch.run", "kind": "function", "doc": "Runs the low-resolution mass spectral match.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks", "modulename": "corems.molecular_id.search.findOxygenPeaks", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks", "kind": "class", "doc": "Class to find Oxygen peaks in a mass spectrum for formula assignment search
\n\nClass to walk 14Da units over oxygen space for negative ion mass spectrum of natural organic matter\nReturns a list of MSPeak class containing the possible Molecular Formula class objects.
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpec class):\nThis is where we store MassSpec class obj,
\n- lookupTableSettings (MolecularLookupTableSettings class):\nThis is where we store MolecularLookupTableSettings class obj
\n- min_O , max_O (int):\nminium and maximum of Oxygen to allow the software to look for\nit will override the settings at lookupTableSettings.usedAtoms\ndefault min = 1, max = 22
\n
\n\nAttributes
\n\n\n- mass_spectrum_obj (MassSpec class):\nThis is where we store MassSpec class obj,
\n- lookupTableSettings (MolecularLookupTableSettings class):\nThis is where we store MolecularLookupTableSettings class obj
\n
\n\nMethods
\n\n\n- run().\nwill be called when the instantiated class method start is called
\n- get_list_found_peaks().\nreturns a list of MSpeaks classes cotaining all the MolecularFormula candidates inside the MSPeak\nfor more details of the structure see MSPeak class and MolecularFormula class
\n- set_mass_spec_indexes_by_found_peaks().\nset the mass spectrum to interate over only the selected indexes
\n
\n", "bases": "threading.Thread"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.__init__", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(\tmass_spectrum_obj,\tsql_db: bool = False,\tmin_O: int = 1,\tmax_O: int = 22)"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.mass_spectrum_obj", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.mass_spectrum_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.min_0", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.min_0", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.max_O", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.max_O", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.run", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.run", "kind": "function", "doc": "Run the thread
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.find_most_abundant_formula", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.find_most_abundant_formula", "kind": "function", "doc": "Find the most abundant formula in the mass spectrum
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpec class):\nMass spectrum object
\n
\n\nReturns
\n\n\n- MolecularFormula class obj: most abundant MolecularFormula with the lowest mass error
\n
\n", "signature": "(self, mass_spectrum_obj):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.find_most_abundant_formula_test", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.find_most_abundant_formula_test", "kind": "function", "doc": "[Test function] Find the most abundant formula in the mass spectrum
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpec class):\nMass spectrum object
\n- settings (MolecularSearchSettings class):\nMolecular search settings object
\n
\n\nReturns
\n\n\n- MolecularFormula class obj: most abundant MolecularFormula with the lowest mass error
\n
\n", "signature": "(self, mass_spectrum_obj, settings):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.find_series_mspeaks", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.find_series_mspeaks", "kind": "function", "doc": "Find a series of abundant peaks in the mass spectrum for a given molecular formula
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpec class):\nMass spectrum object
\n- molecular_formula_obj_reference (MolecularFormula class):\nMolecular formula object
\n- deltamz (float):\ndelta m/z to look for peaks
\n
\n\nReturns
\n\n\n- list: list of MSpeak class objects
\n
\n", "signature": "(self, mass_spectrum_obj, molecular_formula_obj_reference, deltamz=14):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.get_list_found_peaks", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.get_list_found_peaks", "kind": "function", "doc": "Get the list of found peaks
\n\nReturns
\n\n\n- list: list of MSpeak class objects
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.findOxygenPeaks.FindOxygenPeaks.set_mass_spec_indexes_by_found_peaks", "modulename": "corems.molecular_id.search.findOxygenPeaks", "qualname": "FindOxygenPeaks.set_mass_spec_indexes_by_found_peaks", "kind": "function", "doc": "Set the mass spectrum to interate over only the selected indexes.
\n\nNotes
\n\nWarning!!!!\nset the mass spectrum to interate over only the selected indexes\ndon not forget to call mass_spectrum_obj.reset_indexes after the job is done
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.last_error", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "last_error", "kind": "variable", "doc": "\n", "default_value": "0"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.last_dif", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "last_dif", "kind": "variable", "doc": "\n", "default_value": "0"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.closest_error", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "closest_error", "kind": "variable", "doc": "\n", "default_value": "0"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.error_average", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "error_average", "kind": "variable", "doc": "\n", "default_value": "0"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.nbValues", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "nbValues", "kind": "variable", "doc": "\n", "default_value": "0"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas", "kind": "class", "doc": "Class for searching molecular formulas in a mass spectrum.
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- sql_db (MolForm_SQL, optional):\nThe SQL database object, by default None.
\n- first_hit (bool, optional):\nFlag to indicate whether to skip peaks that already have a molecular formula assigned, by default False.
\n- find_isotopologues (bool, optional):\nFlag to indicate whether to find isotopologues, by default True.
\n
\n\nAttributes
\n\n\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- sql_db (MolForm_SQL):\nThe SQL database object.
\n- first_hit (bool):\nFlag to indicate whether to skip peaks that already have a molecular formula assigned.
\n- find_isotopologues (bool):\nFlag to indicate whether to find isotopologues.
\n
\n\nMethods
\n\n\n- run_search().\nRun the molecular formula search.
\n- run_worker_mass_spectrum().\nRun the molecular formula search on the mass spectrum object.
\n- run_worker_ms_peaks().\nRun the molecular formula search on the given list of mass spectrum peaks.
\n- database_to_dict().\nConvert the database results to a dictionary.
\n- run_molecular_formula().\nRun the molecular formula search on the given list of mass spectrum peaks.
\n- search_mol_formulas().\nSearch for molecular formulas in the mass spectrum.
\n
\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.__init__", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.__init__", "kind": "function", "doc": "\n", "signature": "(\tmass_spectrum_obj,\tsql_db=None,\tfirst_hit: bool = False,\tfind_isotopologues: bool = True)"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.first_hit", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.first_hit", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.find_isotopologues", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.find_isotopologues", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.mass_spectrum_obj", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.mass_spectrum_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.run_search", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.run_search", "kind": "function", "doc": "Run the molecular formula search.
\n\nParameters
\n\n\n- mspeaks (list of MSPeak):\nThe list of mass spectrum peaks.
\n- query (dict):\nThe query dictionary containing the possible molecular formulas.
\n- min_abundance (float):\nThe minimum abundance threshold.
\n- ion_type (str):\nThe ion type.
\n- ion_charge (int):\nThe ion charge.
\n- adduct_atom (str, optional):\nThe adduct atom, by default None.
\n
\n", "signature": "(\tself,\tmspeaks: list,\tquery: dict,\tmin_abundance: float,\tion_type: str,\tion_charge: int,\tadduct_atom=None):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.run_worker_mass_spectrum", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.run_worker_mass_spectrum", "kind": "function", "doc": "Run the molecular formula search on the mass spectrum object.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.run_worker_ms_peaks", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.run_worker_ms_peaks", "kind": "function", "doc": "Run the molecular formula search on the given list of mass spectrum peaks.
\n\nParameters
\n\n\n- ms_peaks (list of MSPeak):\nThe list of mass spectrum peaks.
\n
\n", "signature": "(self, ms_peaks):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.database_to_dict", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.database_to_dict", "kind": "function", "doc": "Convert the database results to a dictionary.
\n\nParameters
\n\n\n- classe_str_list (list):\nThe list of class strings.
\n- nominal_mzs (list):\nThe list of nominal m/z values.
\n- mf_search_settings (MolecularFormulaSearchSettings):\nThe molecular formula search settings.
\n- ion_charge (int):\nThe ion charge.
\n
\n\nReturns
\n\n\n- dict: The dictionary containing the database results.
\n
\n", "signature": "(classe_str_list, nominal_mzs, mf_search_settings, ion_charge):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.run_molecular_formula", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.run_molecular_formula", "kind": "function", "doc": "Run the molecular formula search on the given list of mass spectrum peaks.
\n\nParameters
\n\n\n- ms_peaks (list of MSPeak):\nThe list of mass spectrum peaks.
\n
\n", "signature": "(*args, **kw):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulas.search_mol_formulas", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulas.search_mol_formulas", "kind": "function", "doc": "Search for molecular formulas in the mass spectrum.
\n\nParameters
\n\n\n- possible_formulas_list (list of MolecularFormula):\nThe list of possible molecular formulas.
