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
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