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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full.mol
Description: Binary data
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