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

Merge pull request #383 from ghutchis/github-issue-template

Add a default issue template for Open Babel - Suggestions welcome

48116702f5a66f7014ebcfa98fae998fe7bbac47 authored almost 8 years ago

Add a default issue template for Open Babel Suggestions welcome

https://help.github.com/articles/creating-an-issue-template-for-your-repository/

acb448b73e46b81d98f241b1d9ef7236595955cf authored almost 8 years ago

Add an option to the canonical SMILES format to specify the timeout.

117b2e510c3c174e08d4e5dee71314e69ba126ea authored almost 8 years ago

Merge branch 'master' of github.com:openbabel/openbabel

25d4eb9c47f82885179671d992a9825b5457f046 authored almost 8 years ago

Merge branch 'fixglobalstate' of https://github.com/baoilleach/openbabel into fixglobalstate

c27e38c72c9b6c4a680d091c7cf7c52ee11cd02a authored almost 8 years ago

Ensure that the atom typers use the thread-safe SmartsPattern matcher API, and not the legacy one.

5fa93c418d953cc9de24341ecae57ccbf756655b authored almost 8 years ago

Minor fix for gcc compile

73c1301d455858ebc27ede37a6dd1bfe828c168b authored almost 8 years ago

Merge branch 'master' of github.com:dkoes/openbabel

75c3d3ba80c9896bc1e59aae5277fcc540edbaf8 authored almost 8 years ago

1. Avoid use of any "extern" globals in residue.cpp/.h.

2. Remove pointless code that appended missing keys to residue or elem arrays and returned their ...

443f364ba00daade5f3d33fa16f41f69c6b40305 authored almost 8 years ago

Update README.md

ee58e94cc26304f5efd4ff2c6530a7fd6271f4de authored almost 8 years ago

Fix race condition: Class parameter _mlist replaced by local variable

243df96002561f66c061c3aad952e2d87784c503 authored almost 8 years ago

Fix race-conditions: Replace use of object parameter with local variable.

fa7200cc9d4c724a12d591383ec454f253b4958b authored almost 8 years ago

Make OBAromaticTyper thread safe by moving the molecule state to be local to the AssignAromaticFlags() function.

Note: API Change.

697b92180f9f61f738ef3e5c04d30340b9f8ee8e authored about 8 years ago

Usage of ctypes module for RTLD_GLOBAL to achieve python2/3 compatibility

776867aa63c389f3140053f3afd4a0ad8a3c58a7 authored about 8 years ago

Merge branch 'master' of github.com:openbabel/openbabel

98a9c6b8a1beb2a3a80a9d552a5f6028ff66314b authored about 8 years ago

Fix crash when reading more recent GAMESS vibration files.

28c87d9f1e97cd2476da08b1d1db9b9bd2a9f5ed authored about 8 years ago

Merge pull request #371 from nextmovesoftware/aromatictriplebond

Preserve triple bond when reading SMILES with a triple bond in an aromatic ring

e74427dae1965994d656eabb7f794479f5e13056 authored about 8 years ago

Fix bug #368: Python3.6 openbabel: No module named 'DLFCN'

The DLFCN module has been removed from python 3.6, as it is not
documented. Same funtionality ca...

92f4646d5cbf8d3291c66f9bff7ae61b6d535763 authored about 8 years ago

Preserve triple bond when reading SMILES with a triple bond in an aromatic ring.

6d082fe26925c804e8b3a8e70b8d846a45332db0 authored about 8 years ago

rms shenanigans

12bf013f077b6b307202292fabaf5ba1bd981d0d authored about 8 years ago

Merge pull request #343 from razziel89/patch_conformer_search

add support for customizations of filter and rotors used during conformer search and small bugfixes

74fe4f2505fb729252262c1f786cf28bdf61f3d2 authored about 8 years ago

Merge pull request #369 from derekharmon/master

SF #909 - Fix segfault when ReadMolecule() called with PubChem document but...

74b2c6a9537ffef8fffd2b4a586bb377719cc996 authored about 8 years ago

Merge pull request #370 from Acpharis/confab_zero_rotamers

Include original when there are zero rotatable bonds in confab

069d609b01d0d79aaec22241df9c363c2b7df47a authored about 8 years ago

Move to using if statement and different conditional

Move to using if statement at request of devs. I also think checking
for if the number of confor...

