github.com/openbabel/openbabel commits | Ecosyste.ms: OpenCollective

Merge pull request #1954 from baoilleach/obrandom

Remove OBRandom from the public API

fbc4bf36a0d38058ef32062194e2f606f19d24c1 authored over 5 years ago by Noel O'Boyle <[email protected]>

Update usage of GetBO() in Python tests

e3f437edfefceb6ba247ad361e0f37426f0b487e authored over 5 years ago by Noel O'Boyle <[email protected]>

Remove OBBond::GetBO() and SetBO()

9a2c758e51857ccc18996a614c4b5a68d9f76b7c authored over 5 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1964 from baoilleach/RemoveDataFunction

Remove GetGenericValueDef from OBGenericData

04db1f33db81954993dbe86b75305a29eb47c922 authored over 5 years ago by Geoff Hutchison <[email protected]>

Merge pull request #1966 from baoilleach/FixGradientTest

Fix randomly failing Python gradient test

2016d2fe5da247d6008a3175f33c821b2aeff3e2 authored over 5 years ago by Noel O'Boyle <[email protected]>

smilesformat.cpp doesn't actually use OBRandom. It just calls rand().

67316c21aaa1fba25cb14b2277ed3cd144d5ca3c authored over 5 years ago by Noel O'Boyle <[email protected]>

Tidy up by making more methods static

ac77f64f8764b20b7d5c70279ad1b8f7ae00ae45 authored over 5 years ago by Noel O'Boyle <[email protected]>

Update bindings for lack of rand.h

7330eff772ca7aa50bd3312fcf06949ac4dfb2f8 authored over 5 years ago by Noel O'Boyle <[email protected]>

Remove OBRandom from the public API. It is still present in the codebase, and no behaviour has been changed.

00178ce70b98c85047aa247060fbaa30ead9d1f7 authored over 5 years ago by Noel O'Boyle <[email protected]>

The gradient test was failing randomly. This fixes it by ensuring that Energy() is called first.

3f6b0b0a547bcb5496a1ed316e6b93c371ab5ed8 authored over 5 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1963 from baoilleach/updatebindings

Update bindings for changes to headers

4c5a54699ecfc7bc081aa3de94a212ec79b248ca authored over 5 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1961 from dkoes/obrms_enhancement

enhancements to obrms to support optimization of pose alignment

e0ac680eb9ce4e2626f6640e069943d607f34af9 authored over 5 years ago by Geoff Hutchison <[email protected]>

Merge pull request #4 from baoilleach/myobrms

Add include for obutil.h now required on git master

365bc41add16b671e0071908053d3e0aacfb1eaf authored over 5 years ago by David Koes <[email protected]>

Update bindings for changes to headers

3b63eed7b26db36d98bf73950b1712d5dd1441e2 authored over 5 years ago by Noel O'Boyle <[email protected]>

Add include for obutil.h now required on git master

7d4caabadf405987f25f01a4e983a4e7f669d7db authored over 5 years ago by Noel O'Boyle <[email protected]>

Merge pull request #3 from baoilleach/myobrms

Fix MSVC build

5cba863890635034fdce5460b0d0d0f7d3a68745 authored over 5 years ago by David Koes <[email protected]>

Ensure that obrms is compiled with getopt.c. Simplify the logic for the three tools that need this handling.

75cf2f73232a42f1792d5fcc5c2c267803c55d3a authored over 5 years ago by Noel O'Boyle <[email protected]>

Ensure that obrms is compiled with getopt.c. Simplify the logic for the three tools that need this handling.

e486f8a0561b1f0a1302d2122e662291a901bbb1 authored over 5 years ago by Noel O'Boyle <[email protected]>

Remove GetGenericValueDef from OBGenericData

b00c7beec138ba09cd7d55246074b0ae90c10dcf authored almost 6 years ago by Noel O'Boyle <[email protected]>

try alloca for windows build

f124c6e50e2b7c6528bde68b247d65b355864882 authored almost 6 years ago by David Koes <[email protected]>

Merge pull request #1958 from baoilleach/MolHeader

Remove miscellanous headers from mol.h, atom.h and bond.h

6aff822f8d37074eebcd1901628623ea1b97f6ae authored almost 6 years ago by Noel O'Boyle <[email protected]>

Merge branch 'master' into TryRebase

455554ace650b8c5477c748ae2ac706b65f5421c authored almost 6 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1 from openbabel/master

Update upstream commits

f63e1037882812ea9a8c16518d3498371613b337 authored almost 6 years ago by Yi-Shu Tu <[email protected]>

remove boost dependency from cmake file

173c33e686c7eb4fcd6c0899f447b1e258eb0552 authored almost 6 years ago by David Koes <[email protected]>

remove boost dependency

"this shouldn't take too much time" <--- WRONG!

