Torsion Distribution plotting/analysis

[RiesBen]

This PR contains the Torsion Distribution plotting/analysis for for openFE trajectories.

Features:

• read-out alchemical states from the trajectories
• find all rotatable bonds
• calculate trajectory torsions
• plot torsion distribution

Todo:

• [x] Initial running version for torsion Distribution plotting
• [ ] Initial Compare Torsion Distributions
• [x] Test Code on more complex systems
• [x] Implement Tests

Example plots:

[pep8speaks]

Hello @RiesBen! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file src/openfe_analysis/torsions_distributions.py:

Line 20:1: E302 expected 2 blank lines, found 1 Line 20:47: E225 missing whitespace around operator Line 32:42: E225 missing whitespace around operator Line 46:80: E501 line too long (87 > 79 characters) Line 56:80: E501 line too long (92 > 79 characters) Line 59:5: E731 do not assign a lambda expression, use a def Line 59:80: E501 line too long (84 > 79 characters) Line 67:80: E501 line too long (93 > 79 characters) Line 80:80: E501 line too long (116 > 79 characters) Line 81:80: E501 line too long (116 > 79 characters) Line 86:1: W391 blank line at end of file

• In the file src/openfe_analysis/utils/__init__.py:

Line 2:1: W391 blank line at end of file

• In the file src/openfe_analysis/utils/lassoo_highlights.py:

Line 2:80: E501 line too long (101 > 79 characters) Line 7:1: E265 block comment should start with '# ' Line 12:1: E402 module level import not at top of file Line 13:1: E402 module level import not at top of file Line 14:1: E402 module level import not at top of file Line 15:1: E402 module level import not at top of file Line 16:1: E402 module level import not at top of file Line 17:1: E402 module level import not at top of file Line 18:1: E402 module level import not at top of file Line 19:1: E402 module level import not at top of file Line 20:1: E402 module level import not at top of file Line 24:80: E501 line too long (87 > 79 characters) Line 35:80: E501 line too long (115 > 79 characters) Line 67:80: E501 line too long (117 > 79 characters) Line 99:80: E501 line too long (94 > 79 characters) Line 105:13: E303 too many blank lines (2) Line 108:80: E501 line too long (86 > 79 characters) Line 123:80: E501 line too long (88 > 79 characters) Line 129:80: E501 line too long (102 > 79 characters) Line 139:80: E501 line too long (94 > 79 characters) Line 141:80: E501 line too long (85 > 79 characters) Line 143:80: E501 line too long (82 > 79 characters) Line 148:80: E501 line too long (81 > 79 characters) Line 151:80: E501 line too long (104 > 79 characters) Line 153:80: E501 line too long (94 > 79 characters) Line 161:80: E501 line too long (93 > 79 characters) Line 167:80: E501 line too long (105 > 79 characters) Line 170:80: E501 line too long (107 > 79 characters) Line 176:80: E501 line too long (82 > 79 characters) Line 198:80: E501 line too long (85 > 79 characters) Line 221:80: E501 line too long (83 > 79 characters) Line 257:80: E501 line too long (104 > 79 characters) Line 258:80: E501 line too long (105 > 79 characters) Line 259:80: E501 line too long (80 > 79 characters) Line 260:80: E501 line too long (80 > 79 characters) Line 265:80: E501 line too long (120 > 79 characters) Line 275:80: E501 line too long (93 > 79 characters) Line 281:80: E501 line too long (114 > 79 characters) Line 287:80: E501 line too long (107 > 79 characters) Line 293:80: E501 line too long (91 > 79 characters) Line 333:54: W292 no newline at end of file

• In the file src/openfe_analysis/visualization.py:

Line 3:13: E222 multiple spaces after operator Line 4:19: E127 continuation line over-indented for visual indent Line 21:80: E501 line too long (89 > 79 characters) Line 50:80: E501 line too long (110 > 79 characters) Line 50:110: E703 statement ends with a semicolon Line 67:80: E501 line too long (94 > 79 characters)

[codecov[bot]]

Codecov Report

All modified lines are covered by tests :white_check_mark:

:exclamation: No coverage uploaded for pull request base (main@2a5900e). Click here to learn what that means.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #20 +/- ## ======================================= Coverage ? 47.01% ======================================= Files ? 8 Lines ? 368 Branches ? 0 ======================================= Hits ? 173 Misses ? 195 Partials ? 0 ```

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[RiesBen]

Original Task description #11 :

Type System sampling check Question Is phase space well sampled? How Minima sampled ~60% Tool MDA + rdkit Note Ideally what you should be looking at here is a combination of the solvent, vacuum, and complex differences and the variation in dihedral sampling across lambda states. I.e. is there a major change happening in my transformation that isn't being sampled across all states -- @IAlibay

[mikemhenry]

Those plots look really nice :star_struck:

[RiesBen]

@RiesBen Remove the hydrogens.

[RiesBen]

@jameseastwood, @hannahbaumann and @IAlibay we should reassign this issue. The implementation should be stable, it is mainly about adressing the comments and merging it.