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69 Commits

Author SHA1 Message Date
Maciej Wójcikowski
72ea0bcd56 Fix Python 2 unicode 2016-07-19 11:41:40 +02:00
Noel O'Boyle
a170a4e5ad Fix comment symbol in swig interfaces 2016-06-25 21:08:13 +01:00
David Hall
673dd2e864 Swig3 patch from Fedora 2015-02-12 08:50:23 -05:00
Noel O'Boyle
1e87704d58 Update Java, Perl and Python bindings to work without Eigen installed. More bindings to come.~ 2013-11-26 14:03:24 +00:00
Reinis Danne
1d94ecf505 scripts/openbabel-python.i: Revert shared_ptr changes 
This reverts part of ce178cbbd3.
 2013-11-22 00:50:20 +02:00
Noel O'Boyle
ce178cbbd3 1. Use obsharedptr instead of shared_ptr. obsharedptr is #defined to the appropriate value 
2. Add support for shared_ptrs to Python bindings. The following code now works:

r = OBReaction()
m = OBMol()
r.AddReactant(m)
 2013-08-26 12:18:26 +01:00
Reinis Danne
dbbfd1d341 scripts/openbabel-python.i: Alias __next__ with next 
Avoids an extra function call on every iteration.
 2013-06-12 00:01:49 +03:00
Noel O'Boyle
46426d64b5 Fix for Eigen problems with the bindings reported by Reinis Danne on openbabel-devel. Now supports Eigen3 as well as Eigen2. 2012-09-27 19:03:59 +00:00
Noel O'Boyle
1e7430d52e scripts/openbabel-python.i: I forgot to check this in. It enables access to OBChemTsfm from Python. 2012-09-05 12:11:04 +00:00
Tim Vandermeersch
b4a88c3281 Move include/openbabel/stereo/python.h to 
include/openbabel/stereo/bindings.h. Move stereo bindings code to
scripts/stereo.i and update openbabel-python.i and openbabel-java.i
 2012-08-08 13:34:31 +00:00
Tim Vandermeersch
fb06dab0cb Add support for OBXXXStereo::SetConfig for python bindings 2012-08-06 18:12:06 +00:00
Tim Vandermeersch
19db57a8ef Add support for OBXXXStereo::GetConfig for the python bindings. 2012-08-06 18:11:43 +00:00
Noel O'Boyle
baee593b55 openbabel-java.i, openbabel-python.i: Synch the Python and Java interface files. 2011-06-10 08:39:44 +00:00
Noel O'Boyle
b5f8848c56 scripts/openbabel-python.i: Add support for toAliasData in Python bindings. 2011-05-14 16:25:16 +00:00
Noel O'Boyle
3d215e082c openbabel-python.i: Apply patch from My Th (PR3194037) to add support for vectors of OBInternalCoord*. 2011-02-27 19:09:20 +00:00
Noel O'Boyle
b5484f9047 openbabel-python.i: Apply patch from My Th (PR3194050) to fix iterators in Python 3. 2011-02-27 15:40:10 +00:00
Noel O'Boyle
dca7e79a63 Python bindings: Add support for OBStereoFacade. (TODO: look at other stereo classes) 2010-12-07 10:21:29 +00:00
Noel O'Boyle
5277b11c1f scripts/openbabel-python.i: I recently added support for align.h. This is dependent on Eigen and needed another "if" statement added to the interface. 2010-11-17 09:50:10 +00:00
Noel O'Boyle
870a726e98 Add Python bindings for new canonical labelling, isomorphism, OBAlign and OBQuery classes. 2010-11-04 12:17:12 +00:00
Noel O'Boyle
2dd7889739 Adding vector<vector<vector3> > as requested in PR#2969937. 2010-08-16 11:46:26 +00:00
Noel O'Boyle
8a8d86a14e Add OBReaction (as requested in PR#3033204). Get rid of warning about shadowed method in OBRotor. 2010-08-16 11:23:00 +00:00
Noel O'Boyle
b0b23393b1 * scripts/openbabel-python.i: Revert of r3914 (presumably it was a 
mistake to include this file in the commit)
 2010-07-30 08:48:26 +00:00
Tim Vandermeersch
c03e2d9bfc Add mask feature to OBIsomorphismMapper and OBQuery 2010-07-29 16:46:21 +00:00
Geoffrey Hutchison
9db4514cbf * scripts/openbabel-python.i: Add chargemodel to Python bindings. 2010-07-27 17:19:10 +00:00
Noel O'Boyle
c49ce0543d 2010-07-26 Noel O'Boyle 
* scripts/CMakeLists.txt, openbabel-python.i: Pass -DHAVE_EIGEN2 to swig
	and conditionally generate bindings for conformersearch.h.
 2010-07-26 10:42:22 +00:00
Tim Vandermeersch
539df04a8b Add OBConformerSearch class 2010-07-12 12:22:15 +00:00
Hans De Winter
aa6b4b0e48 Initial Spectrophore(TM) code 2010-07-05 13:22:23 +00:00
Noel O'Boyle
5c81329d4c 2010-05-11 Noel O'Boyle 
* scripts/CMakeLists.txt, openbabel-java.i, openbabel-python.i: Bring
	the Java bindings back to life. Bring the python and java SWIG
	interface files into synch. More to be done here.
 2010-05-11 11:30:00 +00:00
Noel O'Boyle
c5621afbb4 Adding ignore for OpenBabel::FptIndex; as it was breaking the linking step. Not sure why. 2010-03-01 17:14:16 +00:00
Noel O'Boyle
9658f5afb9 Avoid error when running SWIG. 2010-02-28 14:27:03 +00:00
Noel O'Boyle
f2c52613ec Revert one of my changes that got rid of warnings 2010-02-16 10:13:51 +00:00
Noel O'Boyle
17e00be9d1 2010-02-15 Noel O'Boyle 
* scripts/openbabel-python.i: Get rid of warnings. Allow access to
	rotors. Tidy up the interface a bit (prevent people calling C++
	iterators, for instance)
 2010-02-15 10:44:09 +00:00
Noel O'Boyle
afb12d1eb7 2009-09-21 Noel O'Boyle <baoilleach@gmail.com> 
* scripts/*: Copied + pasted the scripts directory from 22x as a number
	of commits were never merged.
 2009-09-21 11:12:00 +00:00
Tim Vandermeersch
ba44a484d6 Update headers to enable python bindings to work. 2009-07-18 22:33:52 +00:00
Tim Vandermeersch
e4fa3d172d Updated Python build to that of 22x branch 
Conflicts:

