v1.0.0.dev1

Merge pull request #1103 from hainm/master

add -Wl,--no-undefined

v0.1.2.dev4

What's new?

• add pretty print for DataSetList when having pandas
• enhance speed for frame_iter and chunk_iter
• add 'merge_traj'
• add apply method to change traj's internal data
• add basic math for Trajectory
• add XYZ class as a simple wrapper for numpy ndarray
  traj.xyz is no longer ndarray, just a read-only wrapper
• add TrajectoryMDAnalysisIterator
• add read_data for DataFile and DataSetList
• add frame swap for Trajectory
• add atom coords assignment traj['@ca'] = xyz
• add stack for DataSetList to join 2 datasets
• rename set_frame_m to set_frame_mass
• update to_amber_mask to convert integer array-like to string mask
• add autoimage and rmsfit_to for chunk_iter and frame_iter
• tune speed for chunk_iter and frame_iter for TrajectoryIterator
• add plot method for DataSet
• add write_to_cpptraj_format
• add array for Frame
• introduce array interface to numpy for cpptraj's DataSet
• add median, std, ... for DataSetList
• update run_all_and_find_fails.py for capturing segmetation fault
• add Trajectory joining (traj += traj)
• optimize slicing for TrajectoryIterator
• optimize strip_atoms (1000 times speed up)
• add copy method for DataSet
• add fancy indexing for DataSetList
• add _fast_slice for Trajectory (1000 times faster)
• add regular expression for groupby
• add to_pickle, to_json, read_pickle, read_json
• add _guess_filetype
• change fit_to to rmsfit_to
• enhance smart _frame_iter_master
• create alias rmsd for calc_rmsd in common_actions module
• update loading hd5f file without going through mdtraj
• correctly handle box in api.Trajectory
• add TrajectoryREMDIterator class to handal REMD
• change io.load_remd_iterator to io.iterload_remd
• add io._iterload_from_filelist and io._load_from_filelist
• add count for DataSet_integer
• API CHANGE (05-06-2015):
  • change FrameArray to Trajectory
  • change TrajReadOnly to TrajectoryIterator (issue #262)
    (#262)
  • io.load will return Trajectory instead of TrajectoryIterator
  • io.iterload will return TrajectoryIterator
• add "legend" as property of DataSet
• remove "get_box" from Frame. use "box"
• support autoimage when loading mdtraj object
• bugfix for io.loadpdb_rcsb
• add 'calc_rdf'
• trick to add reference to Action
  • Example: calc_abcxyz([[ref,], traj], command), where ref is a Frame object, abcxyz is a specific action.
• add option to load coords from ParmEd object
• add align_principal_axis
• fix iteration in api.Trajectory: 2 orders of magniture faster
• add "as_ndmatrix" for Matrix_3x3

v0.1.2.dev3

What's new?

• add set_nobox for FrameArray
• add dtype in calculate method to return list, pyarray, dataset or ndarray
• support ParmEd with bonds, dih, angles loading
• add support loading more infor (bonds, box, angles, dihedrals) from MDAnalysis
  and mdtraj
• add bonds, angles and dihedrals iterators for Topology
• support MPI (with mpi4py)
• add calc_rmsd
• rename "do_rotation" to "rotate", "do_translation" to "translate"
  "do_autoimage" to "autoimage"
• add "box" to Topology
• reorganize folders (04-25-2015)
  • moved Atom, Molecule, Residue, Box to pytraj.core
  • moved Trajin_Single to pytraj.trajs
  • moved Matrix_3x3, Vec3, Grid ... to pytraj.math
  • moved all unused files away from main folder
  • dont support Energy routine in cpptraj, use pysander instead
  • move all optional package importing to pytraj.externals.
  • enhance groupby method: dslist.groupby("omega", mode='aspect')
  • added pytraj.api.Trajectory as a new Trajectory object with xyz is a numpy array
• add universal _get_top method
  _get_top(traj, top)
• add DataSet_Mesh
• better setup.py: automatically install libcpptraj
• change API of FrameArray and TrajReadOnly
  traj['CA'] return a stripped-atoms traj (not a xyz coords)
• add calc_temperature

v0.1.2.dev2

what's new

• add "groupby" method for DataSetList
• directly access "calc_..." methods from FrameArray and TrajReadOnly (traj.calc_COM, ...)
• "tolist" in Traj should return 3D list (n_frame, n_atoms, 3)
• "tolist" of Frame should return 2D list (n_atoms, 3)
• add "tolist" for DataSet_Vector
• add "keys()" to DataSetList class. Now we can use this as a list and a dict
• support Grid calculation (calc_volmap, ...)
• enhance speed of AtomMask selection (about 5 times faster)
• add set_error_silent to turn-off (and on) cpptraj' warning
• add attribute indices for AtomMask object (shorter than selected_indices method's name
• support loading MDAnalysis objects (Universe)
• add method load_pseudo_parm to load ParmEd and mdtraj Topology objects
• fully compat with cpptraj, user can get CpptrajState from trajin.in file
  (pytraj.io.load_cpptraj_file)
• add to_ndarray for DataSet, Frame, Vec3,... objects
• introduce memoryview for DataSet
• fix memory for calculate method
• add simple wrapper to pysander to be used with pandas' DataFrame
• add calc_multidihedral for quickly scanning dihedral
• improve code for AtomMask: add_selected_indices could accept memview
• add _frame_iter_master to iterate anything that results Frame objects
• add frame_iter with atom indices (before: only support atom mask): traj(mask=index_array)

v0.1.2.dev0.1

What's new

• Can combine with pysander to get energy
• Update DataSet class inheritance (following cpptraj changes)
• Support Analysis classes in cpptraj (including clustering)
• Introduce dataframe to interact with pandas (to_dataframe)
• Support OPENMP
• Have option to make faster building (less than 2 minutes) by using multiprocess
• load method of FrameArray is much more robust (it can load raw numpy, list, tuple of numbers, any iterable objects that resulting Frame ... and much more)

• Support loading `mdtraj` objects (Trajectory and Topology). Support loading array with ndim=1, 2, 3
  

• Support more than 100 kinds of calculations and analyses in `cpptraj`
  

• Many bugfixs to avoid segmentation fault 
  

v0.1.2.dev0

[check v0.1.2.dev0.1]

v0.1.0.1

What's new?

• Features
  • Turn on profiling
  • Add fit_to method for structure alignment
• Bug fix
  • Turn off AMBERHOME requirement

Install

wget https://github.com/pytraj/pytraj/archive/v0.1.0.1.tar.gz
tar -xf v0.1.0.1.tar.gz
cd pytraj*
python ./setup.py install

0.1.beta.20

wget https://github.com/pytraj/pytraj/archive/0.1.beta.20.tar.gz
tar -xf 0.1.beta.20.tar.gz
cd pytraj*
python setup.py install

What's new?

• faster iterator for loading trajectory
• simpler setup process (not yet supported pip or conda install)
• bug fixes

0.1.beta.9

wget https://github.com/pytraj/pytraj/archive/0.1.beta.9.tar.gz
tar -xf 0.1.beta.9.tar.gz
cd pytraj*
python setup.py install

0.1.beta.10

wget https://github.com/pytraj/pytraj/archive/0.1.beta.10.tar.gz
tar -xf 0.1.beta.10.tar.gz
cd pytraj*
python setup.py install