[Rdkit-discuss] ETKDG conformation generation algorithm and fullerene-like structures.

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

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 119, Issue 6

TJ, Your suggestion solved my problem. Thanks! I need to pay closer attention to the SMARTS documentation! Regards, Jim Metz -Original Message- From: rdkit-discuss-request To: rdkit-discuss

Re: [Rdkit-discuss] ETKDG conformation generation algorithm and fullerene-like structures.

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

Re: [Rdkit-discuss] ETKDG conformation generation algorithm and fullerene-like structures.

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

Re: [Rdkit-discuss] ETKDG conformation generation algorithm and fullerene-like structures.

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 wrote: > > I've