\n- ion_type (str):\nThe ion type.
\n- neutral_molform (bool, optional):\nFlag to indicate whether the molecular formulas are neutral, by default True.
\n- find_isotopologues (bool, optional):\nFlag to indicate whether to find isotopologues, by default True.
\n- adduct_atom (str, optional):\nThe adduct atom, by default None.
\n
\n\nReturns
\n\n\n- list of MSPeak: The list of mass spectrum peaks with assigned molecular formulas.
\n
\n", "signature": "(\tself,\tpossible_formulas_list: List[corems.molecular_formula.factory.MolecularFormulaFactory.MolecularFormula],\tion_type: str,\tneutral_molform=True,\tfind_isotopologues=True,\tadduct_atom=None) -> List[corems.ms_peak.factory.MSPeakClasses._MSPeak]:", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker", "kind": "class", "doc": "Class for searching molecular formulas in a mass spectrum.
\n\nParameters
\n\n\n- find_isotopologues (bool, optional):\nFlag to indicate whether to find isotopologues, by default True.
\n
\n\nAttributes
\n\n\n- find_isotopologues (bool):\nFlag to indicate whether to find isotopologues.
\n
\n\nMethods
\n\n\n- reset_error().\nReset the error variables.
\n- set_last_error().\nSet the last error.
\n- find_formulas().\nFind the formulas.
\n- calc_error().\nCalculate the error.
\n
\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.__init__", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.__init__", "kind": "function", "doc": "\n", "signature": "(find_isotopologues=True)"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.find_isotopologues", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.find_isotopologues", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.reset_error", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.reset_error", "kind": "function", "doc": "Reset the error variables.
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n
\n", "signature": "(self, mass_spectrum_obj):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.set_last_error", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.set_last_error", "kind": "function", "doc": "Set the last error.
\n\nParameters
\n\n\n- error (float):\nThe error.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n
\n", "signature": "(self, error, mass_spectrum_obj):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.calc_error", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.calc_error", "kind": "function", "doc": "Calculate the error.
\n\nParameters
\n\n\n- mz_exp (float):\nThe experimental m/z value.
\n- mz_calc (float):\nThe calculated m/z value.
\n- method (str, optional):\nThe method, by default 'ppm'.
\n
\n\nRaises
\n\n\n- Exception: If the method is not ppm or ppb.
\n
\n\nReturns
\n\n\n", "signature": "(mz_exp, mz_calc, method='ppm'):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulaWorker.find_formulas", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulaWorker.find_formulas", "kind": "function", "doc": "Find the formulas.
\n\nParameters
\n\n\n- formulas (list of MolecularFormula):\nThe list of molecular formulas.
\n- min_abundance (float):\nThe minimum abundance threshold.
\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- ms_peak (MSPeak):\nThe mass spectrum peak.
\n- ion_type (str):\nThe ion type.
\n- ion_charge (int):\nThe ion charge.
\n- adduct_atom (str, optional):\nThe adduct atom, by default None.
\n
\n\nReturns
\n\n\n- list of MSPeak: The list of mass spectrum peaks with assigned molecular formulas.
\n
\n\nNotes
\n\nUses the closest error the next search (this is not ideal, it needs to use confidence \nmetric to choose the right candidate then propagate the error using the error from the best candidate).\nIt needs to add s/n to the equation.\nIt need optimization to define the mz_error_range within a m/z unit since it is directly proportional \nwith the mass, and inversely proportional to the rp. It's not linear, i.e., sigma mass.\nThe idea it to correlate sigma to resolving power, signal to noise and sample complexity per mz unit.\nMethod='distance'
\n", "signature": "(\tself,\tformulas,\tmin_abundance,\tmass_spectrum_obj,\tms_peak,\tion_type,\tion_charge,\tadduct_atom=None):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC", "kind": "class", "doc": "Class for searching molecular formulas in a LC object.
\n\nParameters
\n\n\n- lcms_obj (LC):\nThe LC object.
\n- sql_db (MolForm_SQL, optional):\nThe SQL database object, by default None.
\n- first_hit (bool, optional):\nFlag to indicate whether to skip peaks that already have a molecular formula assigned, by default False.
\n- find_isotopologues (bool, optional):\nFlag to indicate whether to find isotopologues, by default True.
\n
\n\nMethods
\n\n\n- run_untargeted_worker_ms1().\nRun untargeted molecular formula search on the ms1 mass spectrum.
\n- run_target_worker_ms1().\nRun targeted molecular formula search on the ms1 mass spectrum.
\n
\n", "bases": "SearchMolecularFormulas"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.__init__", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.__init__", "kind": "function", "doc": "\n", "signature": "(lcms_obj, sql_db=None, first_hit=False, find_isotopologues=True)"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.first_hit", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.first_hit", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.find_isotopologues", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.find_isotopologues", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.lcms_obj", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.lcms_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.run_untargeted_worker_ms1", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.run_untargeted_worker_ms1", "kind": "function", "doc": "Run untargeted molecular formula search on the ms1 mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.molecularFormulaSearch.SearchMolecularFormulasLC.run_target_worker_ms1", "modulename": "corems.molecular_id.search.molecularFormulaSearch", "qualname": "SearchMolecularFormulasLC.run_target_worker_ms1", "kind": "function", "doc": "Run targeted molecular formula search on the ms1 mass spectrum.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment", "modulename": "corems.molecular_id.search.priorityAssignment", "kind": "module", "doc": "\n"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment", "kind": "class", "doc": "A class for assigning priority to oxygen classes in a molecular search.
\n\nParameters
\n\n\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- sql_db (bool, optional):\nWhether to use an SQL database. The default is False.
\n
\n\nAttributes
\n\n\n- mass_spectrum_obj (MassSpectrum):\nThe mass spectrum object.
\n- sql_db (MolForm_SQL):\nThe SQL database object.
\n
\n\nMethods
\n\n\n- run().\nRun the priority assignment process.
\n- create_data_base().\nCreate the molecular database for the specified heteroatomic classes.
\n- run_worker_mass_spectrum(assign_classes_order_tuples).\nRun the molecular formula search for each class in the specified order.
\n- get_dict_molecular_database(classe_str_list).\nGet the molecular database as a dictionary.
\n- ox_classes_and_peaks_in_order_().\nGet the oxygen classes and associated peaks in order.
\n- get_classes_in_order(dict_ox_class_and_ms_peak)
\nGet the classes in order. \n
\n", "bases": "threading.Thread"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.__init__", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.__init__", "kind": "function", "doc": "This constructor should always be called with keyword arguments. Arguments are:
\n\ngroup should be None; reserved for future extension when a ThreadGroup\nclass is implemented.
\n\ntarget is the callable object to be invoked by the run()\nmethod. Defaults to None, meaning nothing is called.
\n\nname is the thread name. By default, a unique name is constructed of\nthe form \"Thread-N\" where N is a small decimal number.
\n\nargs is the argument tuple for the target invocation. Defaults to ().
\n\nkwargs is a dictionary of keyword arguments for the target\ninvocation. Defaults to {}.
\n\nIf a subclass overrides the constructor, it must make sure to invoke\nthe base class constructor (Thread.__init__()) before doing anything\nelse to the thread.
\n", "signature": "(mass_spectrum_obj, sql_db=False)"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.mass_spectrum_obj", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.mass_spectrum_obj", "kind": "variable", "doc": "\n"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.run", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.run", "kind": "function", "doc": "Run the priority assignment process.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.create_data_base", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.create_data_base", "kind": "function", "doc": "Create the molecular database for the specified heteroatomic classes.
\n\nReturns
\n\n\n- assign_classes_order_str_dict_tuple_ (list):\nA list of tuples containing the class names and dictionaries of class attributes.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.run_worker_mass_spectrum", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.run_worker_mass_spectrum", "kind": "function", "doc": "Run the molecular formula search for each class in the specified order.
\n\nParameters
\n\n\n- assign_classes_order_tuples (list):\nA list of tuples containing the class names and dictionaries of class attributes.
\n
\n", "signature": "(self, assign_classes_order_tuples):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.get_dict_molecular_database", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.get_dict_molecular_database", "kind": "function", "doc": "Get the molecular database as a dictionary.
\n\nParameters
\n\n\n- classe_str_list (list):\nA list of class names.
\n
\n\nReturns
\n\n\n- dict: A dictionary containing the molecular database.
