Dear Mailinglist-members,
in rdkit, when doing a MCS search for molecules bearing a chirality
center, (how) is it possible to preserve the stereochemical information
when exporting the subgraph to a SMARTS string?
Consider the following three molecules:
>>> mol_ccw = Chem.MolFromSmiles('C1=C[C@H](Cl)CCC1')
>>> mol_cw = Chem.MolFromSmiles('C1=C[C@@H](Cl)CCC1')
>>> mol_lin = Chem.MolFromSmiles('C=C[C@H](Cl)CCC')
Doing a chirality-sensitive subgraph search leads to the somewhat
expected result:
>>> rdFMCS.FindMCS([mol_ccw, mol_cw], matchChiralTag=True).smartsString
'[#6](=[#6])-[#6]-[#6]-[#6]-[#6]-[#17]'
>>> rdFMCS.FindMCS([mol_ccw, mol_lin], matchChiralTag=True).smartsString
'[#6]=[#6]-[#6](-[#17])-[#6]-[#6]-[#6]'
>>> rdFMCS.FindMCS([mol_cw, mol_lin], matchChiralTag=True).smartsString
'[#6]-[#6]-[#6]-[#6]-[#6]'
The subgraph over mol_cw and mol_lin includes the stereocenter. But
unfortunately, the chirality information is not stored in the SMARTS
string, and using [#6]=[#6]-[#6](-[#17])-[#6]-[#6]-[#6] for a
chirality-sensitive substructure match leads to the expected result of
the pattern made from that SMARTS string matching all three molecules:
>>> patt = Chem.MolFromSmarts('[#6]=[#6]-[#6](-[#17])-[#6]-[#6]-[#6]')
>>> len({mol_cw, mol_ccw, mol_lin}.GetSubstructMatches(patt,
useChirality=True))
1
Manually inserting a lazy @H or a &*&H1 at the stereocenter leads -of
course- to the desired result:
>>> patt = Chem.MolFromSmarts('[#6]=[#6]-[#6@H](-[#17])-[#6]-[#6]-[#6]')
>>> len({mol_ccw, mol_lin}.GetSubstructMatches(patt, useChirality=True))
1
>>> len(mol_cw.GetSubstructMatches(patt, useChirality=True))
0
Now, when matching mol_ccw and mol_lin, how do I get the
stereochemistry-aware SMARTS string
[#6]=[#6]-[#6&*&H1](-[#17])-[#6]-[#6]-[#6] as the substructure in the
first place?
Thank you & kind regards,
Thilo
--
Dr. Thilo Bauer
Computer-Chemie-Centrum
Friedrich-Alexander-Universität
Nägelsbachstr. 25
91052 Erlangen
+49 170 9738141
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