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Rules

Minimum bond length

The method .absorb_overclose (from _overclose.py) has a default length of 0.8.

The atom to be absorbed is determined by the line

sort_indices = lambda i: self._get_atom_valence(self.rwmol.GetAtomWithIdx(i)) + 10 * commonality[i]

where the ad-hoc 10x-weighted penalty commonality is the number of times the atom violates bond lengths.

NB. This happens before the method call has_issues.

Rings

The method ._fix_aromatic_rings (from (_ring.py)[molecular_rectifier/_ring.py]) does a bunch of checks, if issues are present. If the ring is a spiro ring, or a carbocyclic ring without 6 or 18 rings, the ring is reduced. With a special case of 5-atom rings (_fix_penta_aromatic) wherein a carbon is made into a nitrogen (ie. a pyrrole).

The method .fix_rings (from _ring.py) is called regardlessly of issues and enforces several rules that prevent unusual structures, not all illegal:

  • The method ._prevent_bonded_to_bridgeheads prevents a carbon forming 3-aromatic-bond and a bond to something else.
  • The method .fix_aromatic_radicals fixes radicals due to aromaticity.
  • The method ._prevent_conjoined_ring prevents 3- and 4- membered rings fused to another ring.
  • The method ._prevent_weird_rings prevents benzo-cyclopropane or benzo-azetine kind of molecules (legal, but weird).

The method triage_rings (from _valence.py) fixes mixed bond issues

Allene

An allene is normal... but weird (_prevent_allene from _odd.py correct it).

Unspecified bonds

An unspecified bond (not racemic, but with unknown bond order) is corrected to a single bond (.ununspecified_bonds see _valence.py).

Radical protons

The method _adjust_Hs (from _valence.py) fixes radical protons.

Valence

This is a nightmare. The method .fix_issues (from _valence.py) iterates around the violating atoms and tries to find a workable protonation state.