> > I either start from SMILES and/or add atoms and bonds to an obmol object. > I can change the tetrahedral stereochemistry of the molecules with ease, > but I can't seem to do it for cis/trans isomers. > …
> I tried to change the configuration of the OBStereoFacade for the bond in > question, but it did nothing. > I tried rotating the atoms around the bond and minimizing the > molecule, but nothing. > If you start from a SMILES string, you can easily change the stereoisomers around a double bond by changing the ‘/‘ or ‘\’ characters as needed. If you’re modifying the underlying coordinates, you will need to make sure stereo is re-perceived from the 3D coordinates, as indicated in the manual: https://open-babel.readthedocs.io/en/latest/Stereochemistry/stereo.html#stereo-perception "If operations are performed on the molecule that require stereo is be reperceived, then OBMol::SetChiralityPerceived(false) should be called.” Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: https://hutchisonlab.org/
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