> I had to generate a 3D molecule from SMILES to xyz. But i have noticed that,
> 'sometimes', if i give a SMILES input for a cyclic molecule, ('c1ccccc1' for
> benzene) and convert it into xyz (3d) coordinates and take the data to
> visualize in Avogadro, it is not showing a cyclic molecule at all (showing an
> acyclic hexatriene type of thing). I, again, want to say the word "sometimes",
This is a known bug that's much less likely to occur in OB-3.0 - which has a
much larger set of ring fragments. When generating 3D coordinates, if a ring
isn't matched, it falls back to the atom-by-atom builder. If you use the
'better' or 'best' levels of 3D coordinate generation, the force field will
clean this up before writing the XYZ file.
But again, if you have examples, that's extremely helpful. Saying 'sometimes
this works' is extremely frustrating from a debugging perspective because it
gives us nothing to test, debug and improve.
If you have a specific example with OB-3.0, please submit the bug report and
example SMILES to https://github.com/openbabel/openbabel/issues
Thanks and best regards,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/
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