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4b5d4c426f7f78271844ce3fec07a98a5d48ee34
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37 Commits
Author SHA1 Message Date
David KoesandDavid Koes 4b5d4c426f IsElement implemention, make OBElements::Element enum (#1754) 
* IsElement implemention, make OBElements::Element enum

* Fix php include.  Consistent renaming.

Resname all the single character residue constants.  Do this instead of
defining natively in python since the actual constants are arbitrary and
so could change (unlike elements)

Co-authored-by: David Koes <dkoes@beefy.dcb.private.net>
 2020-05-03 15:25:03 -04:00
Noel O'Boyle f96f03580e Update bindings for lack of ChiralData 2019-04-16 09:21:03 +01:00
Noel O'Boyle 7330eff772 Update bindings for lack of rand.h 2019-04-15 20:54:45 +01:00
Noel O'Boyle 3b63eed7b2 Update bindings for changes to headers 2019-04-14 21:16:00 +01:00
Noel O'Boyle 71128d38a8 Revert "Remove outdated stereo code" 2019-04-07 17:57:22 +01:00
Noel O'Boyle 7cc1d51331 Update bindings for lack of ChiralData 2019-03-17 20:20:43 +00:00
an.nguyen 46df170c65 Remove OBChemTsfm.Init 2018-04-19 07:34:05 +02:00
an.nguyen e4752e459a Add stereo + obfunctions + kekulize to ruby binding 2018-04-18 10:47:34 +02:00
Noel O'Boyle 65074163ee Compiling the Python bindings (at least) failed as OBBitVec was not yet defined. I've moved it before the mol.h include. 2018-01-10 20:39:37 +00:00
Noel O'Boyle bb4bc5f521 Update bindings 2017-12-28 21:02:27 +00:00
Noel O'Boyle a170a4e5ad Fix comment symbol in swig interfaces 2016-06-25 21:08:13 +01:00
David Hall 673dd2e864 Swig3 patch from Fedora 2015-02-12 08:50:23 -05:00
Noel O'Boyle 8cf5f20dc7 Ruby bindings: Get rid of warning about shadowed function and enable compiling without Eigen 2013-11-28 21:19:15 +00:00
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