Hi Andrew, On Mon, Apr 30, 2012 at 10:32 PM, Andrew Dalke <[email protected]> wrote: > >>>> from rdkit import Chem >>>> writer = Chem.SDWriter("/dev/stdout") >>>> for mol in Chem.ForwardSDMolSupplier("CHEMBL1269997.sdf"): > ... writer.write(mol) > ... > [22:11:05] > > **** > Invariant Violation > > Violation occurred on line 388 in file > /tmp/homebrew-rdkit-HEAD-Ebdo/Code/GraphMol/FileParsers/MolFileStereochem.cpp > Failed Expression: pick >= 0 > **** > > Traceback (most recent call last): > File "<stdin>", line 2, in <module> > RuntimeError: Invariant Violation [snip] > This error was previously reported in the thread JP started, titled > "Invariant violation...", dated July 6, 2011. Greg replied: > >> 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). > > but I see no posting of a failing structure. I hope the attached structure > helps resolve this problem.
I fixed this today and checked in the changes. Here's the bug report: https://sourceforge.net/tracker/index.php?func=detail&aid=3525000&group_id=160139&atid=814650# Please give it a try and let me know how it looks. -greg ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
