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7caab0c0f78ee77bd1274476e81fb9df5b53a164
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38 Commits

Author SHA1 Message Date
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
Noel O'Boyle
a3a65728b5 setup.py can now find the relevant libraries, whereever they are! 2005-12-16 11:18:14 +00:00
Noel O'Boyle
417b79770f Added find_likely_directory to setup.py based on the same function in pydaylight's setup.py. Not yet finished, but the general idea is there. 2005-12-15 17:06:02 +00:00
Noel O'Boyle
47ac0166f8 Added GetVar() methods to pyopenbabel.py. 2005-12-09 09:22:46 +00:00
Noel O'Boyle
2edfaa096f Documented the design of the Atom class so far, and started on the Molecule class. 2005-12-07 17:13:43 +00:00
Noel O'Boyle
96461e3f02 Initial import of pyopenbabel.py, a more Pythonic interface to openbabel, and pyopenbabel.txt, where notes on design decisions should be added. 2005-12-07 11:23:49 +00:00
Noel O'Boyle
d6bb5750c9 Renamed the created extension from openbabel.so to _openbabel.so. 2005-12-07 11:18:08 +00:00
Geoffrey Hutchison
cbc4695bc0 Updated mainline with openbabel-new-framework branch. Will create a new openbabel-2-0-x release branch soon. 2005-11-18 00:53:15 +00:00