David Koes
59a8d6c4de
Merge branch 'obrms_enhancement'
2019-05-03 17:17:03 -04:00
David Koes
b7d7a0690a
Merge branch 'obrms_enhancement' of github.com:dkoes/openbabel into obrms_enhancement
2019-04-25 16:36:15 -04:00
David Koes
85ccd84950
fix firstonly logic and extend man page
2019-04-25 16:35:48 -04:00
David Koes
365bc41add
Merge pull request #4 from baoilleach/myobrms
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Add include for obutil.h now required on git master
2019-04-14 19:01:24 -04:00
Noel O'Boyle
7d4caabadf
Add include for obutil.h now required on git master
2019-04-14 21:05:34 +01:00
David Koes
5cba863890
Merge pull request #3 from baoilleach/myobrms
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Fix MSVC build
2019-04-14 09:17:05 -04:00
Noel O'Boyle
75cf2f7323
Ensure that obrms is compiled with getopt.c. Simplify the logic for the three tools that need this handling.
2019-04-14 08:16:53 +01:00
Noel O'Boyle
e486f8a056
Ensure that obrms is compiled with getopt.c. Simplify the logic for the three tools that need this handling.
2019-04-13 21:12:56 +01:00
David Koes
f124c6e50e
try alloca for windows build
2019-04-11 12:08:11 -04:00
David Koes
173c33e686
remove boost dependency from cmake file
2019-04-10 15:32:05 -04:00
David Koes
92281ff4d8
remove boost dependency
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"this shouldn't take too much time" <--- WRONG!
This also fixes the incorrect documentation for the -f option.
2019-04-10 15:28:39 -04:00
David Koes
32c9c5e125
enhancements to obrms to support optimization of pose alignment
2019-04-09 15:52:07 -04:00
David Koes
0167820fa8
edit
2019-04-09 15:47:11 -04:00
David Koes
d0951662e3
Merge branch 'openbabel'
2019-04-09 15:07:25 -04:00
Noel O'Boyle
dd3d14a312
Merge pull request #1960 from openbabel/revert-1952-updatestereo
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Revert "Remove outdated stereo code"
2019-04-07 19:06:51 +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Revert "Remove outdated stereo code"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Remove outdated stereo code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
355ddf945f
Merge pull request #1951 from baoilleach/flags
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Tidy setting/unsetting of molecule perception flags
2019-04-07 14:09:28 +01:00
Noel O'Boyle
cd85a984a4
Merge pull request #1946 from baoilleach/refactorpython
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Refactor python bindings so that openbabel.py and pybel.py are within an openbabel folder
2019-03-25 20:01:17 +00:00
Noel O'Boyle
d02ff77546
Merge pull request #1 from mcs07/refactorpython
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Fix independent python bindings install
2019-03-23 13:09:21 +00:00
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
230b6138c4
Merge pull request #1948 from baoilleach/cmakewarnings
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Address CMake build warning about policy CMP0005 being set to OLD
2019-03-21 20:49:30 +00:00
Noel O'Boyle
1b2a68d9e1
Get rid of unused stereo flags in OBBond and their associated methods. Comment out bitrotted code that still used old stereo IsUp() and IsDown().
2019-03-19 20:53:14 +00:00
Noel O'Boyle
f41e8915fc
Get rid of OBEdgeBase typedef.
2019-03-19 20:33:22 +00:00
Noel O'Boyle
3fae840b97
Drive-by fix for Python tests on Windows
2019-03-19 13:53:58 +00:00
Noel O'Boyle
699b4eed28
Correct setting of environment variables for tests
2019-03-19 13:39:21 +00:00
Noel O'Boyle
d1958e571d
Update one of the Python tests for the API changes
2019-03-19 07:30:45 +00:00
Noel O'Boyle
3c3e23c781
In the interests of time, retain current behavior of OBMol::IsChiral in mdlformat.cpp and reportformat.cpp. File bug to fix it.
2019-03-19 07:21:27 +00:00
Noel O'Boyle
df6af57484
Part of previous commit
2019-03-17 21:23:44 +00:00
Noel O'Boyle
e6c72e167d
Remove OBMol::IsChiral(). It doesn't check whether the molecule is chiral, nor is there any easy way to implement this quickly.
2019-03-17 21:20:30 +00:00
Noel O'Boyle
3a851128d3
Remove obchiral executable as it uses the old chirality. Also, it's functionality is covered by the report format. I think. In theory.
2019-03-17 21:18:37 +00:00
Noel O'Boyle
7cc1d51331
Update bindings for lack of ChiralData
2019-03-17 20:20:43 +00:00
Noel O'Boyle
31318d0f75
Remove stereo code deprecated since Tim's rewrite back in 2009.
2019-03-17 14:23:33 +00:00
Noel O'Boyle
cf0f7ac915
1. Remove "Unset" methods for mol flag perception flags. [API break]
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2. Ensure that all mol flag perception settings methods take a boolean for setting/unsetting. [API extension]
3. Move HasFlag and SetFlag to the public API. Consider the case where the user wants to set a custom flag. [API addition]
2019-03-17 12:19:50 +00:00
Noel O'Boyle
8cd1e9723a
Merge pull request #1949 from baoilleach/FixStaticInit
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Fix clang warning about in-class init of a non-static data member
2019-03-10 21:29:46 +00:00
Noel O'Boyle
150a9a06cc
Fix clang warning about in-class init of a non-static data member
2019-03-10 11:17:46 +00:00
Noel O'Boyle
43ae14e932
Remove policy statement for CMP0005 as no longer needed
2019-03-09 21:07:41 +00:00
Noel O'Boyle
31cb9a3062
Don't cache OB_MODULE_PATH as it can get stuck on the wrong value even if you change . Don't define it with add_definitions, as it's already set in babelconfig.h and it causes a redefinition warning.
2019-03-09 21:01:15 +00:00
Noel O'Boyle
82396bb9fa
Set cmake policy CMP0005 to NEW to get rid of warning
2019-03-09 20:46:38 +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
David Koes
Noel O'Boyle
Matt Swain