* scripts/CMakeLists.txt, openbabel-java.i, openbabel-python.i: Bring
the Java bindings back to life. Bring the python and java SWIG
interface files into synch. More to be done here.
* scripts/openbabel-java.i, scripts/openbabel-perl.i,
scripts/openbabel-ruby.i: Fix script bindings. Now compile
cleanly. Perl still needs work to pass tests.
* include/openbabel/math/spacegroup.h, include/openbabel/plugin.h:
Minor updates for SWIG compatibility.
* */Makefile.in: Regenerate UNIX build files.
* src/plugin.cpp: Make sure to #include <iterator> to solve GCC
compile problem.
* src/descriptor.cpp: Change _isnan to IsNan, as discussed on the
list to solve GCC compile problem.
* scripts/*: Updated to compile. May have removed functionality
because of plugin changes.
* tools/obminimize.cpp, tools/obgen.cpp, tools/obenergy.cpp:
Switch to OBPlugin::List().
* scripting interfaces: added a method to cast OBGenericData to
OBPairData
* pybel: added dictionary-like support for accessing molecule data,
and updated the tests and the API documentation
handle
the new pluginiter.h, and in particular, its use in
OBFingerprint.Iter. Also, regenerated all of the dependent
files.
* scripts/openbabel-python.i: Removed python code added on
2006-12-20
to set BABEL_DATADIR as it actually had no effect.
iterators in obiter.h. Note: there is a problem getting
OBMolPairIter to work even if std_pair.i is included and a template
<int, int> created (compile of openbabel_python.cpp fails in this case
so these additions have not been included).
references to classes in obiter.h (e.g. there's no such thing
as OBResidueBondIter). Added some comments. Added wrappers for Python
to allow iteration over atoms in a molecule, etc.
This involved renaming the original OB method, and replacing
it by a Python class implementing the iterator protocol.
src/ring.h, src/mol.cpp, src/base.cpp, src/obiter.h: Remove
OBNodeBase, OBEdgeBase, and OBGraphBase classes, contributed by
Gerd Menche.
* tools/obprop.cpp: Ditto. Example of changing iterators to new format.
* scripts/*: Updated based on above changes.