This also fixes the incorrect documentation for ...

92281ff4d8dcfea75b2606545feecd283558e611 authored almost 6 years ago by David Koes <[email protected]>

Merge pull request #1959 from baoilleach/testoutput

For Travis builds, include output for build failures

4b043767b65881572f3a2c2aa4454efbe3d28703 authored almost 6 years ago by Geoff Hutchison <[email protected]>

enhancements to obrms to support optimization of pose alignment

32c9c5e125213846bd4981fab3a2ea7a0687e31f authored almost 6 years ago by David Koes <[email protected]>

edit

0167820fa80a7d69a62b509836bad1376254ad56 authored almost 6 years ago by David Koes <[email protected]>

Merge branch 'openbabel'

d0951662e34de071f8601d2b4ca2549c7ba324b8 authored almost 6 years ago by David Koes <[email protected]>

Merge pull request #1960 from openbabel/revert-1952-updatestereo

Revert "Remove outdated stereo code"

dd3d14a312845e200d0b99cf02cb8d91a8838b5c authored almost 6 years ago by Noel O'Boyle <[email protected]>

Revert "Remove outdated stereo code"

71128d38a8012216b8e87b2fe33721f1f86e0c04 authored almost 6 years ago by Noel O'Boyle <[email protected]>

For Travis builds, include output for build failures

b9f62eec9c101353ec4bba01656de09a0081679b authored almost 6 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1952 from baoilleach/updatestereo

Remove outdated stereo code

e72f2e400be200d118ac287bf80da85003e750ef authored almost 6 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1951 from baoilleach/flags

Tidy setting/unsetting of molecule perception flags

355ddf945f52a7090c5b6d9e063f7303bc07b125 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Use hex encoding for cent symbol as causing compile problems

cf3b851d49ffc519ef52688493372fb588151931 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Fix genbank format

971955597166fcae195b1a52fb02d1bcda2aca9a authored almost 6 years ago by Noel O'Boyle <[email protected]>

Add c standard libs required for g++ builds.

63b166249f1ec5df4d8326cd41fb187bf08b1a4a authored almost 6 years ago by Noel O'Boyle <[email protected]>

Fix compile problem and get rid of warnings.

1951ea9b80923ec68d3e818dedf604b365a57a67 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Fix linking problem regarding multiply defined stringbuf symbol by including oberror.h (!?). It looks like having OBMessageHandler subclass std::stringbuf may be the root cause.

58c1feea046265301c73c7c14ef7e8cd57b9c6bb authored almost 6 years ago by Noel O'Boyle <[email protected]>

Everything else

c047a594aeb4933add432ab5f09420e626d15cc9 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Add descs, charges, ffs

b02db7c0c423009bcb86fba9fb2788cf233e4f15 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Charges

aa2cbf0ebdcbaeab843f2aef74e4aa8632e208d1 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Final misc

bd20e68893cb4875ee45d033da7c0577ed0c422e authored almost 6 years ago by Noel O'Boyle <[email protected]>

Misc part I

450b4a77be1b9ea42929affa5196bfe6c0936217 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Utility formats

b27a5b96d372a734715c08cabbae4aac16f0194b authored almost 6 years ago by Noel O'Boyle <[email protected]>

Update tools

50944923976a1a7ef47056406f67104ada2dab77 authored almost 6 years ago by Noel O'Boyle <[email protected]>

More formats

c28c7dc86db1f415c0a60abeb94497d49161ff8d authored almost 6 years ago by Noel O'Boyle <[email protected]>

More formats

a7e4083902be92681f5d04b99d6ee7951a08304f authored almost 6 years ago by Noel O'Boyle <[email protected]>

Get compchem formats to compile

1f111e32f9c34be0c27b59d1acea8f8e1fe10971 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Move the externs from mol.h into wherever their class is declared. Get the first few formats compiling.

a3f5515981066abee1f2b46aa55484f7585d329d authored almost 6 years ago by Noel O'Boyle <[email protected]>

Remove more includes in headers

9c8579b638a7ef32f184437fcce81bbb0ac6b423 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1946 from baoilleach/refactorpython

