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533 Commits
Author SHA1 Message Date
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 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 79bdb42114 * config.sub, config.guess, configure, Makefile.* Update with 
automake-1.10 and autoconf-2.61.
 2007-03-13 12:24:21 +00:00
Geoffrey Hutchison 7078f7c5a8 Added test program. 2007-03-13 12:21:48 +00:00
Geoffrey Hutchison 250f0f5b7c Regenerated from recent plugin and force field changes. 2007-02-26 21:51:27 +00:00
Geoffrey Hutchison 6369377128 Fix Java compile from previous revision. 2007-02-20 15:27:03 +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
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 0426d61e76 * scripts/openbabel-python.i: quick fix to allow the openbabel module 
to be imported without errors. The OBFingerprintIter issue remains
	unresolved.
 2007-01-12 14:33:29 +00:00
Chris Morley 5225ffa57b Changes in PluginIter and its Python implementation. 2007-01-09 23:31:34 +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
Noel O'Boyle d4052c7ae8 Necessary fixes for pybel tests to pass on Windows. The original problem was that FP3 was unable to find patterns.txt, which means that the installer needs to install the data files somewhere, and BABEL_DATADIR needs to be set appropriately. The following changes were made: 
* windows-vc2005/OBPython/setup.py: Install data files (e.g.
	patterns.txt needed for FP3) into site-packages/openbabel_data

	* scripts/openbabel-python.i: For Windows installs, set BABEL_DATADIR
	to the location into which the binary installer installs the data files

	* src/fingerprints/finger3.cpp: Replace instances of "/" by
	FILE_SEP_CHAR
 2006-12-20 09:26:16 +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 3b3e9be82b Updates for Java targets. 2006-12-15 15:36:18 +00:00
Geoffrey Hutchison 9d98c5e948 Fixed Java (JNI) interfaces to compile cleanly. Updated other SWIG interfaces. 2006-12-14 23:17:34 +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
Geoffrey Hutchison b47b3c689d * scripts/: Regenerated files based on Noel's changes today. 2006-12-13 19:43:43 +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
Noel O'Boyle 9f8af2378d * scripts/openbabel-python.i: Added some SWIG magic that allows the 
creation of a C doubles array. Also added a Python convenience
	function that converts a list to a C doubles array. This will allow
	users to access functions such as OBMol::Rotate.
 2006-11-29 13:55:16 +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 9519c444ec Reorganized names 2006-11-03 22:30:38 +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
Geoffrey Hutchison 19d4b48ec4 Changes for Rich Apodaca's Ruby tests. 2006-10-27 21:49:36 +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