Look at the docs for OBStereoFacade and related classes. Stereo is stored in a Config object with refs to the four IDs of the atoms connected to the atoms of the double bond.
On 19 Nov 2016 11:35 p.m., "Sam Tonddast-Navaei" <s.tondd...@gmail.com> wrote: > Hello all, > > I am trying to break a molecule into two fragments using Pybel yet > keeping the cis/trans stereochemisty information at the cleavage point when > I substitute it by a dummy atom. Currently I am trying to copy the bond > property (IsUp or IsDown) and assign it to the new bonds (bonds assign tot > he dummy atoms). However I figured out that both functions are returning > False values. > > I did a loop over all bonds and printed the following: > > for temp_bond in openbabel.OBMolBondIter(mol2.OBMol): >> >> print temp_bond.GetIdx(), temp_bond.GetBO(), temp_bond.IsDown(), >> temp_bond.IsUp(), temp_bond.IsCisOrTrans() > > > SMILES: OCCCC#CC#C/C=C/C(=O)OC >> 0 1 False False False >> 1 1 False False False >> 2 1 False False False >> 3 1 False False False >> 4 3 False False False >> 5 1 False False False >> 6 3 False False False >> 7 1 False False False >> 8 2 False False False >> 9 1 False False False >> 10 2 False False False >> 11 1 False False False >> 12 1 False False False > > > Can someone help me what I am missing here and whether there is a smarter > way of doing this? > > Thanks for your time, > Sam > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > >
------------------------------------------------------------------------------
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
