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495 Commits
Author SHA1 Message Date
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
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
Noel O'Boyle 77112c972c OBMol.GetData() returns a pointer to OBGenericData, not an OBGenericData object itself. 2006-06-09 10:00:18 +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 1c24163aa5 * configure, configure.in, Makefile.*: Update to test for Perl and 
"prove" used for new test harness.
 2006-02-20 21:21:21 +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 1a75b13ad5 Fixed misspelling 2005-12-15 17:02:20 +00:00
Noel O'Boyle faa871e561 Added patch from Josh for Geoff's RTLD_GLOBAL fix for problem importing dynamically-loaded libraries for file conversion in Python. 2005-12-15 11:11:42 +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 5b6cb002c7 Updated UNIX build files (configure, Makefile.in, etc.) for 2.0.0 release number. 
Will branch for openbabel-2-0-x soon.
 2005-11-20 21:16:01 +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