	scripts/openbabel-python.i
 2009-07-18 22:23:56 +00:00
Tim Vandermeersch
0082bcde7f Merged revisions 3027-3031 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-2-x

........
  r3027 | ghutchis | 2009-05-22 19:54:18 +0200 (Fri, 22 May 2009) | 2 lines
  
  Make sure to define OB_MODULE_PATH for dlhandler_unix
........
  r3028 | ghutchis | 2009-05-26 19:56:17 +0200 (Tue, 26 May 2009) | 2 lines
  
  Fix bug introduced with 2D code -- many molecules will come in as 0D, not 3D.
........
  r3029 | ghutchis | 2009-05-27 01:23:11 +0200 (Wed, 27 May 2009) | 4 lines
  
          * data/element.txt, data/element.h: Update atomic radii with
          consistent sets from recent publications.
........
  r3030 | ghutchis | 2009-05-27 01:23:54 +0200 (Wed, 27 May 2009) | 2 lines
  
  Backport r3026, removing IMPVAL for alkali and alkaline earth metals.
........
  r3031 | baoilleach | 2009-05-27 15:45:11 +0200 (Wed, 27 May 2009) | 3 lines
  
  2009-05-27  Noel O'Boyle  <baoilleach@gmail.com>
  
          * scripts/openbabel-python.i: Allow access to OBBuilder and matrix3x3
........
 2009-07-17 23:30:46 +00:00
Geoffrey Hutchison
2b849f4282 Merged revisions 2735,2740,2744,2806-2807 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-2-x

