Hi Ling, I can't reproduce this problem on windows using the most recent version of the RDKit. Which version of the RDKit are you using and how did you install it?
Please also share exactly what you see for an error message. -greg On Tue, Feb 21, 2023 at 7:03 AM Ling Chan <lingtrek...@gmail.com> wrote: > Dear colleagues, > > Don't know if this is a bug, or if my input molecule is not good. I > suspect that it is the former. > > If you run the following on the file "full.sdf", it will crash at the > MolToMolBlock line. > > for m1 in Chem.SDMolSupplier(inputsdf, removeHs=False): > m2=Chem.RemoveHs(m1) > print (Chem.MolToMolBlock(m2)) > > You can confirm that the problem is due to the stereo definition of the > double bond, since if you edit the bond line " 4 5 2 3" to " 4 5 2 0" it > will not crash. > > I tried to simplify the situation by boiling the molecule down to > "simple.sdf". Unfortunately it does not crash any more. > > Thanks. > > Ling > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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