\n
\n", "signature": "(self, classe_str_list):", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.ox_classes_and_peaks_in_order_", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.ox_classes_and_peaks_in_order_", "kind": "function", "doc": "Get the oxygen classes and associated peaks in order.
\n\nReturns
\n\n\n- dict: A dictionary containing the oxygen classes and associated peaks.
\n
\n", "signature": "(self) -> dict:", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.get_classes_in_order", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.get_classes_in_order", "kind": "function", "doc": "Get the classes in order.
\n\nParameters
\n\n\n- dict_ox_class_and_ms_peak (dict):\nA dictionary containing the oxygen classes and associated peaks.
\n
\n\nReturns
\n\n\n- list: A list of tuples containing the class names and dictionaries of class attributes.
\n
\n\nNotes
\n\nstructure is \n ('HC', {'HC': 1})
\n", "signature": "(self, dict_ox_class_and_ms_peak) -> [(<class 'str'>, <class 'dict'>)]:", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.get_class_strings_dict", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.get_class_strings_dict", "kind": "function", "doc": "Get the class strings and dictionaries.
\n\nParameters
\n\n\n- all_atoms_tuples (tuple):\nA tuple containing the atoms.
\n- atoms_in_order (list):\nA list of atoms in order.
\n
\n\nReturns
\n\n\n- list: A list of tuples containing the class strings and dictionaries.
\n
\n", "signature": "(all_atoms_tuples, atoms_in_order) -> [(<class 'str'>, <class 'dict'>)]:", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.combine_ox_class_with_other", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.combine_ox_class_with_other", "kind": "function", "doc": "Combine the oxygen classes with other classes.
\n\nParameters
\n\n\n\nReturns
\n\n\n- list: A list of dictionaries.
\n
\n", "signature": "(\tatoms_in_order,\tclasses_strings_dict_tuples,\tdict_ox_class_and_ms_peak) -> [<class 'dict'>]:", "funcdef": "def"}, {"fullname": "corems.molecular_id.search.priorityAssignment.OxygenPriorityAssignment.sort_classes", "modulename": "corems.molecular_id.search.priorityAssignment", "qualname": "OxygenPriorityAssignment.sort_classes", "kind": "function", "doc": "Sort the classes.
\n\nParameters
\n\n\n- atoms_in_order (list):\nA list of atoms in order.
\n- combination_tuples (list):
\n
\n\nReturns
\n\n\n- list: A list of tuples containing the class strings and dictionaries.
\n
\n", "signature": "(atoms_in_order, combination_tuples) -> [(<class 'str'>, <class 'dict'>)]:", "funcdef": "def"}, {"fullname": "corems.ms_peak", "modulename": "corems.ms_peak", "kind": "module", "doc": "\n"}, {"fullname": "corems.ms_peak.calc", "modulename": "corems.ms_peak.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc", "modulename": "corems.ms_peak.calc.MSPeakCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation", "kind": "class", "doc": "Class to perform calculations on MSPeak objects.
\n\nThis class provides methods to perform various calculations on MSPeak objects, such as calculating Kendrick Mass Defect (KMD) and Kendrick Mass (KM), calculating peak area, and fitting peak lineshape using different models.
\n\nParameters
\n\n\n\nAttributes
\n\n\n- _ms_parent (MSParent):\nThe parent MSParent object associated with the MSPeakCalculation object.
\n- mz_exp (float):\nThe experimental m/z value of the peak.
\n- start_scan (int):\nThe start scan index of the peak.
\n- final_scan (int):\nThe final scan index of the peak.
\n- resolving_power (float):\nThe resolving power of the peak.
\n
\n\nMethods
\n\n\n- _calc_kmd(dict_base).\nCalculate the Kendrick Mass Defect (KMD) and Kendrick Mass (KM) for a given base formula.
\n- calc_area().\nCalculate the peak area using numpy's trapezoidal fit.
\n- fit_peak(mz_extend=6, delta_rp=0, model='Gaussian').\nPerform lineshape analysis on a peak using lmfit module.
\n- voigt_pso(w, r, yoff, width, loc, a).\nCalculate the Voigt function for particle swarm optimization (PSO) fitting.
\n- objective_pso(x, w, u).\nCalculate the objective function for PSO fitting.
\n- minimize_pso(lower, upper, w, u).\nMinimize the objective function using the particle swarm optimization algorithm.
\n- fit_peak_pso(mz_extend=6, upsample_multiplier=5).\nPerform lineshape analysis on a peak using particle swarm optimization (PSO) fitting.
\n- voigt(oversample_multiplier=1, delta_rp=0, mz_overlay=1).\n[Legacy] Perform voigt lineshape analysis on a peak.
\n- pseudovoigt(oversample_multiplier=1, delta_rp=0, mz_overlay=1, fraction=0.5).\n[Legacy] Perform pseudovoigt lineshape analysis on a peak.
\n- lorentz(oversample_multiplier=1, delta_rp=0, mz_overlay=1).\n[Legacy] Perform lorentz lineshape analysis on a peak.
\n- gaussian(oversample_multiplier=1, delta_rp=0, mz_overlay=1).\n[Legacy] Perform gaussian lineshape analysis on a peak.
\n- get_mz_domain(oversample_multiplier, mz_overlay).\n[Legacy] Resample/interpolate datapoints for lineshape analysis.
\n- number_possible_assignments().\nReturn the number of possible molecular formula assignments for the peak.
\n- molecular_formula_lowest_error().\nReturn the molecular formula with the smallest absolute mz error.
\n- molecular_formula_highest_prob_score().\nReturn the molecular formula with the highest confidence score.
\n- molecular_formula_earth_filter(lowest_error=True).\nFilter molecular formula using the 'Earth' filter.
\n- molecular_formula_water_filter(lowest_error=True).\nFilter molecular formula using the 'Water' filter.
\n- molecular_formula_air_filter(lowest_error=True).\nFilter molecular formula using the 'Air' filter.
\n- cia_score_S_P_error().\nCompound Identification Algorithm SP Error - Assignment Filter.
\n- cia_score_N_S_P_error().\nCompound Identification Algorithm NSP Error - Assignment Filter.
\n
\n"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.calc_area", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.calc_area", "kind": "function", "doc": "Calculate the peak area using numpy's trapezoidal fit
\n\nuses provided mz_domain to accurately integrate areas independent of digital resolution
\n\nReturns
\n\n\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.fit_peak", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.fit_peak", "kind": "function", "doc": "Lineshape analysis on a peak using lmfit module.
\n\nModel and fit peak lineshape by defined function - using lmfit module\nDoes not oversample/resample/interpolate data points \nBetter to go back to time domain and perform more zero filling - if possible.
\n\nParameters
\n\n\n- mz_extend (int):\nextra points left and right of peak definition to include in fitting
\n- delta_rp (float):\ndelta resolving power to add to resolving power
\n- model (str):\nType of lineshape model to use.\nModels allowed: Gaussian, Lorentz, Voigt
\n
\n\nReturns
\n\n\n- mz_domain (ndarray):\nx-axis domain for fit
\n- fit_peak (lmfit object):\nfit results object from lmfit module
\n
\n\nNotes
\n\nReturns the calculated mz domain, initial defined abundance profile, and the fit peak results object from lmfit module\nmz_extend here extends the x-axis domain so that we have sufficient points either side of the apex to fit.\nTakes about 10ms per peak
\n", "signature": "(self, mz_extend=6, delta_rp=0, model='Gaussian'):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.voigt_pso", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.voigt_pso", "kind": "function", "doc": "Voigt function for particle swarm optimisation (PSO) fitting
\n\nFrom https://github.com/pnnl/nmrfit/blob/master/nmrfit/equations.py.\nCalculates a Voigt function over w based on the relevant properties of the distribution.
\n\nParameters
\n\n\n- w (ndarray):\nArray over which the Voigt function will be evaluated.
\n- r (float):\nRatio between the Guassian and Lorentzian functions.
\n- yoff (float):\nY-offset of the Voigt function.
\n- width (float):\nThe width of the Voigt function.
\n- loc (float):\nCenter of the Voigt function.
\n- a (float):\nArea of the Voigt function.
\n
\n\nReturns
\n\n\n- V (ndarray):\nArray defining the Voigt function over w.
