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57 Commits
Author SHA1 Message Date
Eisuke Kawashima 8a8ede202b Update INSTALL and READMEs under scripts/ [ci skip] 
- perl
    - assume perl-binding version is different from Open Babel's
- python
    - assume tarball from github release page
    - note: `python scripts/python/setup.py install` does not work since `__init__.py` is missing
 2019-10-11 16:06:16 +09:00
Jeff Janes 2ccf8f70f4 Fix include directory for building Chemistry::OpenBabel 
The header file openbabel/babelconfig.h is not in ../../include,
but rather is in ../../build/include.
 2017-11-09 10:06:49 -08:00
Jeff Janes 438474f24d Correct spelling of file name for Perl bindings 
The MANIFEST file has openbabel-perl.cpp spelled with
an underscore rather than a dash.  This causes a
confusing but otherwise harmless warning when running
`perl Makefile.PL`.
 2017-11-09 09:55:09 -08:00
Geoffrey Hutchison 0ffd9199f1 Patches from Fedora packaging. 2010-12-15 21:45:57 +00:00
Geoffrey Hutchison 3e71f5a35b Update website to openbabel.org (long overdue). 2010-10-10 01:24:39 +00:00
Noel O'Boyle 042b1e3d1b Fix problem compiling Perl bindings on Linux PR#3059516 2010-09-23 14:55:22 +00:00
Geoffrey Hutchison ee0dedc62a Further refinement. Definitely compiles on Mac OS X now. 2010-08-03 17:11:08 +00:00
Geoffrey Hutchison c6f220e0e4 Updates to Perl bindings makefile -- should now have reasonabel fallbacks for CMake build directories. 2010-08-03 16:53:30 +00:00
Noel O'Boyle 4a6d3571bc 2010-06-07 Noel O'Boyle 
* scripts/CMakeLists.txt, scripts/perl/Makefile.PL: Now perl bindings
	seem to 'make install' correctly.
 2010-06-07 12:16:16 +00:00
Noel O'Boyle eccb35e446 2010-06-06 Noel O'Boyle 
* scripts/CMakeLists.txt, scripts/perl/Makefile.PL: Now perl bindings seem to 'make' correctly.
 2010-06-06 20:33:04 +00:00
Geoffrey Hutchison 6f7c6cb1de Makefile.PL update from Noel. 2008-07-01 18:18:40 +00:00
Geoffrey Hutchison 024240cd78 Split python bindings into multiple pieces. Should solve PR#1905826. 2008-06-05 22:42:47 +00:00
Geoffrey Hutchison 0044d9545e * scripts/openbabel-perl.i, scripts/perl/Makefile.PL: 
Fix up Perl scripting. Now works on Mac OS X and appears to have
        clean converisons via "make test." Fixes PR#1795155 and 1881688.
 2008-05-28 16:32:56 +00:00
Geoffrey Hutchison 73e7b5c204 * scripts/perl: Add dependency checking for libopenbabel. This 
prevents people trying to run automated CPAN tests without the
        library.
 2008-03-02 17:20:48 +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
Geoffrey Hutchison 657e845594 Removing auto-generated SWIG files from trunk 2007-04-19 20:47:06 +00:00
Geoffrey Hutchison 1a078891f2 Merged revisions 1900-1914 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-1-x

........
  r1900 | ghutchis | 2007-03-24 14:17:59 -0400 (Sat, 24 Mar 2007) | 4 lines
  
    * include/openbabel/atom.h, src/atom.cpp: Change SetVector to
    const parameter.
........
  r1901 | ghutchis | 2007-03-25 09:16:53 -0400 (Sun, 25 Mar 2007) | 2 lines
  
  Fix missing Makefile updates when I removed MMFF94 parameter files.
........
  r1902 | timvdm | 2007-03-25 09:38:42 -0400 (Sun, 25 Mar 2007) | 2 lines
  
  removed unused code from forcefield.cpp
........
  r1903 | ghutchis | 2007-03-25 11:46:16 -0400 (Sun, 25 Mar 2007) | 2 lines
  
