Dear Greg, I have generated 265 isomers of zadirachtin, a natural product. When I tried to use RDKit for the creation of 2D depictions, one of the structures failed to be read. The corresponding SD file with the only problematic structure is attached.I generated a depiction by myself that is also attached (as a postscript file).
The problem arises by running the following script:
from rdkit import Chem
suppl = Chem.SDMolSupplier("mol226.sdf")
imol = 0
for mol in suppl:
if mol is None: continue
imol += 1
print "Count:", imol
that results in:
[22:30:46] Unexpected error hit on line 114
[22:30:46] ERROR: moving to the begining of the next molecule
Count: 0
The 264 other molecules in my isomer collection are OK.
Any idea about the origin of this problem?
Best regards,
Jean-Marc Nuzillard
mol226.sdf
Description: StarMath document
mol226.ps
Description: PostScript document
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