20fade0c026e55e59b222d514a71809cbe254ea6 authored about 8 years ago

Include original when there are zero rotatable bonds

If you don't include the original coordinates, confab currently
will give you no conformers for ...

343af15c9bd4583234128db2408b9a7688bd7416 authored about 8 years ago

Fix segfault when ReadMolecule() called with PubChem document but file extension was generic .xml (bug #909)

e3f2d08c8c3e2398b2561a0428d642b4f6898fa8 authored about 8 years ago

Merge pull request #367 from psavery/space-groups-fixed

Fixed a few errors in space-groups.txt

1b55749c9323d2e9dbbe50536c77fd96a79c8660 authored about 8 years ago

Fixed a few errors in space-groups.txt

As was pointed out in issue number 153 on
https://github.com/openchemistry/avogadrolibs, there
a...

7534c4626f1c72187472cada055b3176048040a5 authored about 8 years ago

Merge pull request #339 from ntropia2/patch-1

Added line for -NO2 group

33a068cf0dbb1994fe0ae565787beeb6dce6d726 authored about 8 years ago

Merge pull request #361 from langner/patch-2

Avoid IndexError for plugins with empty names

ab7b281935aaf6cdafcccbd8099bfeb5b963c3da authored about 8 years ago

Avoid IndexError for plugins with empty names

4c3fe03b571d4740957ec4115992be75019ddc76 authored about 8 years ago

fix build error in VisualC++ (explicit conversion to bool)

84414145eb97ec151cb75eb37a33b5af52e4f7a6 authored about 8 years ago

removed pattern overriding hypervalence of nitro

I've removed the incriminating pattern that is incompatible with hypervalent nitrogen (O=N=O).

259200ca5809a2992e3aeb5c34f03033c3a6b6bc authored about 8 years ago

Fix GCC version check, resolves #353.

1bde79933149fb02c2e5b50d3a2f80a82f39c508 authored about 8 years ago

Merge pull request #359 from tgaudin/patch-1

Updating CMakeLists.txt

b6bb17c5fff6f77f818fe14dad9dba04ec4b2696 authored about 8 years ago

Merge pull request #360 from ghutchis/improve-svg-ball-and-stick

Improve svg ball and stick

1560a5de02895604470456681d6ee5ef888ad501 authored about 8 years ago

Decrease transparency ramp for atoms.

643765fb45dce47d4d0b1b2385057b8a4efa804e authored about 8 years ago

Fix compile error.

Also fixed aromatic bonds and a few other style improvements.

df3eea9ade387a06d1b7e0bb6c4220ea600b61f9 authored about 8 years ago

Improve the pseudo-3D ball and stick depiction.

Now uses opacity to bonds and atoms to imply some perspective.
Also scales bonds slightly to imp...

3b9bb4a1b984e2cf313b4074df98f041c6c22d6a authored about 8 years ago

Adding depict_headers to the installation

5766ff00cb8003296a2468147e4d34ab0a3c38ef authored about 8 years ago

Merge pull request #352 from baoilleach/DefaultBuildType

Change default build type to RELEASE and add -O3 switch

1d6c6a24c2ea73ee5cabf53f5653b1bf855bc393 authored over 8 years ago

Merge pull request #357 from philthiel/msvc_zlib_fix

Fix for missing ZLIB on win32

ea8c735e6d941fadb68bcd067aa2bd1175abe743 authored over 8 years ago

Fix for missing ZLIB on win32

c63685becff3df3067a84d993044e8eb60b5aada authored over 8 years ago

Change default build type to RELEASE and add -O3 switch

039fe5250c8300087b642d8283e79b928ce1a96f authored over 8 years ago

Bump for 2.4.1 with correct library version and SWIG wrappers.

486b27e48d187ad213a0ff40d2d3029a9512ee52 authored over 8 years ago

Merge pull request #348 from mcs07/python

Python setup.py fixes for 2.4.0 (and future) release

f9669b50758423735eb8483a1ff18575d0f67b4c authored over 8 years ago

Python setup.py fixes for 2.4.0 release

This commit contains a few minor changes to the Python setup.py file that is used for independen...

