Hi,
I am new to rdkit, sorry if I am missing something obvious.
I am trying to pair matching substructures for a list of molecules. The plan is
to:1) do MCS on a list of molecules2) use GetSubstructMatch to get pairing for
each molecule and MCS result
However, GetSubstructMatch returns empty tuple, despite an obvious match.
Here is a toy example:
from rdkit import Chemfrom rdkit.Chem import MCSfrom rdkit.Chem.Draw import
IPythonConsole mol1 = Chem.MolFromSmiles("Cc1ccccc1")mol2 = Chem.MolFromSmiles(
"CCc1ccccc1" )mol3 = Chem.MolFromSmiles( "Oc1ccccc1" )mol4 =
Chem.MolFromSmiles( "COc1ccccc1" )
res = MCS.FindMCS([mol1,mol2,mol3,mol4])# MCS is a benzenemy_mcs =
Chem.MolFromSmiles(res.smarts)# turn MCSResult into Mol object
benzene = Chem.MolFromSmiles("c1ccccc1")
# build benzene manually
Chem.Draw.MolsToGridImage([mol1,mol2,mol3,mol4,my_mcs,benzene]).show()
# All molecules share a benzene ring. Mol #5 is an actual MCS result. Mol #6 is
a benzene built manually. Mol #5 and #6 seem identical
mol1.HasSubstructMatch(my_mcs)mol2.HasSubstructMatch(my_mcs)
mol3.HasSubstructMatch(my_mcs)
mol4.HasSubstructMatch(my_mcs)
# Returns false
mol1.HasSubstructMatch(benzene)
mol2.HasSubstructMatch(benzene)
mol3.HasSubstructMatch(benzene)
mol4.HasSubstructMatch(benzene)
# returns true
my_mcs.HasSubstructMatch(benzene)# truebenzene.HasSubstructMatch(my_mcs)# false
What am I missing?
Thanks!Ondrej.
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