On 11/17/10 5:35 PM, Imran Haque wrote: > Hi, > > I have a large set of C++ molecule-manipulation libraries that > internally use OpenBabel to handle molecule input and structure, and I'm > trying to wrap them into a Python library using standard Python C API > techniques. These routines work fine when called from a C program, but > when called from the .so used for the Python library, > OBConversion::FindFormat segfaults. I don't know how to follow the code > path in the source code, as it appears to be generated by macros and > eventually calls down into an independent set of .so's for each file > format. Does anyone know how to get the molecule loader routines to work > from dynamic libraries?
We do something similar: we link OpenBabel (C++) into the Postgres database (written in C). We discovered that it is *critical* that you use the C++ linker, NOT the C linker, to link the final shared library. There's a lot of linker magic that goes on behind the curtains regarding different versions of system libraries. C++ has a lot of constructors and initialization that is triggered by the loader/linker, but if you link the shared object with the ordinary C linker, that stuff doesn't get initialized. It causes all sorts of weird and unexplainable segfaults. Simply replacing gcc with g++ to create the .so solved our problem. Craig > > I've put up a minimal test case at > http://cs.stanford.edu/people/ihaque/ob_bug_repro.tar. You may have to > adjust the paths in the Makefile to correspond to your Python and OB > installations. Here's sample output (note that I added a tracing printf > to OBConversion::FormatFromExt that isn't in the mainline OB 2.3.0 source): > > $ python numatoms.py test.sdf > Molecule hasFilename test.sdf > FormatFromExt calling FindFormat with arg sdf > Segmentation fault > > $ ./numatoms test.sdf > Filename test.sdf > FormatFromExt calling FindFormat with arg sdf > Detected format: MDL MOL format > Reads and writes V2000 and V3000 versions > Read Options, e.g. -as > s determine chirality from atom parity flags > This is valid only for 0D information. Atom > parity is always ignored on reading for MOL files > containing 2D or 3D information. > T read title only > P read title and properties only > When filtering an sdf file on title or properties > only, avoid lengthy chemical interpretation by > using the T or P option together with copy format. > > Write Options, e.g. -x3 > 3 output V3000 not V2000 (used for>999 atoms/bonds) > m write no properties > w recalculate wedge and hash bonds(2D structures only) > A output in Alias form, e.g. Ph, if present > > > Molecule has 27 atoms. > > > Thanks, > > Imran Haque > http://cs.stanford.edu/people/ihaque > iha...@stanford.edu > > > PS - Using Pybel is not an option here because I don't want to > reimplement all the C++ functionality in Python - I just need to be able > to call into it. > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today > http://p.sf.net/sfu/msIE9-sfdev2dev > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
