File renaming documentation by talagayev · Pull Request #149 · wolberlab/OpenMMDL

talagayev · 2025-05-17T15:30:19Z

Changes made:

Adjusted code in multiple places

PR Checklist

renaming

…ovchains.py renaming

adjusted

adjust

fixed naming

move update_dict

use update_dict from utils

create utils.py

moved combine_subdict_values

row_name added to update_values to make it more broad

added update_values name

adjusted the binding modes and markov chains for frame selection

moved update_values

moved positions

addition of utils.rst

added core docs

added figures.rst correct

added visualization modules

in prgrs

added

small docs fix

added numpy doc for class

change location

fix

typo fix

fix

added pharmacophore.rst

remove specific PLIP mention

added barcodes.rst

added visulaization rsts

created visualization.rst

added visualization

fix for parameters

fix with the typo adjusting

talagayev added 30 commits April 30, 2025 12:36

Rename barcode_generation.py to barcodes.py

bbccbb7

Rename find_stable_waters.py to stable_waters.py

24af3ba

Rename trajectory_saving.py to trajectories.py

8423b75

renaming

Rename stable_waters.py to wateranalysis.py

ae006fe

Rename markov_state_figure_generation.py to markovchains.py

fa94df8

renaming

Rename rmsd_calculation.py to rmsd.py

9ec91fb

renaming

Rename binding_mode_processing.py to bindingmodes.py

2d679c5

renaming

Rename image_handler.py to imagehandler.py

280420a

renaming

Rename interaction_gathering.py to interactions.py

d56011a

renaming

Update and rename rdkit_figure_generation.py to highlighter.py

990d2bd

renaming

Rename highlighter.py to highlight.py

3fee743

Update and rename visualization_functions.py to visualization.py

79c5147

Rename imagehandler.py to imagehandling.py

01f8f41

Update and rename test_barcode_generation.py to test_barcodes.py

833aa77

Update and rename imagehandling.py to figures.py

16ef413

renaming

Update and rename test_image_handler.py to test_figures.py

f8ca796

renaming

Update and rename test_markov_state_figure_generation.py to test_mark…

7dbf711

…ovchains.py renaming

Update and rename test_rdkit_figure_generation.py to test_highlight.py

cef5a06

adjusted

Update and rename test_rmsd_calculation.py to test_rmsd.py

6e62ff4

adjust

Update and rename test_trajectory_saving.py to test_trajectories.py

1b943a1

Update openmmdlanalysis.py

c3fe1e1

fixed naming

Update highlight.py

6e9b229

move update_dict

Update openmmdlanalysis.py

c466fde

use update_dict from utils

Create utils.py

e0c99f3

create utils.py

Update utils.py

79a5fa4

moved combine_subdict_values

Update bindingmodes.py

22079fc

moved combine_subdict_values

Update bindingmodes.py

47111aa

row_name added to update_values to make it more broad

Update openmmdlanalysis.py

61451df

added update_values name

Update openmmdlanalysis.py

22e19e4

adjusted the binding modes and markov chains for frame selection

Update utils.py

b5175a6

moved update_values

talagayev added 28 commits May 16, 2025 19:15

Update pharmacophore.py

25b0554

moved positions

Create utils.rst

d78b93c

addition of utils.rst

Update api.rst

d1615a6

added core docs

Update api.rst

b3d7966

Update figures.rst

0f2d662

added figures.rst correct

Update api.rst

b608080

added visualization modules

Update figures.rst

8aa9ddc

Update trajectories.py

18b4dc2

Update trajectories.rst

4ca5e6c

in prgrs

Update highlighting.rst

127233d

in prgrs

Update highlighting.rst

2997680

added

Update highlighting.py

18468f2

small docs fix

Update pharmacophore.rst

e66213a

added numpy doc for class

Update pharmacophore.py

a58299c

added numpy doc for class

Update pharmacophore.py

5109d73

change location

Update pharmacophore.py

d8c022c

fix

Update pharmacophore.py

119e15c

typo fix

Update pharmacophore.py

774043c

typo fix

Update pharmacophore.py

e6b749e

fix

Update pharmacophore.rst

27b7ba8

added pharmacophore.rst

Update barcodes.py

ad66803

remove specific PLIP mention

Create barcodes.rst

e5a2ce2

added barcodes.rst

Update api.rst

020e7c3

added visulaization rsts

Create visualization.rst

d719127

created visualization.rst

Update api.rst

54e78f5

added visualization

Update visualization.py

b7f0964

fix for parameters

Update test_pharmacophore.py

eb7db78

fix with the typo adjusting

Update CHANGELOG.md

1eb170e

talagayev merged commit c3773e2 into wolberlab:openmmdl-1.1.0 May 22, 2025

talagayev deleted the file_renaming_documentation branch May 22, 2025 10:21

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File renaming documentation#149

File renaming documentation#149
talagayev merged 247 commits intowolberlab:openmmdl-1.1.0from
talagayev:file_renaming_documentation

talagayev commented May 17, 2025

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talagayev commented May 17, 2025

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