Re: [Rdkit-discuss] newbie help cleaning up sterochemistry in SMILES string

[Greg L. <gre...@gm...>]

Dear Hari,

On Thu, Sep 16, 2010 at 8:44 PM, hari jayaram <ha...@gm...> 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('Cl[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 = 'Cl[C@H](F)Br'

[5]>>> smi.replace('@','')
Out[5] 'Cl[CH](F)Br'

Hope this helps,
-greg