Hi all,
I'm trying to remove the MCS between two molecules (attached, 02.pdb and
12.pdb) using rdFMCS.FindMCS and AllChem.DeleteSubstructs using the following
code:
#########################################
from rdkit import Chem
from rdkit.Chem import AllChem, rdmolfiles, rdFMCS
#########################################
# load molecules:
lig02_pdb = open("02.pdb", 'r').read()
lig12_pdb = open("12.pdb", 'r').read()
lig02_mol = rdmolfiles.MolFromPDBBlock(lig02_pdb)
lig12_mol = rdmolfiles.MolFromPDBBlock(lig12_pdb)
# make list of molecules to map the MCS to:
perturbation_pair = []
perturbation_pair.append(lig02_mol)
perturbation_pair.append(lig12_mol)
MCS_object = rdFMCS.FindMCS(perturbation_pair, completeRingsOnly=True)
MCS_SMARTS = Chem.MolFromSmarts(MCS_object.smartsString)
# remove MCS from each molecule:
lig02_stripped = AllChem.DeleteSubstructs(lig02_mol, MCS_SMARTS)
lig12_stripped = AllChem.DeleteSubstructs(lig12_mol, MCS_SMARTS)
# print SMILES of each stripped molecule:
print("lig02: " + str(Chem.MolToSmiles(lig02_stripped)))
print("lig12: " + str(Chem.MolToSmiles(lig12_stripped)))
#print(Chem.MolToMolBlock(MCS_SMARTS),file=open('./MCS.mol','w+'))
#########################################
I attached the MCS.mol file as well. The lig12.pdb contains an extra Cl atom,
and lig12_stripped should thus contain a single Cl atom after deletion of the
MCS substructure (the MCS substructure is equal to lig02.pdb). When running the
script it actually contains 0 atoms.
I haven't been able to locate the source of the issue in the
AllChem.DeleteSubstructs documentation, does anyone have a suggestion?
I'm using a conda install of rdkit (2018.09.1.0).
Best,
Jenke
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12.pdb
Description: 12.pdb
02.pdb
Description: 02.pdb
MCS.pdb
Description: MCS.pdb
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