linear torsion angle fix

[davidfarinajr]

I added a method within get_torsions that checks for linear (or near-linear within a tolerance) angles in a torsion. If an angle is near 180 degrees, we look farther down the molecule for an atom to define the torsion. I also added angles, description, and center_atoms attribute to torsion class.

[davidfarinajr]

It's helpful for molecules like FCC#CC. Previously, the get_torsions method would return 2 torsions. With this PR, 1 torsion is returned where the terminal carbons are the pivot atoms.

[codecov[bot]]

Codecov Report

Merging #69 into master will increase coverage by 0.28%. The diff coverage is 90.78%.

@@            Coverage Diff             @@
##           master      #69      +/-   ##
==========================================
+ Coverage   63.78%   64.07%   +0.28%     
==========================================
  Files          27       27              
  Lines        4667     4721      +54     
==========================================
+ Hits         2977     3025      +48     
- Misses       1690     1696       +6

Impacted Files	Coverage Δ
autotst/species_test.py	98.73% <100%> (+0.06%)	:arrow_up:
autotst/geometry.py	89.13% <100%> (+0.49%)	:arrow_up:
autotst/species.py	72.5% <89.39%> (+1.25%)	:arrow_up:

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[nateharms]

Also, testing failed and coverage is down, these will need to be addressed before we can merge this in.

[davidfarinajr]

This is rotor scan for SMILES FCC#CCF with C1 and C2 as the pivot atoms (F1-C1-C2-F2). Currently, AutoTST generates 2 torsions for this molecule: (F1-C1-C3-C4) and (F2-C2-C4-C3). However, both of these scans failed because C1-C3-C4 and C2-C4-C3 are linear. The goal of this PR is to identify rotors where the axis of rotation has more than 2 atoms (pivot atoms are not directly connected in graph).

The center_atoms are the atoms in between the pivot atoms (in this case C3 and C4).

[davidfarinajr]

@nateharms, I added center_atoms test. I also realized we need to consider the center_atoms when getting the mask, so I modified the get_mask method and refactored the get_torsions method a bit. Can you take a look at the new changes?

[nateharms]

Will do, I'll wait a sec for the checks to pass, then I'll review and merge if it's all good.