Hi JP, On Wed, Jul 6, 2011 at 1:32 PM, JP <[email protected]> wrote: > Can anyone explain what this means: > Writing results to ./top1000.sdf > [12:05:46] > **** > Invariant Violation > Violation occurred on line 294 in file > /share/apps/RDKit_2011_03_2/Code/GraphMol/FileParsers/MolFileStereochem.cpp > Failed Expression: pick >= 0 > ****
Wow that is certainly an error I never expected to see. From the code, I guess the molecule has a stereocenter that is surrounded by other stereocenters and something extremely unfortunate is happening with the way decisions are being made about which bonds to wedge. As Eddie requested in an earlier message, it would be helpful to have the input that produced the error so that it can be added to the test cases (and so that I can be sure the problem is fixed once I figure out how to). -greg > Traceback (most recent call last): > File "./best_result.py", line 168, in <module> > main() > File "./best_result.py", line 163, in main > w.write(result[2]) > RuntimeError: Invariant Violation > The python code... > w = AllChem.SDWriter(output_file) > for result in res: > # the molecule is in the second position > w.write(result[2]) > w.close() > Where result[2] is an RDKit molecule... > Thanks > JP > ------------------------------------------------------------------------------ > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
