When I try obgen on
OCC(=O)[C@@]1(O)CC[C@@H]2[C@]1(C)C[C@H](O)[C@]1([C@H]2CCC2=CC(=O)CC[C@]12C)F
I get a message
WARNING: damped steplength 16.7257 to 2.25803
on stdout rather than stderr (so dumped into the SDF file making it invalid)
If I edit the SDF file to remove that message, and run o
I usually run 3D generation as follows:
obabel -:OCC(=O)[C@@]1(O)CC[C@@H]2[C@]1(C)C[C@H](O)[C@]1([C@H
]2CCC2=CC(=O)CC[C@]12C)F --gen3d -osdf
==
*** Open Babel Warning in OpenBabel::OBBuilder::CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule ()
> This is discussed in the OB paper. 3D structure generation fails stereo in
> many cases of bridged rings, as we use ring templates of a particular stereo.
The only good solution to this is distance geometry like RDKit.
-Geoff
