Hi RDKitters,
I am having trouble with chirality conservation during fragmentation of
molecules. Is there a simple way of preserving chirality during splits on
chiral atoms? Am I missing a simple function? Andrew has brought this topic
has come up on the mailing list before, but so far there has not been a
simple answer...
Here is an example where chirality is not preserved:
-------------------
> import rdkit
> rdkit.__version__
Out[2]: '2016.03.1'
> from rdkit import Chem
> mol = Chem.MolFromSmiles("F[C@](Cl)(Br)I")
> Chem.MolToSmiles(mol,isomericSmiles=True)
Out[5]: 'F[C@](Cl)(Br)I'
> emol = Chem.EditableMol(mol)
> emol.RemoveBond(1,0)
> emol.AddAtom(Chem.Atom(0))
Out[8]: 5
> emol.AddAtom(Chem.Atom(0))
Out[9]: 6
> emol.AddBond(0,5,Chem.BondType.SINGLE)
Out[10]: 4
> emol.AddBond(1,6,Chem.BondType.SINGLE)
Out[11]: 5
> new_mol = emol.GetMol()
> Chem.MolToSmiles(new_mol,isomericSmiles=True)
Out[13]: '[*]F.[*][C@@](Cl)(Br)I'
---------------------
Best regards,
Christian
*Dr. Christian Kramer*
Computer-Aided Drug Design (CADD) Scientist
F. Hoffmann-La Roche Ltd
Pharma Research and Early Development
Bldg. 092/2.56
CH-4070 Basel.
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