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70 Commits

Author SHA1 Message Date
Noel O'Boyle
e160ab259a Fix for MacOSX to allow compilation of Python bindings against local build tree. 2008-03-31 12:43:41 +00:00
Noel O'Boyle
33495778f2 * scripts/python/pybel.py: First attempts at incorporating the recent work by Tim, Geoff and others on geometry optimisation and 3D coordinate generation. 2008-03-23 20:07:00 +00:00
Noel O'Boyle
a093a951ce Made pybel test suite compatible with Python 2.3 2008-02-01 16:28:33 +00:00
Noel O'Boyle
24ccf30c1b Updating perl wrapper to the same as Python. Fixing setup.py for Python as wasn't finding openbabel.so on my system 2008-01-29 09:38:22 +00:00
Noel O'Boyle
37588a1d49 * scripts/python/pybel.py, scripts/python/examples/testpybel.py: 
Updated to use plugin descriptors. Changed to create a single instance
	of plugin descriptors and fingerprinters. Also, readfile now raises an
	IOError if the file does not exist.
	* scripts/python/examples/findcoverage.bat: Add .bat file to automate
	calculation of code coverage for pybel
 2008-01-17 12:08:31 +00:00
Geoffrey Hutchison
858f8a39f9 * Merged in changes from 2.1.x branch. 2007-09-03 20:53:06 +00:00
Noel O'Boyle
49f5d2915c Final changes for Windows release of OBPython 1.2 
* windows-vc2005/OBPython/setup.py: bumped version up to 1.2
	* scripts/python/pybelapi.py: updated API doc
 2007-06-01 09:05:04 +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
Noel O'Boyle
5d1cdec9c3 * pybel.py: Added support for unitcell, and deletion of OBPairData 
(need to update the tests and the API docs)
 2007-05-10 11:00:13 +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
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
a3e96d91d4 * configure.in, configure, Makefiles: Bump version number to 
2.1.0b5.
 2007-01-14 21:47:03 +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
Noel O'Boyle
7f65eec16a * fingerprint.cpp/.h: Changed the FindFingerprint method to 
accept
	const string& instead of string&. This is necessary for access 
to this
	function from Python.
	
	* scripts/python/pybel.py, testpybel.py, pybelapi.html: Added a 
method
	to Molecule for calculating a molecular fingerprint, handled by 
a new
	Fingerprint class.
 2006-12-16 21:51:22 +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
Noel O'Boyle
7caab0c0f7 * scripts/python/pybel.py, testpybel.py, pybelapi.html: Added a 
.close() method to the Outputfile class of Pybel. This uses the
	CloseOutFile() method added by Chris Morley in r1606. This is
	necessary to ensure that all tests pass on Windows.
 2006-11-25 09:49:50 +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
Noel O'Boyle
abfcaa6132 * scripts/python/testpybel.py: Needed to relax one of the tests of 
molecular weight, as it was failing for the OB2.1b2 snapshot (there
	must have been some changes to the atomic masses). Also,
	corrected tolerance tests to use the absolute value of the difference
	rather than the actual value.
 2006-11-18 18:30:02 +00:00
Noel O'Boyle
71b835bcad * scripts/python/setup.py, pyopenbabel.py, testpyopenbabel.py, 
pyopenbabelapi.html: Changed all references to pyopenbabel to 
pybel
        (new name). Also, corrected minor typo in docstring in pybel.py.
 2006-11-18 13:31:04 +00:00
Noel O'Boyle
22b0bb1053 2006-11-15 Noel O'Boyle <baoilleach@gmail.com> 
* scripts/python/pyopenbabel.py: Updated to be consistent, fast, pass all unit tests, and to have API documentation in docstrings.
	* scripts/python/testpyopenbabel.py: Added complete coverage unit tests	for pyopenbabel.py
	* scripts/python/test/*: Removed previous attempts at testing
	* scripts/python/pyopenbabel.txt: Removed previous attempts at providing documentation (we now have a wiki, and API documentation)
	* scripts/python/head.sdf: Added small test file, used by testpyopenbabel.py
	* scripts/python/pyopenbabelapi.html: Added API documentation for pyopenbabel.py, automatically generated using "pydoc -w"
 2006-11-15 21:25:14 +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
f3e581955f * src/main.cpp, src/obutil.cpp, src/fingerprints/finger3.cpp, 
src/format/fastsearchformat.cpp: Patch from Martin Vogt to address
  PR#1590609. Crashes due to incorrect handling of string parsing on
  64-bit platforms.
 2006-11-06 16:30:35 +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
Noel O'Boyle
4c2d054823 Adding smarts pattern matching stuff. 2006-05-23 14:15:02 +00:00