def set_atom_feat(a: Atom, key: str, val: int):
if key == 'atomic_num':
a.SetAtomicNum(val)
elif key == 'formal_charge':
a.SetFormalCharge(val)
elif key == 'chiral_tag':
a_chiral = rdchem.ChiralType.values[val]
a.SetChiralTag(a_chiral)
elif key == 'num_explicit_hs':
a.SetNumExplicitHs(val)
elif key == 'is_aromatic':
a.SetIsAromatic(bool(val))
return a
def downgrade_ring(self, atom: Chem.Atom):
## very crappy way of doing this
log.debug(f'downgrading whole ring!')
atom.SetIsAromatic(False)
ringinfo = self._get_ring_info(mode='atom')
get_atomrings = lambda ai: [ring for ring in ringinfo if ai in ring]
atomrings = get_atomrings(atom.GetIdx())
for atomring in atomrings:
rnieghs = self._get_ring_neighbors(atomring)
for n1, n2 in rnieghs:
self.mol.GetAtomWithIdx(n1).SetIsAromatic(False)
self.mol.GetAtomWithIdx(n2).SetIsAromatic(False)
self.mol.GetBondBetweenAtoms(n1, n2).SetBondType(
Chem.BondType.SINGLE)
for atomring in atomrings:
rnieghs = self._get_ring_neighbors(atomring)
for n1, n2 in rnieghs:
if self._get_valence_difference(self.mol.GetAtomWithIdx(n1)) <= -2 and \
self._get_valence_difference(self.mol.GetAtomWithIdx(n2)) <= -2:
self.mol.GetBondBetweenAtoms(n1, n2).SetBondType(
Chem.BondType.DOUBLE)