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
--------------------------------------------------------------
University of Edinburgh
David Brewster road
Edinburgh, EH9 3FJ
United Kingdom
-------------------------------------------------------------

The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336.

Attachment: 12.pdb
Description: 12.pdb

Attachment: 02.pdb
Description: 02.pdb

Attachment: MCS.pdb
Description: MCS.pdb

_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to