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
full.sdf
Description: application/vnd.openmolecules.sdf
simple.sdf
Description: application/vnd.openmolecules.sdf
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