  Removed unused mmff94validate (no MMFF94 support, so no reason to keep for 2.1)
........
  r1904 | ghutchis | 2007-03-26 11:37:13 -0400 (Mon, 26 Mar 2007) | 4 lines
  
    * tools/obprop.cpp (main): Fix PR#1688251 with while/for loop on
    CML files. Thanks to Tapani Kinnunen for the report.
........
  r1905 | ghutchis | 2007-03-26 11:41:08 -0400 (Mon, 26 Mar 2007) | 4 lines
  
    * src/formats/mol2format.cpp: Fix problem reported by Noel with
    "USER_CHARGES" appearing instead of Gasteiger.
........
  r1906 | ghutchis | 2007-03-26 11:41:28 -0400 (Mon, 26 Mar 2007) | 3 lines
  
    * src/data.cpp, src/groupcontrib.cpp: Fix doxygen warnings.
........
  r1907 | ghutchis | 2007-03-26 16:58:44 -0400 (Mon, 26 Mar 2007) | 7 lines
  
    * include/openbabel/groupcontrib.h: Documentation fixes.
  
    * NEWS: Minor fixes.
  
    * doc/*.1, doc/*.html: Documentation updates.
........
  r1908 | ghutchis | 2007-03-26 16:59:12 -0400 (Mon, 26 Mar 2007) | 2 lines
  
  Minor doc fix.
........
  r1909 | ghutchis | 2007-03-26 17:00:55 -0400 (Mon, 26 Mar 2007) | 2 lines
  
  Updates for change to OBAtom::SetVector const parameter
........
  r1910 | ghutchis | 2007-03-26 21:59:57 -0400 (Mon, 26 Mar 2007) | 4 lines
  
    * src/obconversion.cpp: Make sure to always return from any
    exception. Otherwise we could crash running code.
........
  r1911 | ghutchis | 2007-03-26 22:00:17 -0400 (Mon, 26 Mar 2007) | 4 lines
  
    * src/formats/mdlformat.cpp: Avoid infinite loop in
    ParseAliasText.
........
  r1912 | ghutchis | 2007-03-26 22:00:35 -0400 (Mon, 26 Mar 2007) | 3 lines
  
    * src/formats/acrformat.cpp: Minor formatting change.
........
  r1913 | ghutchis | 2007-03-26 22:08:00 -0400 (Mon, 26 Mar 2007) | 7 lines
  
    * test/Makefile.am, test/Makefile.in, test/wrapper.sh: Add
    inchiwrite tests to suite.
  
    * test/inchiwrite.cpp, test/inchi.pl: Formatting to integrate into
    Perl "prove" test suite.
........
  r1914 | ghutchis | 2007-03-29 15:31:57 -0400 (Thu, 29 Mar 2007) | 4 lines
  
