On 12 December 2011 22:34, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: > 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?
That would be great. Yes - the previous functions return true. But if I understand correctly, they are setting flags used by later calculations, and it may be that the problem is already caused at this stage? The weird thing is that IdentifyResidue can identify the first serine without any problems; it just doesn't identify the second one. Also, it will identify them both correctly if the --gen3d is omitted (or more precisely, if the call to Builder.Build is omitted). > -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 > ------------------------------------------------------------------------------ Systems Optimization Self Assessment Improve efficiency and utilization of IT resources. Drive out cost and improve service delivery. Take 5 minutes to use this Systems Optimization Self Assessment. http://www.accelacomm.com/jaw/sdnl/114/51450054/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
