Enhance trc class' functionality

[pultar]

Description

Implement mdtraj functions to calculate angles and dihedrals in trajectories. Tests with dummy data are provided. Results can be requested in degrees (default) and radians via a flag.

Todos

• [x] @LaurianeJD please double check if it produces the expected result for your system and if the tests are reasonable (distances, angles, dihedrals)

Status

• [x] Waiting for @LaurianeJD

[codecov[bot]]

Codecov Report

Merging #296 (b011669) into main (7b717d5) will increase coverage by 0.06%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #296      +/-   ##
==========================================
+ Coverage   54.54%   54.60%   +0.06%     
==========================================
  Files          93       93              
  Lines       14358    14372      +14     
==========================================
+ Hits         7831     7848      +17     
+ Misses       6527     6524       -3     

Flag	Coverage Δ
unittests	54.60% <100.00%> (+0.06%)	:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
pygromos/files/trajectory/trc.py	89.96% <100.00%> (+1.60%)	:arrow_up:

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[pultar]

I will need to double check @LaurianeJD It looks like an edge case but we should also account for these cases.

[pultar]

I will need to double check @LaurianeJD It looks like an edge case but we should also account for these cases.

Seems like a problem with numerical precision. We double checked with another system (menthol, included in test files) and re-calculated dihedrals with Chemcraft and Pymol. Values seem to be consistently stable but slightly off.

I believe it's close enough.