\n
\n\nReferences
\n\n\n- https://github.com/pnnl/nmrfit
\n
\n\nNotes
\n\nParticle swarm optimisation (PSO) fitting function can be significantly more computationally expensive than lmfit, with more parameters to optimise.
\n", "signature": "(self, w, r, yoff, width, loc, a):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.objective_pso", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.objective_pso", "kind": "function", "doc": "Objective function for particle swarm optimisation (PSO) fitting
\n\nThe objective function used to fit supplied data. Evaluates sum of squared differences between the fit and the data.
\n\nParameters
\n\n\n- x (list of floats):\nParameter vector.
\n- w (ndarray):\nArray of frequency data.
\n- u (ndarray):\nArray of data to be fit.
\n
\n\nReturns
\n\n\n- rmse (float):\nRoot mean square error between the data and fit.
\n
\n\nReferences
\n\n\n- https://github.com/pnnl/nmrfit
\n
\n", "signature": "(self, x, w, u):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.minimize_pso", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.minimize_pso", "kind": "function", "doc": "Minimization function for particle swarm optimisation (PSO) fitting
\n\nMinimizes the objective function using the particle swarm optimization algorithm.\nMinimization function based on defined parameters
\n\nParameters
\n\n\n- lower (list of floats):\nLower bounds for the parameters.
\n- upper (list of floats):\nUpper bounds for the parameters.
\n- w (ndarray):\nArray of frequency data.
\n- u (ndarray):\nArray of data to be fit.
\n
\n\nNotes
\n\nParticle swarm optimisation (PSO) fitting function can be significantly more computationally expensive than lmfit, with more parameters to optimise.\nCurrent parameters take ~2 seconds per peak.
\n\nReferences
\n\n\n- https://github.com/pnnl/nmrfit
\n
\n", "signature": "(self, lower, upper, w, u):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.fit_peak_pso", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.fit_peak_pso", "kind": "function", "doc": "Lineshape analysis on a peak using particle swarm optimisation (PSO) fitting
\n\nFunction to fit a Voigt peakshape using particle swarm optimisation (PSO).\nShould return better results than lmfit, but much more computationally expensive
\n\nParameters
\n\n\n- mz_extend (int, optional):\nextra points left and right of peak definition to include in fitting. Defaults to 6.
\n- upsample_multiplier (int, optional):\nfactor to increase x-axis points by for simulation of fitted lineshape function. Defaults to 5.
\n
\n\nReturns
\n\n\n- xopt (array):\nvariables describing the voigt function.\nG/L ratio, width (fwhm), apex (x-axis), area.\ny-axis offset is fixed at 0
\n- fopt (float):\nobjective score (rmse)
\n- psfit (array):\nrecalculated y values based on function and optimised fit
\n- psfit_hdp (tuple of arrays):\n0 - linspace x-axis upsampled grid\n1 - recalculated y values based on function and upsampled x-axis grid\nDoes not change results, but aids in visualisation of the 'true' voigt lineshape
\n
\n\nNotes
\n\nParticle swarm optimisation (PSO) fitting function can be significantly more computationally expensive than lmfit, with more parameters to optimise.
\n", "signature": "(self, mz_extend: int = 6, upsample_multiplier: int = 5):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.voigt", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.voigt", "kind": "function", "doc": "[Legacy] Voigt lineshape analysis function\nLegacy function for voigt lineshape analysis
\n\nParameters
\n\n\n- oversample_multiplier (int):\nfactor to increase x-axis points by for simulation of fitted lineshape function
\n- delta_rp (float):\ndelta resolving power to add to resolving power
\n- mz_overlay (int):\nextra points left and right of peak definition to include in fitting
\n
\n\nReturns
\n\n\n- mz_domain (ndarray):\nx-axis domain for fit
\n- calc_abundance (ndarray):\ncalculated abundance profile based on voigt function
\n
\n", "signature": "(self, oversample_multiplier=1, delta_rp=0, mz_overlay=1):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.pseudovoigt", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.pseudovoigt", "kind": "function", "doc": "[Legacy] pseudovoigt lineshape function
\n\nLegacy function for pseudovoigt lineshape analysis. \nNote - Code may not be functional currently.
\n\nParameters
\n\n\n- oversample_multiplier (int, optional):\nfactor to increase x-axis points by for simulation of fitted lineshape function. Defaults to 1.
\n- delta_rp (float, optional):\ndelta resolving power to add to resolving power. Defaults to 0.
\n- mz_overlay (int, optional):\nextra points left and right of peak definition to include in fitting. Defaults to 1.
\n- fraction (float, optional):\nfraction of gaussian component in pseudovoigt function. Defaults to 0.5.
\n
\n", "signature": "(\tself,\toversample_multiplier=1,\tdelta_rp=0,\tmz_overlay=1,\tfraction=0.5):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.lorentz", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.lorentz", "kind": "function", "doc": "[Legacy] Lorentz lineshape analysis function
\n\nLegacy function for lorentz lineshape analysis
\n\nParameters
\n\n\n- oversample_multiplier (int):\nfactor to increase x-axis points by for simulation of fitted lineshape function
\n- delta_rp (float):\ndelta resolving power to add to resolving power
\n- mz_overlay (int):\nextra points left and right of peak definition to include in fitting
\n
\n\nReturns
\n\n\n- mz_domain (ndarray):\nx-axis domain for fit
\n- calc_abundance (ndarray):\ncalculated abundance profile based on lorentz function
\n
\n", "signature": "(self, oversample_multiplier=1, delta_rp=0, mz_overlay=1):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.gaussian", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.gaussian", "kind": "function", "doc": "[Legacy] Gaussian lineshape analysis function\nLegacy gaussian lineshape analysis function
\n\nParameters
\n\n\n- oversample_multiplier (int):\nfactor to increase x-axis points by for simulation of fitted lineshape function
\n- delta_rp (float):\ndelta resolving power to add to resolving power
\n- mz_overlay (int):\nextra points left and right of peak definition to include in fitting
\n
\n\nReturns
\n\n\n- mz_domain (ndarray):\nx-axis domain for fit
\n- calc_abundance (ndarray):\ncalculated abundance profile based on gaussian function
\n
\n", "signature": "(self, oversample_multiplier=1, delta_rp=0, mz_overlay=1):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.get_mz_domain", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.get_mz_domain", "kind": "function", "doc": "[Legacy] function to resample/interpolate datapoints for lineshape analysis
\n\nThis code is used for the legacy line fitting functions and not recommended.\nLegacy function to support expanding mz domain for legacy lineshape functions
\n\nParameters
\n\n\n- oversample_multiplier (int):\nfactor to increase x-axis points by for simulation of fitted lineshape function
\n- mz_overlay (int):\nextra points left and right of peak definition to include in fitting
\n
\n\nReturns
\n\n\n- mz_domain (ndarray):\nx-axis domain for fit
\n
\n", "signature": "(self, oversample_multiplier, mz_overlay):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.number_possible_assignments", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.number_possible_assignments", "kind": "variable", "doc": "\n"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.molecular_formula_lowest_error", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.molecular_formula_lowest_error", "kind": "function", "doc": "Return the molecular formula with the smallest absolute mz error
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.molecular_formula_highest_prob_score", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.molecular_formula_highest_prob_score", "kind": "function", "doc": "Return the molecular formula with the highest confidence score score
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.molecular_formula_earth_filter", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.molecular_formula_earth_filter", "kind": "function", "doc": "Filter molecular formula using the 'Earth' filter
\n\nThis function applies the Formularity-esque 'Earth' filter to possible molecular formula assignments.\nEarth Filter:\n O > 0 AND N <= 3 AND P <= 2 AND 3P <= O
\n\nIf the lowest_error method is also used, it will return the single formula annotation with the smallest absolute error which also fits the Earth filter. \nOtherwise, it will return all Earth-filter compliant formulas.
\n\nParameters
\n\n\n- lowest_error (bool, optional.):\nReturn only the lowest error formula which also fits the Earth filter. \nIf False, return all Earth-filter compliant formulas. Default is True.
