Thanks a tonne Greg and Paul,
I didnt realize that removing stereochemistry was as simple as
removing the "@" characters.
So now with the replace function in python I can easily remove
sterochem information from the molecule.
smiles_corrected = smiles_broken.replace("@","")
Once I remove the stereochemistry , libcheck does the right thing and
gives me the right 3D coordinates.
Thanks for your help
Hari
On Thu, Sep 16, 2010 at 11:36 PM, Greg Landrum <greg.land...@gmail.com> wrote:
> Dear Hari,
>
> On Thu, Sep 16, 2010 at 8:44 PM, hari jayaram <hari...@gmail.com> 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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