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openbabel

We're on a mission to speak the many languages of chemical data
Collective - Host: opensource - https://opencollective.com/openbabel - Code: https://github.com/openbabel/openbabel

Merge pull request #2456 from SebastianWellig/patch-1

Fix search of coordinate system in Gaussian

github.com/openbabel/openbabel - 125cb0111ba615449b21363576d0ffefa9321a15 authored over 2 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2475 from szlepermarcin/fix_log_conformers

fix verbose stdout write of GetConformers

github.com/openbabel/openbabel - 59daa945fa998264cf6cec14dbaf0664e1d847ce authored over 2 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2477 from szlepermarcin/verbosity_level

verbose flag in OBForceField for all stdout writes

github.com/openbabel/openbabel - e5172d2774a0c75d82210c14007817a59b3aa802 authored over 2 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2486 from ghutchis/chemicaljson-format

Initial support for Avogadro's ChemicalJSON (.cjson)

github.com/openbabel/openbabel - f3b9783b155cd158d7dde8b230a9381df4ab6c96 authored over 2 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2463 from nicolasfella/work/install

Fix CMake config install location on Windows

github.com/openbabel/openbabel - a512973b12308a32261a3c4d1d2af0d0a6747590 authored over 2 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2380 from dkoes/ammonium_fix

Fix for ammonium xyz parsing.

github.com/openbabel/openbabel - eb034d2f266e0780415674689bb22ff0f0417c37 authored over 2 years ago by Geoff Hutchison <[email protected]>
Initial support for Avogadro's ChemicalJSON (.cjson)

Supports atoms / bonds, coordinate sets, vibrations and charges

Signed-off-by: Geoff Hutchison ...

github.com/openbabel/openbabel - 4b9ef350d73733033e6fde0d345a74252ed2e0d1 authored over 2 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2387 from e-kwsm/ISSUE_TEMPLATE

Separate issue templates [skip ci]

github.com/openbabel/openbabel - ea4710f04120df713a6806ffb56baae29f16f58f authored over 2 years ago by Geoff Hutchison <[email protected]>
verbose flag in OBForceField for all stdout writes

github.com/openbabel/openbabel - acb6ce906179b442efb410753c9504c2925617f7 authored over 2 years ago by Marcin Szleper <[email protected]>
fix verbose stdout write of GetConformers

github.com/openbabel/openbabel - 45e4f00fe677412ddb497906c6dea444dabb3f48 authored over 2 years ago by Marcin Szleper <[email protected]>
Do not release OpenBabel::OBConformerSearch::m_filter

github.com/openbabel/openbabel - 49dc44e3a82bdd4eb624cd2d439c7328f9e9d2f1 authored over 2 years ago by Marcin Szleper <[email protected]>
test(python): improve usages of unitest.TestCase methods

github.com/openbabel/openbabel - 0f4af753d466d9c548da09e50794d5c065a61aaf authored over 2 years ago by Eisuke Kawashima <[email protected]>
test(python): fix misuse of unittest.TestCase.assert_

github.com/openbabel/openbabel - 7488cec43e34a51ba4a8439bb65a27590e07f3a2 authored over 2 years ago by Eisuke Kawashima <[email protected]>
python: replace IOError with OSError

https://peps.python.org/pep-3151/

github.com/openbabel/openbabel - 77530fb0aad7f8a52eaa7321aef50a27efb3e83b authored over 2 years ago by Eisuke Kawashima <[email protected]>
ci: rearrange tar options properly

github.com/openbabel/openbabel - 916d4f95902d72a5458241c473166f2a8e5df922 authored over 2 years ago by Eisuke Kawashima <[email protected]>
Fix CMake config install location on Windows

LIB_INSTALL_DIR is 'bin' on Windows, resulting in an unsuitable install location

Instead use th...

github.com/openbabel/openbabel - 41c0c157fb16f08a67a3fedf4638c725f74a5712 authored over 2 years ago by Nicolas Fella <[email protected]>
regex has been in C++11 std, so it may be used directly,and it can be compiled with msys2 successfully.

github.com/openbabel/openbabel - d994b40b9725781c252633a7faf2f167ae6cb2e8 authored over 2 years ago by Qing-Dong Wang <[email protected]>
Exclude dipole orientation as match

github.com/openbabel/openbabel - efe7bdaaefb0c389d37e3b120bb21aac58f8c8b9 authored almost 3 years ago by Sebastian Wellig <[email protected]>
Minor fix in test suite. Forgot the break statement.

github.com/openbabel/openbabel - d6eaced9f83994e387422eb70d3e633dbe928aec authored almost 3 years ago by Noel O'Boyle <[email protected]>
Fix segfault in OBMol.CopySubstructure sometimes triggered when using option '2'

github.com/openbabel/openbabel - da67a871aeb8a7788cd136c49c719e87b530f961 authored almost 3 years ago by Noel O'Boyle <[email protected]>
Handle implicit hydrogens in cdxml, fixes #2416

github.com/openbabel/openbabel - f23fc59f625746a760cf1d8c4915448d46f97d5e authored about 3 years ago by Fredrik Wallner <[email protected]>
Merge pull request #2383 from GregCT/master

Fix typo

github.com/openbabel/openbabel - f3ed2a9a5166dbd3b9ce386e636a176074a6c34c authored over 3 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2400 from StashOfCode/patch-1

Add missing #

github.com/openbabel/openbabel - e9bb6142a4637221073c4506ac1133e9bebbff0f authored over 3 years ago by Geoff Hutchison <[email protected]>
Fix bug in tautomer code

