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:

• Initial running version for torsion Distribution plotting
• Initial Compare Torsion Distributions
• Test Code on more complex systems
• 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
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• In the file src/openfe_analysis/utils/__init__.py:

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

Line 2:80: E501 line too long (101 > 79 characters)
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• 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)
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Line 50:110: E703 statement ends with a semicolon
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[codecov]

Codecov Report

All modified lines are covered by tests ✅

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

Additional details and impacted files

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

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[richardjgowers]

How is this different from the definition in Lipinski?

[richardjgowers]

We're going to ignore hydrogen torsions right? Does slicing the zeroth element here potentially miss a heavy atom torsion?

[richardjgowers]

Can we put plotting into openfe main repo please?

[RiesBen]

This could actually be a dependency, it's vendored code:
https://github.com/c-feldmann/lassohighlight/tree/master

[richardjgowers]

This won't work for our trajectories right?

[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 🤩

[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.