On Sat, Sep 18, 2010 at 12:05 AM, Geoffrey Hutchison
<ge...@geoffhutchison.net> wrote:
>> 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.
>
> This doesn't make chemical sense, though. If libcheck is operating on a
> SMILES without stereochemistry, there's no way it can always give "the right
> 3D" coordinates. If you have "N" stereo centers, the chance of a correct 3D
> structure will be (0.5)^N.
>
> I'd suggest using a different tool. For example, the upcoming Open Babel 2.3
> will handle 3D coordinate generation while ensuring stereochemistry.
>
> But you don't have to use OB -- I'm just saying that your 3D coordinates
> won't respect stereo with your approach.
Geoff's point is a good one: if you remove the stereochemistry
information from the SMILES and then generate 3d coordinates, your
odds of getting a correct 3d structure are not good. I had assumed
that you had bad stereochemistry info in the SMILES that you wanted to
get rid of. If the stereochem is correct, then it might be a good idea
to try Geoff's idea and use OB 2.3 when it's released or to use the
RDKit's 3D coordinate generation (also respects stereochemistry),
write the files as SDF, and then use the current version of OB to
translate to a PDB if you need things in that format.
Best,
-greg
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