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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