          * scripts/: Updated interface wrappers, including new Java
          README. (Java is confirmed to work on Mac OS X.)
........
 2007-04-13 18:57:13 +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 67790a7a4e Updated with recent changes (including list of available formats.) 2007-03-23 18:55:34 +00:00
Geoffrey Hutchison 9517b6b0d6 Updated for recent library changes. 2007-03-15 00:02:18 +00:00
Geoffrey Hutchison 250f0f5b7c Regenerated from recent plugin and force field changes. 2007-02-26 21:51:27 +00:00
Geoffrey Hutchison bb3c908eed * scripts/*.i, scripts/*: Add access to OBForceField classes and methods. 2007-02-20 15:05:35 +00:00
Geoffrey Hutchison 5ac27fb442 Updates with DataSource => DataOrigin 2007-02-12 16:15:46 +00:00
Noel O'Boyle a697b20c0a Regenerating bindings for scripting languages 2007-02-08 20:06:59 +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
Geoffrey Hutchison d0470afd50 Updates after documentation changes. 2007-01-16 05:25:18 +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
Geoffrey Hutchison 9d2edcdea1 Regenerate Makefiles to eliminate some build problems. 2007-01-04 13:49:27 +00:00
Geoffrey Hutchison abc1f2ead3 Updates for recent changes. 2006-12-28 19:51:38 +00:00
Geoffrey Hutchison 08f782aea6 * scripts/python/setup.py, scripts/perl/Makefile.PL: Updates from 
Rathann Mierzejewski to check for src/.libs directories. Prevents
  "chicken and egg" problem with what component is built first.
 2006-12-18 21:00:58 +00:00
Geoffrey Hutchison 9d98c5e948 Fixed Java (JNI) interfaces to compile cleanly. Updated other SWIG interfaces. 2006-12-14 23:17:34 +00:00
Geoffrey Hutchison b47b3c689d * scripts/: Regenerated files based on Noel's changes today. 2006-12-13 19:43:43 +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 ddd3f40be1 * scripts/*: Regenerate for continuing API changes (e.g., vector3, 
etc.)
 2006-11-27 22:16:08 +00:00
Geoffrey Hutchison 8dad311517 * src/atom.h, src/base.h, src/bond.h, src/residue.h, src/mol.h, 
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.
 2006-11-20 18:43:41 +00:00
Geoffrey Hutchison 3e4bd6ae3c Updated with automated Java generation and SWIG 1.3.30. 2006-11-06 17:44:10 +00:00
Geoffrey Hutchison 7b29e5c152 * scripts/openbabel.i, scripts/*: Updated with changes from Martin 
Vogt to fix break (likely dating back to header split of atom.h,
  bond.h, residue.h).
 2006-10-27 21:10:17 +00:00
Geoffrey Hutchison 822ff3c93f * scripts/openbabel.i: Add output string for 
OBTypeTable::Translate().

  * scripts/*: Regenerate.
 2006-10-17 20:36:33 +00:00
Geoffrey Hutchison 771aaf9678 * scripts/ruby: Add new ruby interface -- probably needs to be 
moved to allow compilation into main libopenbabel.

  * scripts/*: Updated for above changes.
 2006-09-26 18:21:02 +00:00
Geoffrey Hutchison 02b6bb6c65 * scripts/*: Regenerate for latest header changes. 2006-06-28 21:02:05 +00:00
Geoffrey Hutchison 4b4ba5a579 * scripts/*: Regenerate to add new OBAtom::CountRingBonds() 
method.
 2006-06-21 20:01:58 +00:00
Geoffrey Hutchison 170e0af579 * src/base.h, src/base.cpp: Add "const" qualifiers to 
OBGenericData methods.

        * scripts/*/*.cpp: Regenerated using SWIG for above changes.
 2006-06-14 21:42:00 +00:00
Geoffrey Hutchison d640e740c8 * scripts/openbabel.i: Update from Noel to use 
vector<OBGenericData*> instead of vector<OBGenericData>.

        * scripts/*.cpp: Regenerate using SWIG 1.3.29.
 2006-06-12 15:07:50 +00:00
Geoffrey Hutchison 77c3b8b621 * src/generic.h (Clone): Change from a pure virtual function to a 
virtual which returns NULL as a default. Allows building script
        wrappers with vector<OBGenericData>.

        * scripts/*: Regenerate to solve compilation problems, addressed
        by generic.h changes above.
 2006-06-07 15:58:11 +00:00
Geoffrey Hutchison 75553332f1 * scripts/openbabel.i: Added template support for 
vector<OBGeneric> to address iterating through generic data for
        PR#1484029.

        * scripts/*: Regenerate as above.
 2006-06-06 16:28:28 +00:00
Geoffrey Hutchison f7a808dbed * scripts/*: Regenerate to add Craig's UnsetHash() and 
UnsetWedge() calls.
 2006-06-02 22:12:20 +00:00
Geoffrey Hutchison 4a7db87676 * scripts/*: Regenerate using SWIG. 2006-05-08 18:38:43 +00:00