72be31f3fa15b7a85fa6806200b451a93eead732 authored over 8 years ago

Merge branch 'master' of github.com:openbabel/openbabel

3c440a5e27a9516f1240db4d01fabb14665f9d59 authored over 8 years ago

Bump version number for 2.4.0

6845211259bc0d79732a85a9e93abf7a7b50223a authored over 8 years ago

add support for customizations of filter and rotors used during conformer search

b5039467435efbc824bc75b412528a420fce45a2 authored over 8 years ago

Updated proposed change

Included also cases where no bond order has been determined (i.e., all single bonds)

b1bea58b1dd50e52cf7d25a34ae27f6ecaf51c4c authored over 8 years ago

Updated proposed change

Included incorrect cases where the nitrogen has two double bonds

4368fb1c14e3792840fcde5e23c14499f7a731df authored over 8 years ago

Added line for -NO2 group

Added an entry for the -NO2 group to preserve the explicit charge localization [N+](=O)[O-] when...

98b4fbc473c8abf6f550139c49233698732e7f77 authored over 8 years ago

Merge branch 'master' of https://github.com/openbabel/openbabel into upstream

4b4f9eda7f55be10d026523fe71eef9503e057c6 authored over 8 years ago

Merge pull request #336 from maw001/patch-1

Add support for reading Jaguar input files to jaguarformat.cpp

0fc251ca61cf896db00b2c842452202bf1692480 authored over 8 years ago

Add support for reading Jaguar input files to jaguarformat.cpp

c09b55dda4ac8098a183a41521bc123748762289 authored over 8 years ago

Merge pull request #318 from mwojcikowski/patch-2

[WIP2] Fix MSVS for current master

db03c52f01c1271a4b156a0c53ed930aad9da5e4 authored over 8 years ago

Merge pull request #319 from psavery/master

Fixed a bug with using the --fillUC feature

3bc7056c9a4725a63a4e6292eb1f636fea0f168e authored over 8 years ago

Merge pull request #332 from Jsunseri/master

Bugfix for multi-model PDB writing

3db8a52c3b6609a98fb005eca71339c174c3891d authored over 8 years ago

Merge pull request #333 from dkoes/numrotors

enable sampleRingBonds option in IsRotor as well

e4d7460f4ec6e80b03c531e7106aadc207c492d0 authored over 8 years ago

sampleRingBonds -> includeRingsBonds

f1cae022b5417f28841d1e20961d7146dfedf67f authored over 8 years ago

enable sampleRingBonds option in IsRotor as well

dbddc7c8bb7283062e7b31701ea29e7b9e428108 authored over 8 years ago

Bugfix for multi-model PDB writing. Previous versions inserted an

'END' tag before the 'ENDMDL' tag after each model. This violates
the PDB spec, which says 'END' ...

638d735d643624bcd212dc1f7c789c6036199a67 authored over 8 years ago

Merge pull request #327 from baoilleach/ChangeAspect

Set the aspect ratio to 2.0 for ASCII depictions in SD files

117ee1c66597146d3837b04ee51a8d23f4c5646f authored over 8 years ago

Merge pull request #328 from nextmovesoftware/ASCIIDepiction_Fix

Fix for logic when there is an existing ASCII depiction in an SD file

9a37e00eed6f289d580208a7437786ecd3eaa193 authored over 8 years ago

Merge pull request #329 from nextmovesoftware/RGroups

Add support for 'M RGP' in mol files

90a7cc2676fb12bcf1f1b0d68a88d1047b32955d authored over 8 years ago

Merge pull request #331 from dkoes/numrotors

restore NumRotors behavior and add rotor count output to obprop

079e252b2925da097e9d73f3b23f4084d67a32f6 authored over 8 years ago

edit info message of obprop

7dc90fb1a7ea6b6ee8dade6455732bff18871222 authored over 8 years ago

restore NumRotors behavior and add rotor count output to obprop

76edfa98edbdfde79df2c6a089424039cd1c299b authored over 8 years ago

Merge branch 'master' of https://github.com/openbabel/openbabel into upstream

e66641f7d4d43a18145c14761871742a1c54c2f5 authored over 8 years ago

restore NumRotors behavior and add rotor count output to obprop

940c0090c0e9127ce75b1d402a6edd271893f38c authored over 8 years ago

Merge branch 'master' of https://github.com/openbabel/openbabel

4897ae1e1eb8d8384a220f5bcea2174291b98523 authored over 8 years ago

Minor fix for compilation with gcc

db9615f4120c2e2b08e12f2fb4d132a65a2d0665 authored over 8 years ago

Add testcase to exercise the R group handling code

fa242a0cc44c7742191201f119908f7cb65ce68a authored over 8 years ago

Minor fix to ensure gcc compilation

43a1fc83b5b233e469869859c450142b8a2c8375 authored over 8 years ago

Merge pull request #316 from baoilleach/obdotnet

Get CSharp build back into shape.

a06458cd336da74f62fb2cfd759a39b2cb47834c authored over 8 years ago

Add support for 'M RGP' in mol files

Numbered R groups (e.g. R1, R2) are currently handled like other atom aliases without special ha...

f15a927e8b24d1969bf3cfb42a7ad62667b0298f authored over 8 years ago

Fix for logic when there is an existing ASCII depiction.

