def sequence_tunable(
mol,
OP_REMOVE_ISOTOPE=True, OP_NEUTRALISE_CHARGE=True,
OP_REMOVE_STEREO=False, OP_COMMUTE_INCHI=False,
OP_KEEP_BIGGEST=True, OP_ADD_HYDROGEN=True,
OP_KEKULIZE=True, OP_NEUTRALISE_CHARGE_LATE=True
):
"""Tunable sequence of filters for standardization.
Operations will made in the following order:
1 RDKit Cleanup -- always
2 RDKIT SanitizeMol -- always
3 Remove isotope -- optional (default: True)
4 Neutralise charges -- optional (default: True)
5 RDKit SanitizeMol -- if 4 or 5
6 Remove stereo -- optional (default: False)
7 Commute Inchi -- if 6 or optional (default: False)
8 Keep biggest -- optional (default: True)
9 RDKit SanitizeMol -- if any (6, 7, 8)
10 Add hydrogens -- optional (default: True)
11 Kekulize -- optional (default: True)
"""
F = Filters()
# Always perform the basics..
Cleanup(mol)
SanitizeMol(mol, sanitizeOps=SanitizeFlags.SANITIZE_ALL, catchErrors=False)
AssignStereochemistry(mol, cleanIt=True, force=True, flagPossibleStereoCenters=True) # Fix bug TD201904.01
#
if OP_REMOVE_ISOTOPE:
mol = F.remove_isotope(mol)
if OP_NEUTRALISE_CHARGE:
mol = F.neutralise_charge(mol)
if any([OP_REMOVE_ISOTOPE, OP_REMOVE_ISOTOPE]):
SanitizeMol(mol, sanitizeOps=SanitizeFlags.SANITIZE_ALL, catchErrors=False)
#
if OP_REMOVE_STEREO:
mol = F.remove_stereo(mol)
OP_COMMUTE_INCHI = True
if OP_COMMUTE_INCHI:
mol = F.commute_inchi(mol)
if OP_KEEP_BIGGEST:
mol = F.keep_biggest(mol)
if any([OP_REMOVE_STEREO, OP_COMMUTE_INCHI, OP_KEEP_BIGGEST]):
SanitizeMol(mol, sanitizeOps=SanitizeFlags.SANITIZE_ALL, catchErrors=False)
#
if OP_NEUTRALISE_CHARGE_LATE:
mol = F.neutralise_charge(mol)
SanitizeMol(mol, sanitizeOps=SanitizeFlags.SANITIZE_ALL, catchErrors=False)
#
if OP_ADD_HYDROGEN:
mol = F.add_hydrogen(mol, addCoords=True)
if OP_KEKULIZE:
mol = F.kekulize(mol)
#
return mol
def sequence_rr_legacy(mol):
"""Sequence of filters applied for the first version of RetroRules
"""
F = Filters()
Cleanup(mol)
SanitizeMol(mol, sanitizeOps=SanitizeFlags.SANITIZE_ALL, catchErrors=False)
AssignStereochemistry(mol, cleanIt=True, force=True, flagPossibleStereoCenters=True) # Fix bug TD201904.01
mol = F.remove_isotope(mol)
mol = F.neutralise_charge(mol)
SanitizeMol(mol, sanitizeOps=SanitizeFlags.SANITIZE_ALL, catchErrors=False)
mol = F.keep_biggest(mol)
mol = F.add_hydrogen(mol, addCoords=True)
mol = F.kekulize(mol)
return mol
def test_kekulize():
mol = Filters.kekulize(MolFromSmiles('c1ccccc1'))
assert MolToSmiles(mol) == 'C1=CC=CC=C1'