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24 Commits
Author SHA1 Message Date
Noel O'Boyle a7b96bf22f Get rid of error messages in perl bindings and synch with ruby bindings 2010-06-06 15:28:22 +00:00
Noel O'Boyle 994b94ce67 Bring Ruby bindings into synch with Python bindings 2010-06-06 15:10:17 +00:00
Noel O'Boyle f6618293e8 2010-06-06 Noel O'Boyle 
* scripts/CMakeLists.txt, scripts/openbabel-ruby.i, scripts/ruby/extconf.rb: Ruby binding support.
 2010-06-06 14:33:53 +00:00
Geoffrey Hutchison fdcd45b468 Merge of svn commits r2707, 2711, 2713, 2717 from 2.2 release branch. 2009-03-23 02:13:53 +00:00
Geoffrey Hutchison 889fba2d20 * scripts/java/OBTest.java: Bring back test program. 
* 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.
 2008-05-16 21:07:13 +00:00
Noel O'Boyle 6cb96812df Applied Rich's fix to Ruby initialisation and updated the interface file for Ruby. Compiles fine now, but fingerprint.h is commented out. 2008-01-24 11:28:04 +00:00
Noel O'Boyle 72b9f5011d Merged changes to the Python SWIG interface to the other scripting languages. Haven't yet been able to test (am trying to set up a VM with a decent amount of RAM...) 2008-01-20 17:55:57 +00:00
Geoffrey Hutchison 858f8a39f9 * Merged in changes from 2.1.x branch. 2007-09-03 20:53:06 +00:00
Geoffrey Hutchison 2b8127c377 Fix UNIX builds of SVN trunk: 
* */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().
 2007-05-22 14:55:46 +00:00
Noel O'Boyle 174b5452bf * SWIG interface files: Added template for vectors of strings 
* pybel.py: Added informats and outformats, dictionaries corresponding
	to the supported input and output format
 2007-05-12 11:45:39 +00:00
Geoffrey Hutchison 56f11e72f9 * scripts/*.i: Added casting from OBGenericData to OBUnitCell. 2007-05-08 17:04:53 +00:00
Noel O'Boyle 503b33dc4a 2007-05-08 Noel O'Boyle <baoilleach@gmail.com> 
* scripting interfaces: added a template for a vector of OBRing*
	which is required for OBMol.GetSSSR()
 2007-05-08 13:03:30 +00:00
Noel O'Boyle 8270b862df 2007-05-08 Noel O'Boyle <baoilleach@gmail.com> 
* 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
 2007-05-08 12:33:05 +00:00
Geoffrey Hutchison 113220be4c Merged revisions 1918-1933 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-1-x

........
  r1918 | ghutchis | 2007-03-30 14:25:42 -0400 (Fri, 30 Mar 2007) | 2 lines
  
  Produce a better "clean" before creating a distribution tar
........
  r1919 | ghutchis | 2007-03-30 16:46:51 -0400 (Fri, 30 Mar 2007) | 7 lines
  
    * include/openbabel/residue.h: Hide some residue names (e.g.,
    _1MG) from SWIG wrappers -- such constants are not valid symbols
    in some languages like Ruby.
  
    * scripts/ Update accordingly.
........
  r1920 | ghutchis | 2007-03-30 16:47:12 -0400 (Fri, 30 Mar 2007) | 4 lines
  
    * src/base.cpp: Additional "What's new" documentation for 2.1
    release.
........
  r1921 | ghutchis | 2007-03-30 16:47:34 -0400 (Fri, 30 Mar 2007) | 2 lines
  
  (missed changelog update.)
........
  r1922 | ghutchis | 2007-03-30 17:53:27 -0400 (Fri, 30 Mar 2007) | 2 lines
  
  Updated to use Ruby-style API names via SWIG -autorename
........
  r1923 | ghutchis | 2007-04-02 22:41:53 -0400 (Mon, 02 Apr 2007) | 7 lines
  
    * include/openbabel/residue.h: Undo previous change. Rich Apodaca
    suggested some SWIG-fu instead.
  