\n
\n\nReturns
\n\n\n- list: List of molecular formula objects which fit the Earth filter
\n
\n\nReferences
\n\n\n- Nikola Tolic et al., \"Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra\"\nAnal. Chem. 2017, 89, 23, 12659\u201312665\ndoi: 10.1021/acs.analchem.7b03318
\n
\n", "signature": "(self, lowest_error=True):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.molecular_formula_water_filter", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.molecular_formula_water_filter", "kind": "function", "doc": "Filter molecular formula using the 'Water' filter
\n\nThis function applies the Formularity-esque 'Water' filter to possible molecular formula assignments.\nWater Filter:\n O > 0 AND N <= 3 AND S <= 2 AND P <= 2
\n\nIf the lowest_error method is also used, it will return the single formula annotation with the smallest absolute error which also fits the Water filter.\nOtherwise, it will return all Water-filter compliant formulas.
\n\nParameters
\n\n\n- lowest_error (bool, optional):\nReturn only the lowest error formula which also fits the Water filter.\nIf False, return all Water-filter compliant formulas. Defaults to 2
\n
\n\nReturns
\n\nlist\n List of molecular formula objects which fit the Water filter
\n\nReferences
\n\n\n- Nikola Tolic et al., \"Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra\"\nAnal. Chem. 2017, 89, 23, 12659\u201312665\ndoi: 10.1021/acs.analchem.7b03318
\n
\n", "signature": "(self, lowest_error=True):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.molecular_formula_air_filter", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.molecular_formula_air_filter", "kind": "function", "doc": "Filter molecular formula using the 'Air' filter
\n\nThis function applies the Formularity-esque 'Air' filter to possible molecular formula assignments.\nAir Filter:\n O > 0 AND N <= 3 AND S <= 1 AND P = 0 AND 3(S+N) <= O
\n\nIf the lowest_error method is also used, it will return the single formula annotation with the smallest absolute error which also fits the Air filter.\nOtherwise, it will return all Air-filter compliant formulas.
\n\nParameters
\n\n\n- lowest_error (bool, optional):\nReturn only the lowest error formula which also fits the Air filter.\nIf False, return all Air-filter compliant formulas. Defaults to True.
\n
\n\nReturns
\n\n\n- list: List of molecular formula objects which fit the Air filter
\n
\n\nReferences
\n\n\n- Nikola Tolic et al., \"Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra\"\nAnal. Chem. 2017, 89, 23, 12659\u201312665\ndoi: 10.1021/acs.analchem.7b03318
\n
\n", "signature": "(self, lowest_error=True):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.cia_score_S_P_error", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.cia_score_S_P_error", "kind": "function", "doc": "Compound Identification Algorithm SP Error - Assignment Filter
\n\nThis function applies the Compound Identification Algorithm (CIA) SP Error filter to possible molecular formula assignments.
\n\nIt takes the molecular formula with the lowest S+P count, and returns the formula with the lowest absolute error from this subset.
\n\nReturns
\n\n\n- MolecularFormula: A single molecular formula which fits the rules of the CIA SP Error filter
\n
\n\nReferences
\n\n\n- Elizabeth B. Kujawinski and Mark D. Behn, \"Automated Analysis of Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectra of Natural Organic Matter\"\nAnal. Chem. 2006, 78, 13, 4363\u20134373\ndoi: 10.1021/ac0600306
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.calc.MSPeakCalc.MSPeakCalculation.cia_score_N_S_P_error", "modulename": "corems.ms_peak.calc.MSPeakCalc", "qualname": "MSPeakCalculation.cia_score_N_S_P_error", "kind": "function", "doc": "Compound Identification Algorithm NSP Error - Assignment Filter
\n\nThis function applies the Compound Identification Algorithm (CIA) NSP Error filter to possible molecular formula assignments.
\n\nIt takes the molecular formula with the lowest N+S+P count, and returns the formula with the lowest absolute error from this subset.
\n\nReturns
\n\n\n- MolecularFormula: A single molecular formula which fits the rules of the CIA NSP Error filter
\n
\n\nReferences
\n\n\n- Elizabeth B. Kujawinski and Mark D. Behn, \"Automated Analysis of Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectra of Natural Organic Matter\"\nAnal. Chem. 2006, 78, 13, 4363\u20134373\ndoi: 10.1021/ac0600306
\n
\n\nRaises
\n\n\n- Exception: If no molecular formula are associated with mass spectrum peak.
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.factory", "modulename": "corems.ms_peak.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses", "modulename": "corems.ms_peak.factory.MSPeakClasses", "kind": "module", "doc": "\n"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.ICRMassPeak", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "ICRMassPeak", "kind": "class", "doc": "A class representing a peak in an ICR mass spectrum.
\n", "bases": "_MSPeak"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.ICRMassPeak.__init__", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "ICRMassPeak.__init__", "kind": "function", "doc": "\n", "signature": "(*args, ms_parent=None, exp_freq=None)"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.ICRMassPeak.resolving_power_calc", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "ICRMassPeak.resolving_power_calc", "kind": "function", "doc": "Calculate the theoretical resolving power of the peak.
\n\nParameters
\n\n\n- T (float):\ntransient time
\n- B (float):\nMagnetic Filed Strength (Tesla)
\n
\n\nReturns
\n\n\n- float: Theoretical resolving power of the peak.
\n
\n\nReferences
\n\n\n- Marshall et al. (Mass Spectrom Rev. 1998 Jan-Feb;17(1):1-35.)\nDOI: 10.1002/(SICI)1098-2787(1998)17:1<1::AID-MAS1>3.0.CO;2-K
\n
\n", "signature": "(self, B, T):", "funcdef": "def"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.ICRMassPeak.set_calc_resolving_power", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "ICRMassPeak.set_calc_resolving_power", "kind": "function", "doc": "Set the resolving power of the peak to the calculated one.
\n", "signature": "(self, B: float, T: float):", "funcdef": "def"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.TOFMassPeak", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "TOFMassPeak", "kind": "class", "doc": "A class representing a peak in a TOF mass spectrum.
\n", "bases": "_MSPeak"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.TOFMassPeak.__init__", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "TOFMassPeak.__init__", "kind": "function", "doc": "\n", "signature": "(*args, exp_freq=None)"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.TOFMassPeak.set_calc_resolving_power", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "TOFMassPeak.set_calc_resolving_power", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.OrbiMassPeak", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "OrbiMassPeak", "kind": "class", "doc": "A class representing a peak in an Orbitrap mass spectrum.
\n", "bases": "_MSPeak"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.OrbiMassPeak.__init__", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "OrbiMassPeak.__init__", "kind": "function", "doc": "\n", "signature": "(*args, exp_freq=None)"}, {"fullname": "corems.ms_peak.factory.MSPeakClasses.OrbiMassPeak.set_calc_resolving_power", "modulename": "corems.ms_peak.factory.MSPeakClasses", "qualname": "OrbiMassPeak.set_calc_resolving_power", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient", "modulename": "corems.transient", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.calc", "modulename": "corems.transient.calc", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.calc.TransientCalc", "modulename": "corems.transient.calc.TransientCalc", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations", "kind": "class", "doc": "Transient Calculations
\n\nParameters
\n\n\n- parameters (corems.transient.parameters.TransientParameters):\nThe transient parameters
\n- bandwidth (float):\nThe bandwidth of the transient (Hz)
\n- number_data_points (int):\nThe number of data points of the transient
\n- exc_low_freq (float):\nThe low frequency of the excitation (Hz)
\n- exc_high_freq (float):\nThe high frequency of the excitation (Hz)
\n
\n\nAttributes
\n\n\n- parameters (corems.transient.parameters.TransientParameters):\nThe transient parameters
\n- bandwidth (float):\nThe bandwidth of the transient (Hz)
\n- number_data_points (int):\nThe number of data points of the transient
\n- exc_low_freq (float):\nThe low frequency of the excitation (Hz)
\n- exc_high_freq (float):\nThe high frequency of the excitation (Hz)
\n
\n\nMethods
\n\n\n- cal_transient_time().\nCalculate the time domain length of the transient
\n- zero_fill(transient).\nZero fill the transient
\n- truncation(transient).\nTruncate the transient
\n- apodization(transient).
