Too much symmetry for conformational comparison?
Many or most conformation generators will test new conformations for a
match with previously generated conformations, and will bail out if they
can't exhaust all possibilities.
(I don't know if this is the case RDKit facilities.)
-P.
On Thu, Sep 7, 2017 at 12:59 PM, Jason Biggs <jasondbi...@gmail.com> wrote:
> I've never had success using the ETKDG or KDG methods for fullerenes,
> when trying on C60 it goes for a long time and returns -1. The ETDG method
> works on C60, but fails on your C60H60.
>
> One thing you could try is to embed the hydrogen-suppressed structure,
> then add the hydrogens
>
> RDKit::DGeomHelpers::EmbedParameters params(RDKit::DGeomHelpers::ETDG);
>
> RDKit::DGeomHelpers::EmbedMolecule(*mol, params);
>
> bool explicitOnly = false;
>
> bool addCoords = true;
>
> RDKit::MolOps::addHs(*mol, explicitOnly, addCoords);
>
> seems to work.
>
>
>
> Jason Biggs
>
>
> On Thu, Sep 7, 2017 at 10:49 AM, Dmitry Redkin <red...@acdlabs.ru> wrote:
>
>> Hello all!
>> I've just started to use RDKit, and now I'm trying to generate some 3D
>> conformation for a molecule. ETKDG successfully optimized cyclohexane, so
>> I've tried some more complex example.
>> It was this fullerene-like structure (with all the single bonds and every
>> C
>> atom having H atom attached). I'm attaching it to this email.
>>
>> But whatever I've tried to do with embedding parameters, RDKit whether
>> stalls for several minutes trying to complete operation or just exits with
>> all zero coordinates.
>>
>> Is there any way to generate conformations for this structure? Maybe I did
>> something wrong or there is some flag that can be set to get some result
>> (any result, not necessarily the best one) in a reasonable time?
>>
>> My code is pretty simple, you can see it below.
>>
>>
>> RWMol *mol = MolFileToMol("d:\\temp\\exe32\\full.mol", true, false,
>> false);
>>
>> MolOps::addHs(*mol);
>> DGeomHelpers::EmbedParameters p(DGeomHelpers::ETKDG);
>> p.maxIterations = 100; // if I left it -1, I could not wait long enough
>> for
>> EmbedMolecule to exit.
>> p.useRandomCoords = true;
>> int confid = DGeomHelpers::EmbedMolecule(*((ROMol*)mol), p);
>> MolToMolFile(*((ROMol*)mol), "d:\\temp\\exe32\\full1.mol", true, confid);
>> free(mol);
>>
>>
>> ----------------------------
>> Dmitry Redkin, ACD Inc.
>> red...@acdlabs.ru
>> --
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>>
>>
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>
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