9c18e7c95773cb8100457cc0574c6b6b51b7c1e4 authored over 8 years ago

The default aspect ratio of 1.5 (set selfishly to suit the Windows command prompt) is likely to produce elongated structures when viewing SD files in an editor so I'm setting the ratio to 2.0 here.

8090119551f42a417af76f95227e1d6a87175f82 authored over 8 years ago

Merge pull request #326 from mwojcikowski/patch-3

[MRG] Support Python 2.x Unicode

6c72b8990b69b1aa698ca42945ccb7ccd8836132 authored over 8 years ago

Fix Python 2 unicode

72ea0bcd56bfae247ceabc2adfb8841ce9044a33 authored over 8 years ago

Merge pull request #323 from baoilleach/SDFAscii

Add an option to the MDL format writer to include an ASCII depiction

b6f544adf264be92466e47278ebd117af9970749 authored over 8 years ago

Add an option to the MDL format writer to include an ASCII depiction

e55c0734811b6d63ea530a0c6ec8f0008fc0e305 authored over 8 years ago

Merge pull request #321 from tomjanowski/bugfix1

Fix in OBForceField::WeightedRotorSearch.

Make sure to set the conformer to the correct one a...

8adb967c7eb81d05e2158fb70a2382fd1f2775c6 authored over 8 years ago

Merge branch 'master' of https://github.com/openbabel/openbabel

747791dd2822b8922e15427ab1cabe978f26ad9e authored over 8 years ago

Additional check for data dir

704250e925d765387257d5ee790d24f53803b7c2 authored over 8 years ago

Fix in OBForceField::WeightedRotorSearch.

The WeightedRotorSearch method of the OBForceField class returned wrong
index to the conformer o...

132b3a7e8c205aae962e1f86f0361aa8208ff0b9 authored over 8 years ago

Install python bindings on Windows

575b44feaf4e4efe94339685f201b9ac9f02d6bd authored over 8 years ago

Merge pull request #317 from baoilleach/swigcomments

Fix comment symbol in swig interfaces

3bf30eef3f2af81df4349538cff84e4eb14c6587 authored over 8 years ago

Merge pull request #315 from baoilleach/AmidineImide

Remove OBBond::IsAmidine and IsImide from public API

05818aa13d5837a423ab01a4107b504ddb5689f8 authored over 8 years ago

Merge pull request #314 from baoilleach/IsThiocarboxylSulfur

Remove OBAtom::IsThiocarboxylSulfur from the public API

fa318e7e09e127d8d8913e3a3c345a3a29f94435 authored over 8 years ago

Merge pull request #313 from baoilleach/IsSulfoneOxygen

Remove OBAtom::IsSulfoneOxygen from the public API

a6b1bd330fe573a9baea35853e66c41bd4d2abf5 authored over 8 years ago

Update orcaformat.cpp

0cd54e217019645f937a42b60ac8a226ab11ba06 authored over 8 years ago

Use global namespace (std or regex for MSVS)

a981ad6e63fab0b8c1c09123e1a5fff1e3b217fd authored over 8 years ago

Merge ifs

21712d4a19d1da9af0fdc77b1382177d7169dfc3 authored over 8 years ago

Fix typo

42ef7d7407874dca0a32c45051bedc6f0043aaba authored over 8 years ago

Add isfinite for MSVS 2008

f72c8bda0203b2a000c542695da3c991615fd5ea authored over 8 years ago

Fixed a bug with using the --fillUC feature

If pOptions is not NULL but no transforms are found, then
the SpaceGroup object (spacegroup) wil...

ab1c6572d442e22243d7b6f840f3bb473e7a0df3 authored over 8 years ago

Another fix for VS 2015

b982fb16cec133c275b0232a37e581e2527e40d3 authored over 8 years ago

Fix

474f65848620dd5a8d1ffdad2dad19db39632105 authored over 8 years ago