\nApodization of the transient \n- calculate_frequency_domain(number_data_points).\nCalculate the frequency domain (axis) of the transient
\n- cut_freq_domain(freqdomain_X, freqdomain_Y).\nCut the frequency domain of the transient
\n- phase_and_absorption_mode_ft().\n[Not Functional] Produce a phased absorption mode FT spectrum
\n- magnitude_mode_ft(transient).\nPerform magnitude mode FT of the transient
\n- correct_dc_offset().\n[Not Yet Implemented] Correct the DC offset of the transient
\n
\n"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.cal_transient_time", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.cal_transient_time", "kind": "function", "doc": "Calculate the time domain length of the transient
\n\nReturns
\n\n\n- float: The time domain length of the transient (s)
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.zero_fill", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.zero_fill", "kind": "function", "doc": "Zero fill the transient
\n\nParameters
\n\n\n- transient (numpy.ndarray):\nThe transient data points
\n
\n\nReturns
\n\n\n- numpy.ndarray: The transient data points zerofilled
\n
\n\nNotes
\n\nThe number of zero fills is defined by the transient parameter number_of_zero_fills.\nThe function first calculate the next power of two of the transient length and zero fills to that length, to take advantage of FFT algorithm.\n If the parameter next_power_of_two is set to False, the function will zero fill to the length of the original transient times the number of zero fills
\n", "signature": "(self, transient):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.truncation", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.truncation", "kind": "function", "doc": "Truncate the transient
\n\nParameters
\n\n\n- transient (numpy.ndarray):\nThe transient data points
\n
\n\nReturns
\n\n\n- numpy.ndarray: The truncated transient data points
\n
\n\nNotes
\n\nThe number of truncations is defined by the transient parameter number_of_truncations
\n", "signature": "(self, transient):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.apodization", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.apodization", "kind": "function", "doc": "Apodization of the transient
\n\nParameters
\n\n\n- transient (numpy.ndarray):\nThe transient data points
\n
\n\nReturns
\n\n\n- numpy.ndarray: The apodized transient data points
\n
\n\nNotes
\n\nThe apodization method is defined by the transient parameter apodization_method.\nThe following apodization methods are available:\n Hamming,\n Hanning,\n Blackman,\n Full-Sine,\n Half-Sine,\n Kaiser,\n Half-Kaiser.
\n\nFor Kaiser and Half-Kaiser, an additional parameter 'beta' is required, set by the transient parameter kaiser_beta.
\n", "signature": "(self, transient):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.calculate_frequency_domain", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.calculate_frequency_domain", "kind": "function", "doc": "Calculate the frequency domain (axis) of the transient
\n\nParameters
\n\n\n- number_data_points (int):\nThe number of data points of the transient
\n
\n\nReturns
\n\n\n- numpy.ndarray: The frequency domain of the transient (Hz)
\n
\n", "signature": "(self, number_data_points):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.cut_freq_domain", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.cut_freq_domain", "kind": "function", "doc": "Cut the frequency domain of the transient
\n\nParameters
\n\n\n- freqdomain_X (numpy.ndarray):\nThe frequency domain of the transient (Hz)
\n- freqdomain_Y (numpy.ndarray):\nThe frequency domain of the transient (Hz)
\n
\n\nReturns
\n\n\n- numpy.ndarray: The frequency domain of the transient (Hz)
\n- numpy.ndarray: The frequency domain of the transient (Hz)
\n
\n", "signature": "(self, freqdomain_X, freqdomain_Y):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.phase_and_absorption_mode_ft", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.phase_and_absorption_mode_ft", "kind": "function", "doc": "[Not Functional] Produce a phased absorption mode FT spectrum
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.perform_magniture_mode_ft", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.perform_magniture_mode_ft", "kind": "function", "doc": "Perform magnitude mode FT of the transient
\n\nParameters
\n\ntransient : numpy.ndarray\n The transient data points
\n\nReturns
\n\n\n- numpy.ndarray: The frequency domain of the transient (Hz)
\n- numpy.ndarray: The magnitude of the transient (a.u.)
\n
\n", "signature": "(self, transient):", "funcdef": "def"}, {"fullname": "corems.transient.calc.TransientCalc.TransientCalculations.correct_dc_offset", "modulename": "corems.transient.calc.TransientCalc", "qualname": "TransientCalculations.correct_dc_offset", "kind": "function", "doc": "[Not Yet Implemented] Correct the DC offset of the transient
\n\nA simple baseline correction to compensate for a DC offset in the recorded transient.\nNot implemented.
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient.factory", "modulename": "corems.transient.factory", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses", "modulename": "corems.transient.factory.TransientClasses", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient", "kind": "class", "doc": "The Transient object contains the transient data and the parameters used to process it
\n\nParameters
\n\n\n- data (numpy.ndarray):\nArray with the transient data
\n- d_params (dict):\nDictionary with the parameters to be set
\n
\n\nAttributes
\n\n\n- calibration_terms (tuple):\nTuple with the calibration terms (A, B, C)
\n- bandwidth (float):\nThe bandwidth of the transient (Hz)
\n- number_data_points (int):\nThe number of data points of the transient
\n- polarity (int):\nThe polarity of the transient
\n- transient_time (float):\nThe time domain length of the transient
\n- d_params (dict):\nDictionary with the parameters to be set
\n- frequency_domain (numpy.ndarray):\nArray with the frequency domain
\n- magnitude (numpy.ndarray):\nArray with the magnitude
\n- _full_filename_path (str):\nThe full path of the transient file
\n- _exc_high_freq (float):\nThe high frequency of the excitation (Hz)
\n- _exc_low_freq (float):\nThe low frequency of the excitation (Hz)
\n- _parameters (corems.transient.parameters.TransientParameters):\nThe transient parameters
\n- _transient_data (numpy.ndarray):\nArray with the transient data
\n
\n\nMethods
\n\n\n- get_frequency_domain(plot_result=True).\nGet the frequency domain and magnitude from the transient data
\n- get_mass_spectrum(auto_process=True, plot_result=True, keep_profile=True).
\nGet the mass spectrum from the transient data \n- set_processing_parameter(apodization_method, number_of_truncations, number_of_zero_fills).
\nSet the processing parameters \n- scale_plot_size(factor=1.5).\nScale the plot size by a factor
\n- plot_transient(ax=None, c='k').\nPlot the transient data
\n- plot_zerofilled_transient(ax=None, c='k').\nPlot the transient data with zero fill
\n- plot_apodized_transient(ax=None, c='k').\nPlot the transient data with apodization
\n- plot_frequency_domain(ax=None, c='k').\nPlot the frequency domain and magnitude
\n- set_parameter_from_toml(parameters_path).\nSet the processing parameters from a toml file
\n- set_parameter_from_json(parameters_path).\nSet the processing parameters from a json file
\n
\n", "bases": "corems.transient.calc.TransientCalc.TransientCalculations"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.__init__", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.__init__", "kind": "function", "doc": "\n", "signature": "(data, d_params)"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.d_params", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.d_params", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.frequency_domain", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.frequency_domain", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.magnitude", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.magnitude", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.scale_plot_size", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.scale_plot_size", "kind": "function", "doc": "Scale the plot size by a factor
\n\nParameters
\n\n\n- factor (float, optional):\nThe factor to scale the plot size, by default 1.5
\n
\n", "signature": "(self, factor=1.5):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.set_processing_parameter", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.set_processing_parameter", "kind": "function", "doc": "Set the processing parameters
\n\nParameters
\n\n\n- apodization_method (str):\nApodization method to be used
\n- number_of_truncations (int):\nNumber of truncations to be used
\n- number_of_zero_fills (int):\nNumber of zero fills to be used
\n
\n", "signature": "(\tself,\tapodization_method: str,\tnumber_of_truncations: int,\tnumber_of_zero_fills: int):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.parameters", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.parameters", "kind": "variable", "doc": "The transient parameters
\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.set_parameter_from_toml", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.set_parameter_from_toml", "kind": "function", "doc": "Set the processing parameters from a toml file
\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.set_parameter_from_json", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.set_parameter_from_json", "kind": "function", "doc": "Set the processing parameters from a json file
\n", "signature": "(self, parameters_path):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.get_frequency_domain", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.get_frequency_domain", "kind": "function", "doc": "Get the frequency domain and magnitude from the transient data
\n\nParameters
\n\n\n- plot_result (bool, optional):\nPlot the frequency domain and magnitude, by default True
