Yi-Shu Tu
a3700549ad
Make pybel compatible with #1975
2019-07-08 15:32:13 +08:00
David Koes
30fcd3163e
Address Ubuntu bug in defining python install dir
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See https://bugs.launchpad.net/ubuntu/+source/python3-defaults/+bug/1814653
Fix might be slightly fragile - not sure if it would be better to check
for Ubuntu 18.04 directly
2019-06-04 15:02:35 -04:00
Noel O'Boyle
532ca37c32
Merge pull request #1970 from e-kwsm/improve-python
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Improve python script
2019-04-18 08:26:25 +01:00
Noel O'Boyle
d28440de93
Merge pull request #1971 from yishutu/pybel_with
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Make `pybel.Outputfile` compatible with `with` statment
2019-04-18 08:24:04 +01:00
Yi-Shu Tu
26f192587f
Add __entry__ and __exit__ methods to pybel.Outputfile
2019-04-18 14:13:00 +08:00
Eisuke Kawashima
6b57788a05
Improve python script
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- `from __future__ import print_function`
- replace deprecated `unittest.TestCase.assertEquals` with
`assertEqual`, `assertTrue`, or `assertFalse`
- use `obj is None` instead of `obj == None`
- remove modules and functions that are imported but not used
2019-04-17 21:59:20 +09:00
Noel O'Boyle
f96f03580e
Update bindings for lack of ChiralData
2019-04-16 09:21:03 +01:00
Noel O'Boyle
7330eff772
Update bindings for lack of rand.h
2019-04-15 20:54:45 +01:00
Noel O'Boyle
00178ce70b
Remove OBRandom from the public API. It is still present in the codebase, and no behaviour has been changed.
2019-04-15 20:54:44 +01:00
Noel O'Boyle
3b63eed7b2
Update bindings for changes to headers
2019-04-14 21:16:00 +01:00
Noel O'Boyle
455554ace6
Merge branch 'master' into TryRebase
2019-04-11 13:10:11 +01:00
Noel O'Boyle
71128d38a8
Revert "Remove outdated stereo code"
2019-04-07 17:57:22 +01:00
Noel O'Boyle
e72f2e400b
Merge pull request #1952 from baoilleach/updatestereo
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Remove outdated stereo code
2019-04-07 14:10:30 +01:00
Noel O'Boyle
c047a594ae
Everything else
2019-04-04 20:20:04 +01:00
Matt Swain
5c8165e496
Simplify OB version check in setup.py
2019-03-23 11:22:43 +00:00
Matt Swain
46c9e1f8fd
Update setup.py to install into openbabel package
2019-03-21 23:56:54 +00:00
Matt Swain
d05a47ede9
Improved OB version check in setup.py
2019-03-21 23:55:23 +00:00
Matt Swain
0910928392
Simplify pkg-config wrapper in setup.py
2019-03-21 23:53:54 +00:00
Matt Swain
59792513e3
Simplify metadata in setup.py
2019-03-21 23:52:09 +00:00
Matt Swain
bd031bcaa8
Find version from __init__.py to avoid hardcoding in setup.py
2019-03-21 23:50:12 +00:00
Matt Swain
9e29155155
Simplify setup.py long_description
2019-03-21 23:48:16 +00:00
Matt Swain
1d71075f19
Fix setup.py indentation
2019-03-21 23:46:51 +00:00
Noel O'Boyle
7cc1d51331
Update bindings for lack of ChiralData
2019-03-17 20:20:43 +00:00
Noel O'Boyle
978bc4f80e
Add the OB version in as a text string to the __init__.py via configure_file
2019-03-07 21:08:02 +00:00
Noel O'Boyle
044cbaafb2
Make sure it works on Windows as before
2019-03-06 21:10:52 +00:00
Noel O'Boyle
0c8c4d8d4e
Use Matt Swain's __init__.py hack to support 'import openbabel' but mark as deprecated
2019-03-06 15:42:45 +00:00
Noel O'Boyle
0cebc5bc08
Use a relative import so that Python 3 (and 2) are happy
2019-03-05 20:49:50 +00:00
Noel O'Boyle
5f58dd2a90
Update tests
2019-03-04 20:45:27 +00:00
Noel O'Boyle
7a109535c1
Install to an open babel subfolder
2019-03-02 20:44:49 +00:00
Noel O'Boyle
717b6567cb
Add init.py
2019-03-02 20:44:06 +00:00
Noel O'Boyle
0f14880c01
Minor fix to Eigen definition
2019-02-28 21:34:03 +00:00
Noel O'Boyle
13fbcc822b
Initial changes
2019-02-27 21:06:04 +00:00
Noel O'Boyle
5937140d08
Merge branch 'master' into smilesrxn
2018-07-18 22:01:18 +01:00
Noel O'Boyle
a4c574a07d
Re-enable vector.clear() to allow wrapped std::vectors to be reused, with some possible (?) performance benefit.
