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
d4826d10c3
Rough implementation of Javascript IPython rendering
2013-09-29 17:48:43 -05:00
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
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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
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
Noel O'Boyle
2c9aa50fef
pybel.py: Fix for previous commit to remove tabs.
2012-06-26 13:49:31 +00:00
Noel O'Boyle
0e6c1f59ee
Simplify installation of Python bindings: Now there is only one version of pybel.py for Py 2.x and Py 3.x. It also includes support for Jython and IronPython.
2012-06-26 13:43:25 +00:00
Tim Vandermeersch
f30e3c476a
Removed pybel.py which has already been replaced
2009-07-18 22:34:38 +00:00
Noel O'Boyle
0f0799c777
2008-07-09 Noel O'Boyle <baoilleach@gmail.com>
...
* scripts/python/pybel.py: Bug fix for make3D for linear molecules.
Fixes bug 2014055. Minor doc fixes. Remember to close output files
in Molecule.write()
2008-07-09 12:04:52 +00:00
Noel O'Boyle
f94eab6d2a
2008-07-01 Noel O'Boyle <baoilleach@gmail.com>
...
* scripts/python/pybel.py: Make pybel use CloneData instead of SetData
2008-07-01 13:49:22 +00:00
Noel O'Boyle
79b8f3db20
Pybel: Synching with cinfony, and getting ready for release as 1.3
2008-05-23 08:19:28 +00:00
Noel O'Boyle
ea6d70b717
* scripts/python/pybel.py: Synch with cinfony
2008-05-07 07:01:06 +00:00
Noel O'Boyle
33495778f2
* scripts/python/pybel.py: First attempts at incorporating the recent work by Tim, Geoff and others on geometry optimisation and 3D coordinate generation.
2008-03-23 20:07:00 +00:00
Noel O'Boyle
37588a1d49
* scripts/python/pybel.py, scripts/python/examples/testpybel.py:
...
Updated to use plugin descriptors. Changed to create a single instance
of plugin descriptors and fingerprinters. Also, readfile now raises an
IOError if the file does not exist.
* scripts/python/examples/findcoverage.bat: Add .bat file to automate
calculation of code coverage for pybel
2008-01-17 12:08:31 +00:00
Geoffrey Hutchison
858f8a39f9
* Merged in changes from 2.1.x branch.
2007-09-03 20:53:06 +00:00
Noel O'Boyle
174b5452bf
* SWIG interface files: Added template for vectors of strings
...
* pybel.py: Added informats and outformats, dictionaries corresponding
to the supported input and output format
2007-05-12 11:45:39 +00:00
Noel O'Boyle
5d1cdec9c3
* pybel.py: Added support for unitcell, and deletion of OBPairData
...
(need to update the tests and the API docs)
2007-05-10 11:00:13 +00:00
Noel O'Boyle
8270b862df
2007-05-08 Noel O'Boyle <baoilleach@gmail.com>
...
* scripting interfaces: added a method to cast OBGenericData to
OBPairData
* pybel: added dictionary-like support for accessing molecule data,
and updated the tests and the API documentation
2007-05-08 12:33:05 +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
Noel O'Boyle
7caab0c0f7
* scripts/python/pybel.py, testpybel.py, pybelapi.html: Added a
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.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
Noel O'Boyle
71b835bcad
* scripts/python/setup.py, pyopenbabel.py, testpyopenbabel.py,
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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