\n
\n\nReturns
\n\n\n- frequency_domain (numpy.ndarray):\nArray with the frequency domain
\n- magnitude (numpy.ndarray):\nArray with the magnitude
\n
\n", "signature": "(self, plot_result=True):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.get_mass_spectrum", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.get_mass_spectrum", "kind": "function", "doc": "Get the mass spectrum from the transient data
\n\nParameters
\n\n\n- auto_process (bool, optional):\nProcess the transient data, by default True
\n- plot_result (bool, optional):\nPlot the frequency domain and magnitude, by default True
\n- keep_profile (bool, optional):\nKeep the profile data, by default True
\n
\n\nReturns
\n\n\n- MassSpecfromFreq: Mass spectrum object
\n
\n", "signature": "(\tself,\tauto_process: bool = True,\tplot_result: bool = True,\tkeep_profile: bool = True) -> corems.mass_spectrum.factory.MassSpectrumClasses.MassSpecfromFreq:", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.filename", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.filename", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.dir_location", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.dir_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.A_therm", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.A_therm", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.B_therm", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.B_therm", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.C_therm", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.C_therm", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.plot_transient", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.plot_transient", "kind": "function", "doc": "Plot the transient data
\n\nParameters
\n\n\n- ax (matplotlib.axes, optional):\nMatplotlib axes object, by default None
\n- c (str, optional):\nColor, by default 'k'
\n
\n\nReturns
\n\n\n- matplotlib.axes: Matplotlib axes object
\n
\n", "signature": "(self, ax=None, c='k'):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.plot_zerofilled_transient", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.plot_zerofilled_transient", "kind": "function", "doc": "Plot the transient data with zero fill
\n\nParameters
\n\n\n- ax (matplotlib.axes, optional):\nMatplotlib axes object, by default None
\n- c (str, optional):\nColor, by default 'k'
\n
\n\nReturns
\n\n\n- matplotlib.axes: Matplotlib axes object
\n
\n", "signature": "(self, ax=None, c='k'):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.plot_apodized_transient", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.plot_apodized_transient", "kind": "function", "doc": "Plot the transient data with apodization
\n\nParameters
\n\n\n- ax (matplotlib.axes, optional):\nMatplotlib axes object, by default None
\n- c (str, optional):\nColor, by default 'k'
\n
\n\nReturns
\n\n\n- matplotlib.axes: Matplotlib axes object
\n
\n", "signature": "(self, ax=None, c='k'):", "funcdef": "def"}, {"fullname": "corems.transient.factory.TransientClasses.Transient.plot_frequency_domain", "modulename": "corems.transient.factory.TransientClasses", "qualname": "Transient.plot_frequency_domain", "kind": "function", "doc": "Plot the frequency domain and magnitude
\n\nParameters
\n\n\n- ax (matplotlib.axes, optional):\nMatplotlib axes object, by default None
\n- c (str, optional):\nColor, by default 'k'
\n
\n\nReturns
\n\n\n- matplotlib.axes: Matplotlib axes object
\n
\n", "signature": "(self, ax=None, c='k'):", "funcdef": "def"}, {"fullname": "corems.transient.input", "modulename": "corems.transient.input", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.input.brukerSolarix", "modulename": "corems.transient.input.brukerSolarix", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix", "kind": "class", "doc": "A class used to Read a single Transient from Bruker's FT-MS acquisition station (fid, or ser)
\n\nParameters
\n\n\n- d_directory_location (str):\nthe full path of the .d folder
\n
\n\nAttributes
\n\n\n- d_directory_location (str):\nthe full path of the .d folder
\n- file_location (str):\nthe full path of the .d folder
\n- parameter_filename_location (str):\nthe full path of the apexAcquisition.method file
\n- transient_data_path (str):\nthe full path of the fid or ser file
\n- scan_attr (str):\nthe full path of the scan.xml file
\n
\n\nMethods
\n\n\n- get_transient().\nRead the data and settings returning a Transient class
\n- get_scan_attr().\nRead the scan retention times, TIC values and scan indices.
\n- locate_file(folder, type_file_name).\nFind the full path of a specific file within the acquisition .d folder or subfolders
\n- parse_parameters(parameters_filename).\nOpen the given file and retrieve all parameters from apexAcquisition.method
\n- fix_freq_limits(d_parameters).\nRead and set the correct frequency limits for the spectrum
\n- get_excite_sweep_range(filename).\nDetermine excitation sweep range from ExciteSweep file
\n
\n"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.__init__", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.__init__", "kind": "function", "doc": "\n", "signature": "(d_directory_location)"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.d_directory_location", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.d_directory_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.file_location", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.file_location", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.get_scan_attr", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.get_scan_attr", "kind": "function", "doc": "Function to get the scan retention times, TIC values and scan indices.
\n\nGets information from scan.xml file in the bruker .d folder.\nNote this file is only present in some .d format - e.g. for imaging mode data, it is not present.
\n\nReturns
\n\n\n- dict_scan_rt_tic (dict):\na dictionary with scan number as key and rt and tic as values
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.get_transient", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.get_transient", "kind": "function", "doc": "Function to get the transient data and parameters from a Bruker Solarix .d folder.
\n\nParameters
\n\n\n- scan_number (int):\nthe scan number to be read. Default is 1.
\n
\n\nReturns
\n\n\n- Transient: a transient object
\n
\n", "signature": "(self, scan_number=1):", "funcdef": "def"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.fix_freq_limits", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.fix_freq_limits", "kind": "function", "doc": "Function to read and set the correct frequency limits for the spectrum
\n\nNotes
\n\nThis is using the excitation limits from the apexAcquisition.method file,\nwhich may not match the intended detection limits in edge cases. \nIn default acquisitions, excitation and detection are the same. \nBut, they may not be in some cases with selective excitation, custom excite waveforms, or in 2DMS applications.
\n\nParameters
\n\n\n- d_parameters (dict):\na dictionary with the parameters from the apexAcquisition.method file
\n
\n", "signature": "(self, d_parameters):", "funcdef": "def"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.get_excite_sweep_range", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.get_excite_sweep_range", "kind": "function", "doc": "Function to determine excitation sweep range from ExciteSweep file
\n\nThis looks at the first and last rows of the ExciteSweep file to determine the excitation frequency range.\nNote that this assumes the excitation sweep was linear and the first and last rows are the lowest and highest frequencies.\nThis is presumably always true, but again may be incorrect for edge cases with custom excitation waveforms.
\n\nParameters
\n\n\n- filename (str):\nthe full path to the ExciteSweep file
\n
\n", "signature": "(filename):", "funcdef": "def"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.locate_file", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.locate_file", "kind": "function", "doc": "Function to locate a file in a folder
\n\nFind the full path of a specific file within the acquisition .d folder or subfolders
\n\nParameters
\n\n\n- folder (str):\nthe full path to the folder
\n- type_file_name (str):\nthe name of the file to be located\nExpected options: ExciteSweep or apexAcquisition.method
\n
\n\nReturns
\n\n\n- str: the full path to the file
\n
\n\nNotes
\n\nadapted from code from SPIKE library, https://github.com/spike-project/spike
\n", "signature": "(folder, type_file_name):", "funcdef": "def"}, {"fullname": "corems.transient.input.brukerSolarix.ReadBrukerSolarix.parse_parameters", "modulename": "corems.transient.input.brukerSolarix", "qualname": "ReadBrukerSolarix.parse_parameters", "kind": "function", "doc": "Function to parse the parameters from apexAcquisition.method file
\n\nOpen the given file and retrieve all parameters from apexAcquisition.method\n None is written when no value for value is found
\n\nstructure : <param name = \"AMS_ActiveExclusion\"><value>0</value></param>\n
\n\nParameters
\n\n\n- parameters_filename (str):\nthe full path to the apexAcquisition.method file
\n
\n\nReturns
\n\n\n- dict: a dictionary with the parameters and values
\n
\n\nNotes
\n\nAdapted from code from SPIKE library, https://github.com/spike-project/spike.\nCode may not handle all possible parameters, but should be sufficient for most common use cases
\n", "signature": "(parameters_filename):", "funcdef": "def"}, {"fullname": "corems.transient.input.midasDatFile", "modulename": "corems.transient.input.midasDatFile", "kind": "module", "doc": "\n"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile", "kind": "class", "doc": "[Not Implemented] Reads MIDAS .dat files (binary transient data)
\n\nThis class will read .dat binary format transient data, e.g. midas format from Predator or Thermo datastations\nThis code is not yet implemented and is not fully functional.
