Hi, I've faced the same problem with Mychem. You should use the following ack:
#if defined(__CYGWIN__) || defined(__MINGW32__) // macro to implement static OBPlugin::PluginMapType& Map() PLUGIN_CPP_FILE(OBFormat) #endif Here is a copy of a mail from Chris about this problem: ========================================= In 2008 OBFormat was made part of the OBPlugin framework, which now manages the map relating the formats IDs and the pointers to the OBFormat objects. FormatFromMime() is a hangover from the old system, with its map managed by OBFormat itself. It seems the latter is working but the OBPlugin framework is not. Building OB on MinGW and CygWin gave similar problems with the formats not being visible, which Tim solved by conditional code in each plugin type's cpp file. See for instance line 26 of format.cpp . Maybe adding to the conditional to get this code to run for your build would be a solution. I'm afraid I don't understand how this fix works; maybe Tim could comment whether this would be worth trying. Chris ========================================= Cheers, Jerome Pansanel Le jeudi 18 novembre 2010 02:35:21, Imran Haque a écrit : > 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 ------------------------------------------------------------------------------ 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
