from rdkit import Chem, RDLogger
from rdchiral.chiral import copy_chirality
from rdkit.Chem.AllChem import AssignStereochemistry
RDLogger.DisableLog('rdApp.*')
def canonicalize2(smiles, isomeric=False, canonical=True, kekulize=False):
# When canonicalizing a SMILES string, we typically want to
# run Chem.RemoveHs(mol), but this will try to kekulize the mol
# which is not required for canonical SMILES. Instead, we make a
# copy of the mol retaining only the information we desire (not explicit Hs).
# Then, we sanitize the mol without kekulization. copy_atom and copy_edit_mol
# are used to create this clean copy of the mol.
def copy_atom(atom):
new_atom = Chem.Atom(atom.GetSymbol())
new_atom.SetFormalCharge(atom.GetFormalCharge())
# Preserve atom mapping number
atom_map_num = atom.GetAtomMapNum()
if atom_map_num:
new_atom.SetAtomMapNum(atom_map_num)
if atom.GetIsAromatic() and atom.GetNoImplicit():
new_atom.SetNumExplicitHs(atom.GetNumExplicitHs())
return new_atom
def copy_edit_mol(mol):
new_mol = Chem.RWMol(Chem.MolFromSmiles(''))
atom_mapping = {}
for atom in mol.GetAtoms():
new_atom = copy_atom(atom)
new_idx = new_mol.AddAtom(new_atom)
atom_mapping[atom.GetIdx()] = new_idx
for bond in mol.GetBonds():
a1 = atom_mapping[bond.GetBeginAtom().GetIdx()]
a2 = atom_mapping[bond.GetEndAtom().GetIdx()]
bt = bond.GetBondType()
new_mol.AddBond(a1, a2, bt)
new_bond = new_mol.GetBondBetweenAtoms(a1, a2)
new_bond.SetBondDir(bond.GetBondDir())
new_bond.SetStereo(bond.GetStereo())
for new_atom in new_mol.GetAtoms():
atom = mol.GetAtomWithIdx(new_atom.GetIdx())
copy_chirality(atom, new_atom)
for atom in mol.GetAtoms():
new_atom = new_mol.GetAtomWithIdx(atom_mapping[atom.GetIdx()])
copy_chirality(atom, new_atom)
return new_mol
smiles = smiles.replace(" ", "")
tmp = Chem.MolFromSmiles(smiles, sanitize=False)
tmp.UpdatePropertyCache()
new_mol = copy_edit_mol(tmp)
if not kekulize:
Chem.SanitizeMol(new_mol, sanitizeOps=Chem.SanitizeFlags.SANITIZE_SETAROMATICITY |
Chem.SanitizeFlags.SANITIZE_PROPERTIES |
Chem.SanitizeFlags.SANITIZE_ADJUSTHS, catchErrors=True)
else:
Chem.SanitizeMol(new_mol, sanitizeOps=Chem.SanitizeFlags.SANITIZE_KEKULIZE |
Chem.SanitizeFlags.SANITIZE_PROPERTIES |
Chem.SanitizeFlags.SANITIZE_ADJUSTHS, catchErrors=True)
AssignStereochemistry(new_mol, cleanIt=False, force=True, flagPossibleStereoCenters=True)
new_smiles = Chem.MolToSmiles(new_mol, isomericSmiles=isomeric, canonical=canonical)
return new_smiles
def canonicalize_molecule_smiles(smiles, return_none_for_error=True, skip_mol=False, sort_things=True, isomeric=True, kekulization=True, allow_empty_part=False, keep_atom_map=True):
things = smiles.split('.')
if skip_mol:
new_things = things
else:
new_things = []
for thing in things:
try:
if thing == '' and not allow_empty_part:
raise ValueError('SMILES contains empty part.')
mol = Chem.MolFromSmiles(thing)
assert mol is not None
if not keep_atom_map:
for atom in mol.GetAtoms():
atom.SetAtomMapNum(0)
thing_smiles = Chem.MolToSmiles(mol, kekuleSmiles=False, isomericSmiles=isomeric)
thing_smiles = Chem.MolFromSmiles(thing_smiles)
thing_smiles = Chem.MolToSmiles(thing_smiles, kekuleSmiles=False, isomericSmiles=isomeric)
thing_smiles = Chem.MolFromSmiles(thing_smiles)
thing_smiles = Chem.MolToSmiles(thing_smiles, kekuleSmiles=False, isomericSmiles=isomeric)
assert thing_smiles is not None
can_in = thing_smiles
can_out = canonicalize2(thing_smiles, isomeric=isomeric)
assert can_out is not None, can_in
thing_smiles = can_out
if kekulization:
thing_smiles = keku_mid = Chem.MolFromSmiles(thing_smiles)
assert keku_mid is not None, 'Before can: %s\nAfter can: %s' % (can_in, can_out)
thing_smiles = Chem.MolToSmiles(thing_smiles, kekuleSmiles=True, isomericSmiles=isomeric)
except KeyboardInterrupt:
raise
except:
if return_none_for_error:
return None
else:
raise
new_things.append(thing_smiles)
if sort_things:
new_things = sorted(new_things)
new_things = '.'.join(new_things)
return new_things
