Hi There, I have calculated the Maximum Common Subgraph (MCS) between the attached mol2 molecules. The MCS seems to be successfully found but if I try to map it back to the original molecules I cannot found the common subgraph in one of the two molecule. My script is:
from rdkit import Chem
from rdkit.Chem import rdFMCS
from rdkit.Chem import AllChem
moli = Chem.MolFromMol2File('moli.mol2')
molj = Chem.MolFromMol2File('molj.mol2')
moli_noh = AllChem.RemoveHs(moli)
molj_noh = AllChem.RemoveHs(molj)
# MCS pattern calculation
mcs = rdFMCS.FindMCS([moli_noh, molj_noh],
timeout=20,
atomCompare=rdFMCS.AtomCompare.CompareAny,
bondCompare=rdFMCS.BondCompare.CompareAny,
matchValences=False,
ringMatchesRingOnly=True,
completeRingsOnly=False,
matchChiralTag=False)
mcs_mol = Chem.MolFromSmarts(mcs.smartsString)
print moli_noh.GetSubstructMatch(mcs_mol)
print molj_noh.GetSubstructMatch(mcs_mol)
This produces the output:
()
(0, 1, 6, 8, 9, 5, 11, 2)
Can someone help me please?
Thanks,
Gaetano
molecules.tar
Description: Unix tar archive
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