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b94f4b7f835777bc182d39a0a9c4f0b2a0fe8030
Commit Graph
341 Commits
Author SHA1 Message Date
Matt Swain b94f4b7f83 Add proper python README 
- Convert README to restructuredtext format so it displays correctly on PyPI
- Update email address to current mailing list
- Tidy up setup.py
 2014-01-20 17:58:42 +00:00
Geoff Hutchison e8ab151bc7 Merge pull request #61 from patrickfuller/pybel-charge 
Added a charge function
 2014-01-15 11:15:47 -08:00
Patrick Fuller 668536d591 Improved error messages of calccharges 2014-01-15 10:52:34 -06:00
Patrick Fuller 1612e84ef9 Small fix 2014-01-15 10:16:39 -06:00
Patrick Fuller e5ef11f521 Improvements to proposed pybel charge method 2014-01-15 10:05:46 -06:00
Geoff Hutchison 1fbaf45048 Make sure to remove the generated openbabel-ruby.txt temporary file. 2014-01-14 15:54:03 -05:00
Patrick Fuller 843ecae262 Added a charge function 2014-01-14 13:04:55 -05:00
S. Joshua Swamidass 42335bd889 missed setup.py in last committ 2014-01-05 08:57:27 -10:00
S. Joshua Swamidass 3cf839f34e Rewrote setup.py so that it can independentley install python bindings. Symbolic links to swig files added to enable this. 2014-01-05 08:51:47 -10:00
Geoff Hutchison 61772629ac Merge pull request #47 from Acpharis/csharp_build 
build CSharp bindings in SOURCE_DIR
 2014-01-05 09:54:30 -08:00
Patrick Fuller e0b2dc2c67 Changed url of 3d molecule viewer 2013-12-24 13:03:37 -05:00
Patrick Fuller d869efe9ac Reduced footprint of 3D ipython rendering 2013-12-23 16:24:52 -05:00
Patrick Fuller d02d57f3f9 2D/3D toggle now accessible by pybel.ipython_3d boolean 2013-12-09 09:38:12 -06:00
Patrick Fuller 995326303f pybel.py made PEP8 compliant 2013-12-08 20:49:10 -06:00
Patrick Fuller 57906e34d8 Merge branch 'master' of https://github.com/openbabel/openbabel into ipython-3d 2013-12-08 16:08:22 -06:00
Geoff Hutchison 155fcd9040 Merge pull request #42 from mwojcikowski/php-binding 
PHP binding enhancements
 2013-12-04 15:35:40 -08:00
Noel O'Boyle 8cf5f20dc7 Ruby bindings: Get rid of warning about shadowed function and enable compiling without Eigen 2013-11-28 21:19:15 +00:00
mwojcikowski 4475745b8f Change openbabel.php path to CMake install prefix in Baphpel. 2013-11-28 17:12:40 +01:00
Maciek Wójcikowski 20ef0d774f PHP binding enhancement. Add BaPHPel interface. 2013-11-28 11:01:12 +01:00
khoran 1a63ab8080 Add R to ALL_BINDINGS, fix EIGEN dependancy issue. 
The forcefield.h file causes a build error if the EIGEN
library is not included, so I move it into the
HAVE_EIGEN section in the openbabe-R.i file.
 2013-11-27 22:20:59 -05:00
khoran 4186ea5776 added README, a test file and an example R package 2013-11-27 22:20:59 -05:00
khoran d30dd4b01c added R swig interface 
all compiles now
 2013-11-27 22:20:59 -05:00
Noel O'Boyle a979ef4992 Update Java, Perl and Python bindings to work without Eigen installed. More bindings to come.~ 2013-11-27 22:20:12 -05:00
Reinis Danne 99c1427c75 scripts/openbabel-python.i: Revert shared_ptr changes 
This reverts part of ce178cbbd3.
 2013-11-27 22:20:11 -05:00
Patrick Fuller cb2af57d4b Merge branch 'master' of https://github.com/openbabel/openbabel into ipython-3d 2013-11-19 19:14:51 -06:00
David Hall 2d7a834456 build CSharp bindings in SOURCE_DIR 2013-11-19 19:50:50 -05:00
David Hall 2ae9cccc76 Use Python Library version of the found Python Interpreter 
If you have python2 at /usr/bin/python , but also
have python3 libraries and header files installed,
CMake will use the python2 interpreter, but the
python3 libraries. This causes the python libraries
found to have the same major and minor version as
the interpreter.
 2013-10-21 18:33:20 -04:00
David Hall 4f6984e55f install python libraries in python site-packages directory instead of /usr/lib 2013-10-21 18:32:23 -04:00
Patrick Fuller d4826d10c3 Rough implementation of Javascript IPython rendering 2013-09-29 17:48:43 -05:00
Reinis Danne 3ca6aa3d6f scala: Add an example program in Scala using Java bindings 2013-09-24 19:13:17 +03:00
Reinis Danne 5537dc3276 cmake: Enable to build PHP bindings only 2013-09-24 16:48:59 +03:00
Reinis Danne ed54d502f7 cmake: Enable to build Java bindings only 2013-09-23 13:48:36 +03:00
Reinis Danne 38d842dec9 cmake: Enable to build Ruby bindings only 2013-09-22 14:09:05 +03:00
Reinis Danne 62b8998850 cmake: Enable to build Perl bindings only 2013-09-22 14:09:05 +03:00
Reinis Danne 5cb0104495 cmake: Enable to build bindings only 
So that don't have to rebuild OB just to add bindings. It allows to,
e.g., test Python bindings against multiple Python versions without
requiring to rebuild OB for each version.

