Add protonation functions

[jonwzheng]

Motivation or Problem

This PR adds several helper functions related to protonation & ionization.

Description of Changes

New "big" functions:

• uncharge_mol(mol, method): Input = charged molecule (ion or zwitterion), output = uncharged form. Provides two algorithms for doing uncharging, default is to try both in case the other fails, starting with the rdkit algorithm.
• is_symmetric_to_substructure(mol, substructure): Check whether a mol is symmetric to a provided substructure, i.e. return "True" for comparing ethylene glycol to "OH" substructure

Helper functions:

• protonate_at_site(mol, site): Add a proton to a mol at a given idx and adjust formal charges
• deprotonate_at_site(mol, site): Remove a proton of a mol at a given idx and adjust formal charges
• is_implicit(mol) : Infer whether a molecule is an implicit or explicit mol object
• find_symmetry_classes(mol): provides a set of symmetry classes for atoms in a mol object, based on code by Greg Landrum.

Testing

I included pytest modules for uncharge_mol and is_symmetric_to_substructure

Other notes

The two uncharging methods have different behaviors regarding explicit hydrogens.

Chem.MolToSmiles(uncharge_mol(mol_from_smiles("[C:1]([C:2]([C:3]([C:4](=[O:5])[O-:6])([H:12])[H:13])([H:10])[H:11])([H:7])([H:8])[H:9]"), method="rdkit"))
>> '[CH3:1][CH2:2][CH2:3][C:4](=[O:5])[OH:6]'

vs.

Chem.MolToSmiles(uncharge_mol(mol_from_smiles("[C:1]([C:2]([C:3]([C:4](=[O:5])[O-:6])([H:12])[H:13])([H:10])[H:11])([H:7])([H:8])[H:9]"), method="nocharge"))
>> '[H][O:6][C:4]([C:3]([C:2]([C:1]([H:7])([H:8])[H:9])([H:10])[H:11])([H:12])[H:13])=[O:5]'

Is the desired behavior to re-number?

They still return the same smiles if you use mol_to_smiles though.

[codecov]

Codecov Report

Attention: Patch coverage is 75.78947% with 23 lines in your changes missing coverage. Please review.

Project coverage is 60.93%. Comparing base (a1db373) to head (7d20e94).

Files	Patch %	Lines
rdtools/mol.py	63.49%	12 Missing and 11 partials ⚠️

Additional details and impacted files

@@             Coverage Diff              @@
##           v1.0/dev      #99      +/-   ##
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+ Coverage     60.62%   60.93%   +0.30%     
============================================
  Files            67       67              
  Lines          4874     4969      +95     
  Branches       1199     1227      +28     
============================================
+ Hits           2955     3028      +73     
- Misses         1779     1790      +11     
- Partials        140      151      +11     

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[jonwzheng]

Based on the codecov, may need to add additional tests to properly test implicit_h logic

[xiaoruiDong]

@jonwzheng, thank you for this addition. I will work on reviewing this PR shortly.

[xiaoruiDong]

Just run into this repo https://github.com/durrantlab/dimorphite_dl about protonation. Maybe worth to incorporate in the future due to its light-weight. It may be also helpful for your work @jonwzheng (just FYI, no action needed).