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Molecular Rectifier

Given an RDKit molecule that does not sanitise, correct it until it does, regardless of the severity of the change.

Install

Requires RDKit.

pip3 install molecular-rectifier

Beyond RDKit Sanitisation

The command rdkit.Chem.SanitizeMol fixes minor issues with the molecule. However, more drastic changes such as valence correction and removal of weird bonds is not done, hence the molecular rectifier!

from molecular_rectifier import Rectifier

recto = Rectifier(wrong_mol)
recto.fix()
fixed_mol = recto.mol
# this works:
Chem.SanitizeMol(fixed_mol, sanitizeOps=Chem.SanitizeFlags.SANITIZE_ALL)

A lot of the corrections are based on arbitrary choices. These choices are manually encoded. I am sure that sooner or later some ML module will do this, but for now the Rectifier does the job.

The attribute valence_correction controls how the valence is fixed up —either by shifting the element ('element') or by adding a charge ('charge')

• protonating ring nitrogens if required
• forcing all atoms/bonds in a ring to be aromatic or not (unless part of another ring)
• Texas carbon -> Sulfur
• Hydrogen -> Fluoride shifted downwards
• Carbon in aromatic ring -> single bond ring
• kills bridging bonds with no atoms in the bridge within rings.
• correcting BondType.UNSPECIFIED
• preventing 3- and 4- membered rings fused to another ring
• preventing allene

For more see (rules note)[rules.md].

Rationale

This is used by Fragmenstein in the automatic merging mode (combine). Originally part of it, but moved apart because it may be useful for other uses, outside of Fragmenstein. Or a better module is found to fix the molecules.