Bindings form separate component to enable their installation using
command like this:
cmake -DCOMPONENT=bindings_python -P cmake_install.cmake

I have not looked at other bindings yet, but I think they should follow
similar approach.

--
In Gentoo we are providing separate packages for bindings and with
distutils it was very simple to build against system installation of OB
with a small change to setup.py:
 obExtension = Extension('_openbabel',
                  [os.path.join(srcdir, "openbabel-python.cpp")],
-                 include_dirs=[os.path.join(srcdir, "..", "..", "include"),
-                               os.path.join("..", "include")],
-                 library_dirs=[os.path.join(srcdir, "..", "..", "lib"),
-                               os.path.join(srcdir, "..", "..", "lib64"),
-                               os.path.join("..", "lib")],
+                 include_dirs=[os.path.join("/usr", "include", "openbabel-2.0")],
                  libraries=['openbabel']
                  )

With new build system for bindings it is not quite that straightforward.
 2013-09-22 14:09:05 +03:00
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
Maciek Wójcikowski c08ee72af1 Switch PHP example to SVG - it's the useful part. Include proper openbabel.php 2013-04-10 11:03:45 +02:00
Maciek Wójcikowski c4992a2286 Add example file. 2013-04-10 11:00:21 +02:00
Maciek Wójcikowski 8de17fb234 Remove PHP library searching by cmake, since it's not used. Remove files generated by SWIG. 2013-04-10 10:52:18 +02:00
Maciek Wójcikowski 2374f74a11 Fix building of PHP module. Ignore undefined symbols, since they're loded by PHP. 2013-04-10 10:17:00 +02:00
Maciek Wójcikowski 83f7091067 Fix filename. 2013-04-09 13:26:32 +02:00
Maciek Wójcikowski 97302b1ec6 Initial commit of PHP compiled via cmake. 2013-04-09 13:05:34 +02:00
Maciek Wójcikowski 9c5bad432e Fix documentation of residues in pybel 2013-03-20 13:33:34 +01:00
Geoff Hutchison e4804d9c26 Merge pull request #1 from mwojcikowski/master 
Fix missing LPMD file in src/format
 2013-03-15 11:10:28 -07:00
Maciek Wójcikowski 7c8a9b6327 Pybel residue support 2013-03-06 13:26:38 +01:00
Björn Grüning 006a9351ad add ConvertDativeBonds to pybel 2013-03-05 23:37:00 +01:00
Geoff Hutchison f01160d071 Fix non-Darwin Makefile generation for Ruby. 
Patch contributed by Christoph Willing, #58
https://sourceforge.net/p/openbabel/patches/58/
 2013-02-28 18:28:20 -05:00
Noel O'Boyle df59c4a630 Drat! Trival fix to re-enable Molecule.draw() after recent changes to PNG2. 2012-10-29 15:26:47 +00:00
Reinis Danne 7366f780bb setup.py: There are no separate pybel_pyX.py files anymore 2012-10-15 12:18:03 +00:00