\n\nParameters
\n\n\n- filename_path (str):\nThe path to the .dat file
\n
\n\nAttributes
\n\n\n- filename_path (str):\nThe path to the .dat file
\n- d_params (dict):\nA dictionary with the parameters of the .dat file
\n- transient_data (numpy.ndarray):\nThe transient data
\n
\n\nMethods
\n\n\n- read_file().\nReads the .dat file and returns the transient data and the parameters
\n- get_transient_data(data_file, d_params).\nReads the transient data from the .dat file
\n- parse_parameter(f).\nParses the parameters from the .dat file
\n
\n\nRaises
\n\n\n- NotImplementedError: This class is not yet implemented.
\n
\n"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile.__init__", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile.__init__", "kind": "function", "doc": "\n", "signature": "(filename_path)"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile.filename_path", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile.filename_path", "kind": "variable", "doc": "\n"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile.read_file", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile.read_file", "kind": "function", "doc": "Reads the .dat file and returns the transient data and the parameters
\n\nReturns
\n\n\n- transient_data (numpy.ndarray):\nThe transient data
\n- d_params (dict):\nA dictionary with the parameters of the .dat file
\n
\n", "signature": "(self):", "funcdef": "def"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile.get_transient_data", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile.get_transient_data", "kind": "function", "doc": "Reads the transient data from the .dat file
\n\nParameters
\n\n\n- data_file (file):\nThe .dat file
\n- d_params (dict):\nA dictionary with the parameters of the .dat file
\n
\n\nReturns
\n\n\n- myarray (numpy.ndarray):\nThe transient data
\n
\n", "signature": "(self, data_file, d_params):", "funcdef": "def"}, {"fullname": "corems.transient.input.midasDatFile.ReadMidasDatFile.parse_parameter", "modulename": "corems.transient.input.midasDatFile", "qualname": "ReadMidasDatFile.parse_parameter", "kind": "function", "doc": "Parses the parameters from the .dat file
\n\nParameters
\n\n\n- f (file):\nThe .dat file
\n
\n\nReturns
\n\n\n- output_parameters (dict):\nA dictionary with the parameters of the .dat file
\n
\n", "signature": "(self, f):", "funcdef": "def"}];
// mirrored in build-search-index.js (part 1)
// Also split on html tags. this is a cheap heuristic, but good enough.
diff --git a/tests/test_molecularFormulaSearch.py b/tests/test_molecularFormulaSearch.py
index 406c02d4..d5818001 100644
--- a/tests/test_molecularFormulaSearch.py
+++ b/tests/test_molecularFormulaSearch.py
@@ -22,11 +22,22 @@ def create_mass_spectrum():
file_location = Path.cwd() / "tests/tests_data/ftms/ESI_NEG_SRFA.d/"
bruker_reader = ReadBrukerSolarix(file_location)
-
+ MSParameters.molecular_search.url_database = ''
MSParameters.mass_spectrum.noise_threshold_method = 'log'
MSParameters.mass_spectrum.noise_threshold_log_nsigma = 10
MSParameters.ms_peak.peak_min_prominence_percent = 1
+ MSParameters.molecular_search.min_ppm_error = -5
+ MSParameters.molecular_search.max_ppm_error = 5
+ MSParameters.molecular_search.mz_error_range = 1
+ MSParameters.molecular_search.isProtonated = True
+ MSParameters.molecular_search.isRadical= False
+ MSParameters.molecular_search.isAdduct= False
+
+ usedatoms = {'C': (1,100) , 'H': (4,200), 'O': (0,10), 'N': (0,1), 'P': (0,1)}
+ MSParameters.molecular_search.usedAtoms = usedatoms
+ MSParameters.molecular_search.usedAtoms = usedatoms
+
bruker_transient = bruker_reader.get_transient()
mass_spectrum_obj = bruker_transient.get_mass_spectrum(
@@ -42,52 +53,49 @@ def create_mass_spectrum():
return mass_spectrum_obj
def test_run_molecular_formula_search():
+ # Test for generating accurate molecular formula from a single mass using the local sql database
+ mz = [760.58156938877]
+ abundance = [1]
+ rp, s2n = [[1],[1]]
- #MSParameters.molecular_search.url_database = ''
- MSParameters.molecular_search.usedAtoms['F'] = (0,0)
- MSParameters.molecular_search.usedAtoms['P'] = (0,0)
- MSParameters.molecular_search.usedAtoms['Cl'] = (0,0)
- MSParameters.molecular_search.isAdduct = False
- MSParameters.molecular_search.isRadical = False
-
- MSParameters.molecular_search.used_atom_valences['P'] = 0
- MSParameters.molecular_search.used_atom_valences['F'] = 0
- MSParameters.molecular_search.used_atom_valences['Cl'] = 0
-
MSParameters.mass_spectrum.noise_threshold_method = 'relative_abundance'
- MSParameters.mass_spectrum.noise_threshold_min_relative_abundance = 0.1
+ MSParameters.mass_spectrum.noise_threshold_absolute_abundance = 0
- mz = [215.09269]
- abundance = [1]
- rp, s2n = [1] ,[1]
- dataname = 'one peak'
- MSParameters.mass_spectrum.noise_threshold_method = 'relative_abundance'
- mass_spectrum_obj = ms_from_array_centroid(mz, abundance, rp, s2n, dataname, auto_process=False)
+ MSParameters.molecular_search.url_database = ''
+ MSParameters.molecular_search.error_method = 'None'
+ MSParameters.molecular_search.min_ppm_error = -5
+ MSParameters.molecular_search.max_ppm_error = 5
+ MSParameters.molecular_search.mz_error_range = 1
+ MSParameters.molecular_search.isProtonated = True
+ MSParameters.molecular_search.isRadical= False
+ MSParameters.molecular_search.isAdduct= False
- SearchMolecularFormulas(mass_spectrum_obj).run_worker_ms_peaks([mass_spectrum_obj[0]])
+ usedatoms = {'C': (1,100) , 'H': (4,200), 'O': (0,10), 'N': (0,1)}
+ MSParameters.molecular_search.usedAtoms = usedatoms
+ MSParameters.molecular_search.usedAtoms = usedatoms
+ mass_spectrum_obj = ms_from_array_centroid(mz, abundance, rp, s2n, 'single mf search', polarity=1, auto_process=True)
+ mass_spectrum_obj.settings.noise_threshold_method = 'relative threshold'
+ mass_spectrum_obj.molecular_search_settings.use_min_peaks_filter = False
+ mass_spectrum_obj.molecular_search_settings.use_min_peaks_filter = 10
+ mass_spectrum_obj.molecular_search_settings.use_isotopologue_filter = False
+ SearchMolecularFormulas(mass_spectrum_obj, find_isotopologues=True).run_worker_ms_peaks([mass_spectrum_obj[0]])
ms_peak = mass_spectrum_obj[0]
- print(ms_peak.mz_exp)
- if ms_peak.is_assigned:
- for formula in ms_peak:
- print(formula.string_formated, formula.mz_error)
+ assert ms_peak[0].string == 'C56 H73 N1'
+
def test_mspeak_search():
mass_spec_obj = create_mass_spectrum()
-
- print("OK")
-
mspeak_obj = mass_spec_obj.most_abundant_mspeak
-
SearchMolecularFormulas(mass_spec_obj).run_worker_ms_peaks([mspeak_obj])
-
- print("OK2")
if mspeak_obj.is_assigned:
-
- print(mspeak_obj.molecular_formula_earth_filter().string)
- print(mspeak_obj.molecular_formula_water_filter().string)
- print(mspeak_obj.molecular_formula_air_filter().string)
+ if len(mspeak_obj.molecular_formula_earth_filter()) > 0:
+ print(mspeak_obj.molecular_formula_earth_filter().string)
+ if len(mspeak_obj.molecular_formula_water_filter()) > 0:
+ print(mspeak_obj.molecular_formula_water_filter().string)
+ if len(mspeak_obj.molecular_formula_air_filter()) > 0:
+ print(mspeak_obj.molecular_formula_air_filter().string)
print(mspeak_obj.cia_score_S_P_error().string)
print(mspeak_obj.cia_score_N_S_P_error().string)
print(mspeak_obj.best_molecular_formula_candidate.string)
@@ -161,5 +169,5 @@ def test_priorityAssignment():
#test_priorityAssignment()
#()
#test_molecular_formula_search_db()
- test_run_molecular_formula_search()
- #test_mspeak_search()
+ #test_run_molecular_formula_search()
+ test_mspeak_search()
+