[OpenBabel-scripting] Open Babel-Ruby (almost)

[richard a. <ric...@ya...>]

I'm trying to get Ruby scripting to work with Open
Babel-2.0.2 and SWIG on Linux.

So far I've been able to generate the
openbabel_wrap.cxx file with SWIG from OB's
openbabel.i file and the OB sources. The bottom of
this file contains all of the Ruby module, class, and
method definitions, as expected.

I created an apparently correct extconf.rb file, which
I then used to create a makefile.

With a little tweaking (I needed to add #include
<math.h> at the top of the .cxx file), I was able to
compile openbabel_wrap.cxx against my installed
OB-2.0.2 library using make.

So far so good.

With irb, however, loading the module segfaults:

BUG] Segmentation fault
ruby 1.8.5 (2006-08-25) [x86_64-linux-gnu]

Aborted

Not really that helpful. I was able to trace the
problem to only three class definitions in
obenbabel_wrap.cxx:

OBAtom
OBBond
OBMol

If I remove these three definitions, I can compile the
module, load it through Ruby, and manipulate OB
objects.

In the case of OBAtom, the offending code is at the
very start of the class stanza:

cOBAtom.klass = rb_define_class_under(mRob, "OBAtom",
((swig_class *)
SWIGTYPE_p_OpenBabel__OBNodeBase->clientdata)->klass);

I suspect the same is true for OBBond and OBMol, but
haven't checked.

I initially thought that maybe this problem was linked
to OBAtom inheriting from another OB object. But so
does OBElementTable, for example, and that definition
doesn't cause a segfault.

Any ideas? I'm not very experienced with Ruby
extensions, C, C++, or make, so any information would
be helpful.

cheers,
Rich


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