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67790a7a4e1530834660044090d6a0468a3ce489
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57 Commits

Author SHA1 Message Date
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
Geoffrey Hutchison
4a7db87676 * scripts/*: Regenerate using SWIG. 2006-05-08 18:38:43 +00:00
Geoffrey Hutchison
fd0d0f1980 Remove un-needed .cvsignore files. 2006-05-03 15:47:07 +00:00
Noel O'Boyle
e79d290296 Added a class to allow molecules to be written to a multiple molecule file. 2006-04-24 11:04:14 +00:00
Noel O'Boyle
a254dc2ecf Adding the ability to iterate over molecules in multiple-molecule input files. Note to self: Need to look at how single-molecule files are handled. 2006-04-20 08:07:52 +00:00
Geoffrey Hutchison
32e8d6d627 Merged changes from 2.0.1 fixes that were not already integrated into 2.1. 2006-04-19 15:37:47 +00:00
Geoffrey Hutchison
5732e175fa * scripts/*: Update scripting wrappers with SWIG 1.3.29. 2006-03-28 22:38:06 +00:00
Noel O'Boyle
8caaa288f5 Reverted rename of the created extension from _openbabel.so to openbabel.so. 2006-03-16 15:18:59 +00:00
Noel O'Boyle
75c680fdf4 Adding a simple test file. 2006-03-16 10:18:36 +00:00
Geoffrey Hutchison
b8d999409a * scripts/* : More changes to allow building, linking, and running 
(again!) with current CVS tree.
 2006-03-15 19:48:37 +00:00
Geoffrey Hutchison
ffa5441823 * scripts/*: Build updates for Perl and Python wrappers. 2006-03-14 00:47:39 +00:00
Noel O'Boyle
ce597aeb68 Modified setup.py to also install pyopenbabel. 2006-02-21 09:33:24 +00:00
Geoffrey Hutchison
f71b7c5d47 * scripts/perl/* : Added more unit tests, fixed bug with 
case-sensitive filesystems, and problems with dynamic loading on
        Linux.

        * scripts/python/*: Updated to fix problem with dynamic loading on
        Linux.
 2006-01-25 20:31:41 +00:00
Noel O'Boyle
4aaf2fbe41 Adding file format conversion. 2006-01-04 15:53:52 +00:00