Hi there, it's me again... :-)
As you asked me to post things looking strange to me......here we go:
When I read in a Tripeptid-Sequence (Lys-Leu-Gln) with isomeric Smiles
and do any Reaction,
suddenly Some alpha-Carbons flip their Chirality. Please have a look at
the code:
>>> from Chem import AllChem as Chem
>>>
InputMol=Chem.MolFromSmiles('nccc...@h](N)C(=O)N[C@@H](CC(C)C)C(n...@h](C(N)=O)CCC(N)=O)=O')
>>> repl=Chem.ReactionFromSmarts('[C:1]=[O:2]>>[C:1]=[S:2]')
>>> out=repl.RunReactants((InputMol,))
>>> print Chem.MolToSmiles(out[0][0], isomericSmiles=True)
NCCCC[C@@H](N)C(=S)n...@h](CC(C)C)C(=O)N[C@@H](C(N)=O)CCC(N)=O
This happens for any reaction i tried so far. I also did the Sanitize()
thing
when reading in the Educt and before writing the Product, but there's
no change.
Doing Chem.AssignAtomChiralcodes() before the reaction does not preserve
the
Chirality
Cheers Markus
