I've done a lot of debugging in chains.cpp, but don't have time for a few days. It's sorta like a specialized SMILES/SMARTS parser.
> result = DetermineHetAtoms(mol) && result; > result = DetermineConnectedChains(mol) && result; > result = DeterminePeptideBackbone(mol) && result; > result = DeterminePeptideSidechains(mol) && result; So based on your comment, everything before this seems to be OK? (i.e., returns a positive result). Then DeterminePeptideSidechains() which calls IdentifyResidue() returns 0? -Geoff On Dec 12, 2011, at 3:24 PM, Noel O'Boyle wrote: > Hi there, > > I've been looking at bug PR#3448379. It's a failure in identifying a > serine when at the C-terminus, after calling --gen3d (it's labelled as > UNK). > > As a simpler testcase, "obabel -:N[C@@H](CO)C(=O)N[C@@H](CO)C(=O)O > --gen3d -opdb" will cause the problem (two serines in a row). To speed > things up, you can comment out everything in gen3d after > "builder.Build(*pmol);". > > The specific problem is that IdentifyResidue returns 0 in chains.cpp. > This is quite a complex area of the code (some sort of tree-like > parsing going on). If any of you are familiar with it, I'd appreciate > a hand here. > > - Noel > > ------------------------------------------------------------------------------ > Learn Windows Azure Live! Tuesday, Dec 13, 2011 > Microsoft is holding a special Learn Windows Azure training event for > developers. It will provide a great way to learn Windows Azure and what it > provides. You can attend the event by watching it streamed LIVE online. > Learn more at http://p.sf.net/sfu/ms-windowsazure > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel ------------------------------------------------------------------------------ Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event for developers. It will provide a great way to learn Windows Azure and what it provides. You can attend the event by watching it streamed LIVE online. Learn more at http://p.sf.net/sfu/ms-windowsazure _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
