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470 Commits
Author SHA1 Message Date
David KoesandDavid Koes 4b5d4c426f IsElement implemention, make OBElements::Element enum (#1754) 
* IsElement implemention, make OBElements::Element enum

* Fix php include.  Consistent renaming.

Resname all the single character residue constants.  Do this instead of
defining natively in python since the actual constants are arbitrary and
so could change (unlike elements)

Co-authored-by: David Koes <dkoes@beefy.dcb.private.net>
 2020-05-03 15:25:03 -04:00
Noel O'Boyle 15552f7f62 Merge pull request #2186 from baoilleach/workaroundswigjava 
Workaround for SWIG 4.0.1 Java source code problem
 2020-05-02 13:50:59 +01:00
Noel O'Boyle 839415aa61 Workaround a problem in SWIG 4.0.1 (at least) where the generated Java source relies on reserve being present 2020-05-02 12:41:42 +01:00
Maksim Rakitin fe72644433 Do not use six 2020-04-06 21:53:11 -04:00
Maksim Rakitin 08b7fc9b59 Fix the import of Tkinter in Python 3+ 2020-04-03 14:03:31 -04:00
kevin aac13e34cf R script updates (#2145) 
* changes for building ChemmineOB
* removed some local changes
 2020-04-03 11:35:26 -04:00
Noel O'Boyle 686ee22f21 Merge pull request #2124 from baoilleach/CastStereoBase 
Enable casting to StereoBase in the Python bindings
 2020-02-20 21:34:45 +00:00
Noel O'Boyle efaa11d91c Add cast to StereoBase 2020-02-03 21:08:06 +00:00
Noel O'Boyle cd07cc0680 Correct the path to the openbabel-python.cpp so that the Python bindings can be built directly from the source release (i.e. without SWIG). 2020-01-20 20:46:21 +00:00
Eisuke Kawashima 7bf2ec203f Update scripts/python/setup.py 2019-10-11 16:43:46 +09:00
Eisuke Kawashima 8a8ede202b Update INSTALL and READMEs under scripts/ [ci skip] 
- perl
    - assume perl-binding version is different from Open Babel's
- python
    - assume tarball from github release page
    - note: `python scripts/python/setup.py install` does not work since `__init__.py` is missing
 2019-10-11 16:06:16 +09:00
Eisuke Kawashima b657ca216c Fix import of openbabel 2019-10-10 16:54:59 +09:00
Geoff Hutchison 72e74f8324 Fix CMake error with R and C# bindings 2019-10-03 16:25:39 -04:00
David Koes 9dc3400028 Merge remote-tracking branch 'openbabel/master' into some_tests 2019-09-19 13:45:41 -04:00
Noel O'Boyle c9daca8f2a Update the CSharp bindings 2019-09-12 15:43:41 +01:00
David Koes 2694e44605 Merge remote-tracking branch 'upstream/master' into some_tests 2019-09-03 22:46:08 +01:00
David Koes 20a47d77c1 Merge branch 'master' into some_tests 2019-07-28 22:36:18 -04:00
Yi-Shu Tu 2a333f90ab typo fix 2019-07-10 11:06:57 +08:00
Yi-Shu Tu 4d312ea42b update the docstring, remove old properties 
old properties will raise the error
 2019-07-10 10:59:21 +08:00
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 
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
dkoes f69ef54441 Merge remote-tracking branch 'openbabel/master' 2019-05-03 19:10:03 -04:00
David Koes 59a8d6c4de Merge branch 'obrms_enhancement' 2019-05-03 17:17:03 -04:00
Noel O'Boyle 532ca37c32 Merge pull request #1970 from e-kwsm/improve-python 
Improve python script
 2019-04-18 08:26:25 +01:00
Noel O'Boyle d28440de93 Merge pull request #1971 from yishutu/pybel_with 
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 
- `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 
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