Refactor python bindings so that openbabel.py and pybel.py are within an openbabel folder

cd85a984a439314d090fab76f0520061939fe6bf authored almost 6 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1 from mcs07/refactorpython

Fix independent python bindings install

d02ff77546be84c059bf0eb907308970f4a5765f authored almost 6 years ago by Noel O'Boyle <[email protected]>

Simplify OB version check in setup.py

5c8165e496c2e081bde3df56d4635bef466dd369 authored almost 6 years ago by Matt Swain <[email protected]>

Update setup.py to install into openbabel package

46c9e1f8fd136ee73d92a3946644259abf17e0c6 authored almost 6 years ago by Matt Swain <[email protected]>

Improved OB version check in setup.py

d05a47ede9f8b731abc5e417bba097d5dfbd9ca6 authored almost 6 years ago by Matt Swain <[email protected]>

Simplify pkg-config wrapper in setup.py

0910928392da28f4957d2a6e14bfedbaea37e1eb authored almost 6 years ago by Matt Swain <[email protected]>

Simplify metadata in setup.py

59792513e37a8979cfaa6957d7450da0a0c8b38f authored almost 6 years ago by Matt Swain <[email protected]>

Find version from __init__.py to avoid hardcoding in setup.py

bd031bcaa85b591df047f3e83b153abb706d3853 authored almost 6 years ago by Matt Swain <[email protected]>

Simplify setup.py long_description

9e2915515551f7afc7cc3d2403af684da4c18817 authored almost 6 years ago by Matt Swain <[email protected]>

Fix setup.py indentation

1d71075f199aff5a7f9e2d1cd173bc2d44fe3f68 authored almost 6 years ago by Matt Swain <[email protected]>

Merge pull request #1948 from baoilleach/cmakewarnings

Address CMake build warning about policy CMP0005 being set to OLD

230b6138c401bebeca1a0e1a2ed47caaba0afa4c authored almost 6 years ago by Noel O'Boyle <[email protected]>

Get rid of unused stereo flags in OBBond and their associated methods. Comment out bitrotted code that still used old stereo IsUp() and IsDown().

1b2a68d9e1893c5c9e29a7aa02a7be0554764345 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Get rid of OBEdgeBase typedef.

f41e8915fc72fccd3357843fdac23cf89f3df3a7 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Drive-by fix for Python tests on Windows

3fae840b97876a1be54b2b702a49a18bc8866450 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Correct setting of environment variables for tests

699b4eed285b73fdc5b68f7fa268fae73d789d53 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Initial attempt

6fedf40dd179f8dc8e6c50ae800e70f192815994 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Update one of the Python tests for the API changes

d1958e571d5126d98eb730f22e93c1122898cf9d authored almost 6 years ago by Noel O'Boyle <[email protected]>

In the interests of time, retain current behavior of OBMol::IsChiral in mdlformat.cpp and reportformat.cpp. File bug to fix it.

3c3e23c781396df82cfde58b3178917324f2486d authored almost 6 years ago by Noel O'Boyle <[email protected]>

Part of previous commit

df6af57484f336a389fc6441ff57d44129deba06 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Remove OBMol::IsChiral(). It doesn't check whether the molecule is chiral, nor is there any easy way to implement this quickly.

e6c72e167d4173734fb96777154142ee2ae604c5 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Remove obchiral executable as it uses the old chirality. Also, it's functionality is covered by the report format. I think. In theory.

3a851128d323e31da19c24bbda2b8d4cb8e20098 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Update bindings for lack of ChiralData

7cc1d51331231a2c888557fa369714f88872bba6 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Remove stereo code deprecated since Tim's rewrite back in 2009.

31318d0f755e133e0ca214abc228e19324b7e18b authored almost 6 years ago by Noel O'Boyle <[email protected]>

1. Remove "Unset" methods for mol flag perception flags. [API break]

2. Ensure that all mol flag perception settings methods take a boolean for setting/unsetting. [AP...

cf0f7ac9154e08b84800724fe2698f159091671f authored almost 6 years ago by Noel O'Boyle <[email protected]>

Fix bug with writing periodic bonds to CIF

The coordinates in the atom and bond fields did not match because wrapping had been applied inco...

a46f12c4d7dcc3ab732e55c884f6e1567f13f3e5 authored almost 6 years ago by Ben Bucior <[email protected]>

Merge branch 'master' into periodic-boundaries

7319dbae3b0ae395a87831a498d66cdc3044e4b7 authored almost 6 years ago by Ben Bucior <[email protected]>

Merge pull request #1949 from baoilleach/FixStaticInit

Fix clang warning about in-class init of a non-static data member

8cd1e9723ae4fe365aa7057973943009a0b93741 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Fix clang warning about in-class init of a non-static data member

150a9a06cc39cae9141a3d0260360dce7f3d8eaf authored almost 6 years ago by Noel O'Boyle <[email protected]>

Remove policy statement for CMP0005 as no longer needed

43ae14e932572e25f1b412e056d073ce40418839 authored almost 6 years ago by Noel O'Boyle <[email protected]>

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.