2018-05-05 20:07:31 +01:00
an.nguyen
46df170c65
Remove OBChemTsfm.Init
2018-04-19 07:34:05 +02:00
Noel O'Boyle
115160c8e6
Move the facade code out into its own class and expand it
2018-04-18 20:24:53 +01:00
Noel O'Boyle
f9e8ba255c
Rename obpairtemplateint to OBPairInteger (like the C++ API typedef). Also might as well add OBPairFloatingPoint at the same time.
2018-04-18 20:24:53 +01:00
an.nguyen
e4752e459a
Add stereo + obfunctions + kekulize to ruby binding
2018-04-18 10:47:34 +02:00
Christoph Hille
56776d15a6
Using pillow instead of PIL
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The problem of PIL: the latest version is of 2009 and so there are dependency problems with the new version of numpy and matplotlib
I'm using python2.7 and conda. With pillow there are no dependency problems with the newest numpy and matplotlib versions and "the molecule drawing functianality" works well (y)
2018-04-18 00:02:59 +02:00
Matt Swain
5ae75deaaa
Fix linking of python bindings
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Don’t link against python on Mac, using “-undefined dynamic_lookup” to allow this.
2018-03-30 19:42:35 +01:00
Geoff Hutchison
615e5f515a
Merge pull request #1775 from baoilleach/DLOpenFlags
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In the Python bindings, reset the DL open flags after importing _openbabel
2018-02-11 20:40:15 -05:00
Noel O'Boyle
3b86b037b4
Move the setting and resetting of the DL open flags to where 'import _openbabel' occurs in openbabel.py
2018-02-11 08:31:02 +00:00
Noel O'Boyle
e287255158
Reset the DL open flags after loading the plugins.
2018-02-08 21:09:53 +00:00
Eloy Felix
336abe5694
removed OASA comment. OASA is not used anymore for 2D coordinates generation
2018-02-04 20:48:22 +00:00
Eloy Felix
4baf8a674b
add Molecule.make2D function, fixed test
2018-01-24 17:30:14 +00:00
Eloy Felix
06e233e2ca
add Molecule.make2D function
2018-01-24 16:49:44 +00:00
Noel O'Boyle
65074163ee
Compiling the Python bindings (at least) failed as OBBitVec was not yet defined. I've moved it before the mol.h include.
2018-01-10 20:39:37 +00:00
Noel O'Boyle
bb4bc5f521
Update bindings
2017-12-28 21:02:27 +00:00
Noel O'Boyle
1d9944fa0b
Refactor handling of atom classes. Store them as "Atom Class" data on
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the atom, rather than in an OBAtomClassData object on the molecule.
2017-12-28 21:02:27 +00:00
Noel O'Boyle
b893521c2e
Reduce Python bindings by 20% by avoiding adding methods from the iterated object to the iterator
2017-12-16 21:31:37 +00:00
Yi-Shu Tu
David Koes
Noel O'Boyle
Eisuke Kawashima
Matt Swain
an.nguyen
Christoph Hille
Geoff Hutchison
Eloy Felix