Dear Hari,
On Thu, Sep 16, 2010 at 8:44 PM, hari jayaram <[email protected]> wrote:
> I am working with several ligands from a database stored in a SMILES
> format. I am using the SMILES string to get three dimensional
> coordinates (pdb format file) using a third-party program called
> libcheck.
>
> For some of these molecules the SMILES string sterochemistry in the
> database is entered in incorrectly such that the SMILES input to
> libcheck returns a mangled coordinate file with rings clashing with
> each other . Inputting SMILES string without the stereochemistry makes
> libcheck behave correctly.
>
> Is there a way to use rdkit to cleanup the stereochemistry in the SMILES
> string.
To be certain I understand: you would like to remove the
stereochemistry from the SMILES string?
One way to do this is to read in the SMILES then generate a new SMILES
without stereochemistry information:
[1]>>> from rdkit import Chem
[2]>>> m = Chem.MolFromSmiles('c...@h](F)Br')
[3]>>> Chem.MolToSmiles(m)
Out[3] 'FC(Cl)Br'
A potential problem with this is that it changes the atom ordering.
However, the simplest way to remove stereochemistry information from
SMILES doesn't use the RDKit at all, you just remove "@" characters
from the string:
[4]>>> smi = 'c...@h](F)Br'
[5]>>> smi.replace('@','')
Out[5] 'Cl[CH](F)Br'
Hope this helps,
-greg
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