On 18/09/10 05:19, Greg Landrum wrote:
> 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.
>
The (additional) useful thing libcheck can do is generate esd geometry
restraints for crystallographic refinement (something like the "spring
constants", e.g. 0.02A for a C-C single bonds, 3 degrees for C-C-C
angles etc. (atom type dependent, of course) - also planes and
torsions). I wonder how hard that would be to get
similar/compatible/corresponding numbers by digging into RDKit's UFF
(presumably that would be the way to do it). Any thoughts/advice?
Thanks,
Paul.
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