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?
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