........
  r2735 | timvdm | 2008-10-04 15:47:45 -0400 (Sat, 04 Oct 2008) | 4 lines
  
          * src/forcefield.cpp: Fix OBForceField::GetAtomTypes() and
          OBForceField::GetPartialCharges()
........
  r2740 | baoilleach | 2008-10-11 10:42:31 -0400 (Sat, 11 Oct 2008) | 5 lines
  
  2008-10-10  Noel O'Boyle  <baoilleach@gmail.com>
  
  	* scripts/openbabel-perl.i: Replaced the C++ iterators by Perl classes
  which can be used for iteration natively in Perl.
........
  r2744 | baoilleach | 2008-10-16 13:27:54 -0400 (Thu, 16 Oct 2008) | 5 lines
  
  2008-10-16  Noel O'Boyle  <baoilleach@gmail.com>
  
  	* scripts/openbabel-python.i: Added casting methods for all of the
  	different types of OBGenericData
........
  r2806 | ghutchis | 2008-12-17 12:39:32 -0500 (Wed, 17 Dec 2008) | 2 lines
  
  Added #include <limits> from r2765. Should solve Noel's build problems.
........
  r2807 | ghutchis | 2008-12-17 15:09:12 -0500 (Wed, 17 Dec 2008) | 2 lines
  
  Added #include <limits> to hopefully help Noel with his compile problems.
........
 2009-03-24 20:49:13 +00:00
Noel O'Boyle
b37217aa52 2008-07-01 Noel O'Boyle <baoilleach@gmail.com> 
* scripts/openbabel-python.i: Make the BFS Iterator return two values,
	the Atom and the depth
 2008-07-01 13:25:05 +00:00
Noel O'Boyle
625a89e365 * Reverted r2535 except for changes to scripts/perl/Makefile.PL 
* scripts/openbabel-python.i: Updated SWIG interface file to ignore 21 methods of each std::vector created. This should substantially reduce the size of the wrapper code
 2008-06-17 19:03:50 +00:00
Geoffrey Hutchison
024240cd78 Split python bindings into multiple pieces. Should solve PR#1905826. 2008-06-05 22:42:47 +00:00
Tim Vandermeersch
844b134f09 * scripts/openbabel-python.i: Add OBBitVec. 2008-05-03 12:39:27 +00:00
Tim Vandermeersch
596d57d9b4 * scripts/openbabel-python.i: Added OBForceField::SetLogToStdOut() and 
OBForceField::SetLogToStdErr() to replace SetLogFile(std::ostream
        *pos) in python.
 2008-04-29 19:02:16 +00:00
Noel O'Boyle
b7eeaf4666 2008-03-24 Noel O'Boyle <baoilleach@gmail.com> 
* scripts/openbabel-python.i: Added griddata.h
 2008-03-24 09:54:17 +00:00
Noel O'Boyle
6b982f8973 scripts/openbabel-python.i: Fix for bug reported by Florian Nigsch. The Python iterators didn't correctly handle the case where there was nothing to iterate over. 2008-03-23 09:28:40 +00:00
Chris Morley
d75ea041e1 Replacement for strcasestr, allow cmlformat to be compiled without shared_ptr, etc 2008-03-14 17:44:00 +00:00
Noel O'Boyle
1ed335313e 2008-02-29 Noel O'Boyle <baoilleach@gmail.com> 
* scripts/openbabel-python.i: Bugfix for "[ 1904345 ] Angle, Pair,
        Torsion iterators dones not have deref() method". Turns out that I
        could have been using the __ref__() method all along. This doesn't
        seem to be in the SWIG documentation though.
 2008-02-29 09:58:15 +00:00
Chris Morley
c6b8d931df Small revision of python bindings 2008-01-19 09:36:23 +00:00
Chris Morley
eb0050dbfe Get SWIG for Python to compile 2008-01-16 18:05:02 +00:00
Noel O'Boyle
0a34b924d0 Updated openbabel-python.i to allow compilation. 2008-01-16 10:55:01 +00:00
Geoffrey Hutchison
858f8a39f9 * Merged in changes from 2.1.x branch. 2007-09-03 20:53:06 +00:00