    * scripts/ Update accordingly. Includes ruby changes, new README
    and examples.
........
  r1924 | ghutchis | 2007-04-03 22:51:43 -0400 (Tue, 03 Apr 2007) | 2 lines
  
  Updated for 2.1 release of scripting interfaces.
........
  r1925 | ghutchis | 2007-04-04 00:06:50 -0400 (Wed, 04 Apr 2007) | 2 lines
  
  Moved examples to subdir (for cleaner-looking dist) and MANIFEST
........
  r1926 | ghutchis | 2007-04-04 20:58:12 -0400 (Wed, 04 Apr 2007) | 2 lines
  
  Updated for new Doxygen update (and new warnings)
........
  r1927 | timvdm | 2007-04-05 17:41:37 -0400 (Thu, 05 Apr 2007) | 4 lines
  
  - documentation update
  - covert to dative bonds (for psa)
  - psa.txt: fix smiles for 3-rings
........
  r1929 | ghutchis | 2007-04-07 14:43:05 -0400 (Sat, 07 Apr 2007) | 3 lines
  
    * NEWS: Minor fixes for 2.1.0 final release.
........
  r1930 | ghutchis | 2007-04-07 15:07:08 -0400 (Sat, 07 Apr 2007) | 2 lines
  
  Minor fixes. Corresponds to 2.1.0 released source.
........
  r1933 | ghutchis | 2007-04-13 13:44:01 -0400 (Fri, 13 Apr 2007) | 8 lines
  
    * src/formats/inchi/strutil.c: Bug reported on the InChI mailing
    list.
  
    * src/formats/inchiformat.cpp: Bug caught during ChemSpotlight
    testing -- some files don't have chirality information (e.g., 3D
    files but with 0.0 coordinates throughout). Warn and give up.
........
 2007-04-13 18:44:10 +00:00
Geoffrey Hutchison bb3c908eed * scripts/*.i, scripts/*: Add access to OBForceField classes and methods. 2007-02-20 15:05:35 +00:00
Noel O'Boyle 51d76550c9 Removed %apply of OUTPUT in the script interface files, and regenerated the bindings 2007-02-05 20:19:01 +00:00
Noel O'Boyle d18872df68 * scripts/openbabel-[python,java,perl,ruby].i: Added ability to 
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.
 2007-01-06 18:19:41 +00:00
Noel O'Boyle b2528f043e * scripts/openbabel-[python,ruby,java,perl].i: Updated to include all 
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).
 2006-12-14 13:15:31 +00:00
Noel O'Boyle d3783a87a9 * scripts/openbabel-[python,ruby,java,perl].i: Tidied up the 
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.
 2006-12-13 13:29:36 +00:00
Noel O'Boyle f95f7182df * scripts/openbabel-[python,ruby,java,perl].i: Added a line to 
create a vector of unisigned ints, required to use the Fingerprint
	class. Also, added lines to prevent warnings due to shadowed classes
	in obiter.h.
 2006-12-12 12:48:54 +00:00
Geoffrey Hutchison 0afe511e34 * include/openbabel: New directory for public headers. Ensures 
internal and external code use the same 
  #include <openbabel/header.h> syntax.
 2006-12-10 13:56:00 +00:00
Geoffrey Hutchison 6bb194a602 * scripts/: Added fingerprint.h header for direct access to 
OBFingerprint classes.
 2006-12-08 00:05:39 +00:00
Geoffrey Hutchison aa011ebe45 * scripts/*: Cleanups and fixes, including for compilation 
problems with Perl. (Derives from some macro expansion for THR.)
 2006-12-02 18:56:04 +00:00
Geoffrey Hutchison 07164cb7be * scripts/*: Split openbabel.i into individual copies for each 
language.

  * scripts/java/*: Initial attempt at a java interface from SWIG. Untested.
 2006-11-03 22:23:31 +00:00