Merging of Code refactoring of Setup & Simulation with Analysis #109

talagayev · 2024-10-02T11:38:26Z

Changes made:

Code refactoring for OpenMMDL Setup
Code refactoring for OpenMMDL Simulation

Moved functions into classes and added smirnoff support

Adjusted the code to functions

Adjusted to classes

Added code with new classes

restructure of code

adjusted to save conf file

Equilibration & Restart changed to Checkbox

Added File and Class to move default configuration settings from openmmdl setup

Added file to mave config creation there

Adjusting to new changes in moval of code

Added function for amber bash script default options

Added remaining config file parts

Adjusted with the moval of the script generation

Added LigandExtractor

Class for Amberscript creation in progress

Adjusting for the new amber script python

Added remainder of amber script functions

Added first function for Request sessions

Adjusted with new sessions script and final amber scripts

Full Amber bash script preparation file

Added additional sessions

full setup options

Added Setup Options

remove blank lines

Added Upload Files function

run by black

Returned to the state before type checking and hinting

returned to previous state

Adjusted the tutorial tabs to the new tab configuration in Simulation Options and added Configuration files naming in the simulation options instead of a python script

Changed OpenMMDL-Setup to OpenMMDL Setup

name changed from receptor_fertig --> AmberOptionSelected.png

name changed from add_membrane_other --> addMembraneMixtures.png

name changed ligand_ausgefüllt --> AmberOptionReceptor.png

changed names of images accordingly to pathway and added 2 images

grammatical change

name changed from neuer_ordener --> PDBFixerPathFolder.png

added image PDBFixerPathFolder.png

Fixing Tutorial figures

Adjusted

returned

Adjusted code for easier config parser

adjusted strings

removed old files

Added new openmmdl simulation files

OpenMMDL Simulation restructure

type hinting and checking

adjusting the code

openmmdlsetup.py: type hinting

talagayev added 30 commits August 1, 2024 12:50

Update forcefield_water.py

9186a63

Moved functions into classes and added smirnoff support

Update protein_ligand_prep.py

6bd6d8b

Adjusted the code to functions

Update post_md_conversions.py

78487ff

Adjusted to classes

Update cleaning_procedures.py

87258cb

Added code with new classes

Update openmmdlsetup.py

0494487

Update configurePdbFile.html

5b0eb7f

Update openmmdlsetup.py

67ee220

restructure of code

Update simulationOptions.html

6fe02c8

adjusted to save conf file

Update openmmdlsetup.py

60cf5fb

Update simulationOptions.html

5856890

Equilibration & Restart changed to Checkbox

Create setup_options.py

93953ce

Added File and Class to move default configuration settings from openmmdl setup

Create configfile_creator.py

ab4af18

Added file to mave config creation there

Update openmmdlsetup.py

fb383eb

Adjusting to new changes in moval of code

Update setup_options.py

8072838

Added function for amber bash script default options

Update configfile_creator.py

8984b4e

Added remaining config file parts

Update openmmdlsetup.py

505c4bb

Adjusted with the moval of the script generation

Create file_operator.py

2dfec82

Added LigandExtractor

Create amberscript_creator.py

0ba9ca4

Class for Amberscript creation in progress

Update openmmdlsetup.py

e5f729d

Adjusting for the new amber script python

Update amberscript_creator.py

0eec5ea

Added remainder of amber script functions

Update setup_options.py

2705bc8

Added first function for Request sessions

Update openmmdlsetup.py

1119b6c

Adjusted with new sessions script and final amber scripts

Update amberscript_creator.py

31f4939

Full Amber bash script preparation file

Update amberscript_creator.py

d8e1e45

Update configfile_creator.py

75c6da1

Update setup_options.py

7150804

Added additional sessions

Update setup_options.py

9a166ca

full setup options

Update setup_options.py

d1d80d2

Added Setup Options

Update file_operator.py

7213161

remove blank lines

Update file_operator.py

5a0886f

Added Upload Files function

Armenia01 and others added 29 commits August 16, 2024 14:08

Update openmmdlsetup.py

d0c2236

run by black

Update amberscript_creator.py

4f10984

Returned to the state before type checking and hinting

Update configfile_creator.py

fed4ecf

returned to previous state

Update configfile_creator.py

47a46ff

Update file_operator.py

3ab533e

returned to previous state

Update file_operator.py

9c25d22

Update setup_options.py

562a444

Update tutorial_amber_path.rst

116a289

Adjusted the tutorial tabs to the new tab configuration in Simulation Options and added Configuration files naming in the simulation options instead of a python script

Update tutorial_pdb_path.rst

9c5311c

Changed OpenMMDL-Setup to OpenMMDL Setup

Rename Rezeptor fertig .png to AmberOptionSelected.png

ace352e

name changed from receptor_fertig --> AmberOptionSelected.png

Rename addMembrane_other.png to addMembraneMixtures.png

1bfe8e1

name changed from add_membrane_other --> addMembraneMixtures.png

Rename normal ligand, ausgefüllt.png to AmberOptionReceptor.png

d99d907

name changed ligand_ausgefüllt --> AmberOptionReceptor.png

Update tutorial_amber_path.rst

3f6aaa9

changed names of images accordingly to pathway and added 2 images

Update tutorial_amber_path.rst

30469e1

grammatical change

Add files via upload

bd6378b

Rename neuer ordner.png to PDBFixerPathFolder.png

48c4099

name changed from neuer_ordener --> PDBFixerPathFolder.png

Update tutorial_pdb_path.rst

ef25d5d

added image PDBFixerPathFolder.png

Merge pull request #97 from Armenia01/4

9ef4bbb

Fixing Tutorial figures

Update configfile_creator.py

a68ff91

Adjusted

Update amberscript_creator.py

495dc81

returned

Update configfile_creator.py

38c1535

Adjusted code for easier config parser

Update configfile_creator.py

9198c18

adjusted strings

Delete openmmdl/openmmdl_simulation/scripts directory

e78ed42

removed old files

Delete openmmdl/openmmdl_simulation/openmmdlsimulation.py

1fa1dc9

Add files via upload

436e09b

Added new openmmdl simulation files

Merge pull request #103 from talagayev/Code_Class_movement_Setup_Sim_2

33a1e4f

OpenMMDL Simulation restructure

Merge pull request #98 from Armenia01/5.5

41e8975

type hinting and checking

Update openmmdlsetup.py

6d3bec2

adjusting the code

Merge pull request #99 from Armenia01/6

2e44afb

openmmdlsetup.py: type hinting

talagayev merged commit b99f1bd into Code_Class_movement Oct 2, 2024
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Merging of Code refactoring of Setup & Simulation with Analysis #109

Merging of Code refactoring of Setup & Simulation with Analysis #109

talagayev commented Oct 2, 2024

Merging of Code refactoring of Setup & Simulation with Analysis #109

Merging of Code refactoring of Setup & Simulation with Analysis #109

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talagayev commented Oct 2, 2024