31cb9a3062267cd88f1a2c6d5eb8c10883723233 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Set cmake policy CMP0005 to NEW to get rid of warning

82396bb9fa05694f5a7aca64c60144ad5430898b authored almost 6 years ago by Noel O'Boyle <[email protected]>

Add the OB version in as a text string to the __init__.py via configure_file

978bc4f80ecbfacf84002fed11ba8cd6af6e41e1 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Make sure it works on Windows as before

044cbaafb2f2c53ed9d1fe53b0e192dd691bbc71 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Use Matt Swain's __init__.py hack to support 'import openbabel' but mark as deprecated

0c8c4d8d4e27faecfc75a7258c015255aa4431cf authored almost 6 years ago by Noel O'Boyle <[email protected]>

Use a relative import so that Python 3 (and 2) are happy

0cebc5bc08090876efd97f84a6c50f54fae3770b authored almost 6 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1931 from n-yoshikawa/fragment-based-builder-update

Update fragment based builder

6771e1042eccf94c82c981f310b1a922efb6c45b authored almost 6 years ago by Geoff Hutchison <[email protected]>

Revert "Update ring fragment template"

This reverts commit d515ebee4c7dd1ee3336a8a3d1c1044e7afaeee6.

aa481737dd3a1fed9470e96c1e94e1c16d7394e7 authored almost 6 years ago by Naruki Yoshikawa <[email protected]>

Update tests

5f58dd2a9035cd762bed4d0eeebb7dc3b207a376 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Do NOT cache the CMAKE_INSTALL_RPATH. Otherwise, if you are doing trying to do a local install but forget to set CMAKE_INSTALL_PREFIX the first time, it's too late! The cached value /usr/local/lib will be used for all RPATHs and you will only discover this when you try to import your Python library and it segfaults as it's found some other one in /usr/local/lib instead of in the local install dir.

a3b636b6f16c28e193245c91e97d43f83a0d1723 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1831 from JasonYCHuang/fix-cdxml-upside-down-format

Fix cdxml upside down format

13f02bd7cad86b2fa466f687cc3c69d1848e99dd authored almost 6 years ago by Geoff Hutchison <[email protected]>

Merge pull request #1945 from n-yoshikawa/fix-obsmartspattern-leak

Fix memory leak in OBSmartsPattern::Init()

1a731859033ae2421d396e60c64ca58fa6c04450 authored almost 6 years ago by Geoff Hutchison <[email protected]>

Merge branch 'master' into periodic-boundaries

fa505c4777c8a11534746e85d713d6297c73d0d1 authored almost 6 years ago by Geoff Hutchison <[email protected]>

Merge pull request #1902 from fredrikw/fix1900

Updated the coordinate generation from templates.

073e455341894ba071244c39e280d4926570f490 authored almost 6 years ago by Geoff Hutchison <[email protected]>

Merge pull request #1944 from pbecherer/cofformat

Add support for COF format plus tests

9d427c95d939a0f3926a618471c38aeb6636fb25 authored almost 6 years ago by Geoff Hutchison <[email protected]>

Install to an open babel subfolder

7a109535c1ecde99f50f0a94bb43be5981278411 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Add init.py

717b6567cbbc489670ddd7d2824716a839b2a919 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Merge pull request #1943 from baoilleach/Fix310

Revert "CMakeLists.txt: Allow configuring BABEL_DATADIR"

9bf3a3906478f44c1f0e51d206b38f6e5e05da46 authored almost 6 years ago by Noel O'Boyle <[email protected]>

Fix memory leak in OBSmartsPattern::Init()

634e08030e93d9ea1dc21abd872939ea5c74b730 authored almost 6 years ago by Naruki Yoshikawa <[email protected]>

Add support for COF format plus tests

Add support for COF format (Culgi object file) and add Python tests for converting COF to and fr...

22326d3abd522ea942339a32076bd2f9fc4f0f09 authored almost 6 years ago by Paul Becherer <[email protected]>