Mhh, your choices of test molecules sounds like going from poster child to 
archenemy of conformation generation algorithms :-)

-------------------------------------
|  Markus Sitzmann
|  markus.sitzm...@gmail.com

> On 7. Sep 2017, at 18:59, 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 
>> -- 
>> This message has been scanned for viruses and
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>> believed to be clean.
>> 
>> 
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