When all atoms were assigned and there were still unassigned double bonds left,
a random bond wa...

github.com/openbabel/openbabel - ef88904df96efb2aff6b81dea088a8200d693959 authored over 3 years ago by timvdm <[email protected]>
Fix undefined name discovered by flake8

github.com/openbabel/openbabel - a9b40d9733cafac98b6f4c593567ababb8c8969b authored over 3 years ago by Christian Clauss <[email protected]>
GitHub Action to lint Python code

github.com/openbabel/openbabel - 3a4a11a66f52ee146ae4d0e2583e0f3e328d6f69 authored over 3 years ago by Christian Clauss <[email protected]>
Add missing #

They had this in the paper `[O]=C(C)[A#X]` which translates to [O]=[CH0](C)[A;!#6]. # was missing

github.com/openbabel/openbabel - c77136439aa5fff14ee0d1cfc1141ba1fed84dbf authored over 3 years ago by Arso <[email protected]>
More robust pdb reading.

Not all istream implementations support tell/seek so use peek when
consuming blank lines.

github.com/openbabel/openbabel - cd8990452e27ba7ee68fef763f1fee537f088291 authored over 3 years ago by dkoes <[email protected]>
Separate issue templates [skip ci]

https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-reque...

github.com/openbabel/openbabel - 860853b4fa7dbdf1710fab4593d1b051100aa3e5 authored over 3 years ago by Eisuke Kawashima <[email protected]>
Replace deprecated C headers with C++ alternatives

github.com/openbabel/openbabel - 74a000f30f8d2b21f6ef4e17fa55ce4d00d24af8 authored over 3 years ago by Eisuke Kawashima <[email protected]>
clang-tidy: readability-delete-null-pointer

github.com/openbabel/openbabel - 2b2ac7464d900f57e5b7a50e9eeb6833c60ba3b0 authored over 3 years ago by Eisuke Kawashima <[email protected]>
Fix bond perception of ring nitrogens.

There are two rules in bondtyp.txt that I don't understand the
justification of and I don't see ...

github.com/openbabel/openbabel - 5d5f6d50af30c65e62b24262c9bc19456012b831 authored over 3 years ago by David Koes <[email protected]>
Fix for bond order detection for azete

This is a bug reported by Madeleine Walz on the openbabel-devel list. Given a file format witho...

github.com/openbabel/openbabel - 501a3335e877f61786695834c2fe66218691d490 authored over 3 years ago by dkoes <[email protected]>
Fix for ammonium xyz parsing.

This is a bug report from Stefano Forli on the openbabel-devel list.
When calling obabel with -p...

github.com/openbabel/openbabel - d154b30d3fff72c3116428922bc0a70eb4e857d1 authored over 3 years ago by dkoes <[email protected]>
Resolve ImportError with make test

This change will build _openbabel.so in scripts/python/openbabel instead
of the default build/li...

github.com/openbabel/openbabel - 4ba2fec17b786afebadfae800a015704ad533843 authored over 3 years ago by dkoes <[email protected]>
Make FASTA conversion really connect the atoms.

Should fix #2367

github.com/openbabel/openbabel - ee68092e06503e65170d1067d35931f7a9abb826 authored over 3 years ago by Fredrik Wallner <[email protected]>
Allow for multiple-word titles for Tinker files

github.com/openbabel/openbabel - fa89f6f12959506ae2b300186426101af2f18e73 authored over 3 years ago by Michael Quevillon <[email protected]>
Merge pull request #2243 from baoilleach/javadoc

Support Javadoc from doxygen for SWIG 4.0 Java bindings

github.com/openbabel/openbabel - c3143e6235788ddd2c0a9d8298ad4873a5dbc81d authored over 3 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2242 from baoilleach/enable_pydoc

Support Doxygen comments in SWIG Python bindings

github.com/openbabel/openbabel - af94e4f2edb8d1dc2f592c449b6742310e45c29f authored over 3 years ago by Geoff Hutchison <[email protected]>
Create config.yml

Welcomebot config

github.com/openbabel/openbabel - dd458fca5dd762dad34fc5f6db8df638bb00ad13 authored over 3 years ago by Geoff Hutchison <[email protected]>
Clean up tinkerformat and allow for no comment

github.com/openbabel/openbabel - 760b651fa42b84a990f581af797fed0a45b17eac authored over 3 years ago by Michael Quevillon <[email protected]>
Merge pull request #2345 from openbabel/imgbot

[ImgBot] Optimize images

github.com/openbabel/openbabel - 2ff5b1089ee0d69b5694cf305e4a121b153340c5 authored almost 4 years ago by Geoff Hutchison <[email protected]>
[ImgBot] Optimize images

*Total -- 670.15kb -> 560.54kb (16.36%)

/data/splash.png -- 52.43kb -> 40.58kb (22.6%)
/doc/spl...

github.com/openbabel/openbabel - 2c09cfcd6d25a9c9fc1c4b86fafc43c17e7a9ce2 authored almost 4 years ago by ImgBotApp <[email protected]>
Merge pull request #2342 from catenacyber/ossfuzz

First fuzz targets for integration with oss-fuzz

github.com/openbabel/openbabel - 972d4de77572ef0250fe310b4ba18136c5065671 authored almost 4 years ago by Geoff Hutchison <[email protected]>
First fuzz targets for integration with oss-fuzz

github.com/openbabel/openbabel - 0d9b6659ce9beb736f0ded80fb807b4a0b3282fe authored almost 4 years ago by Philippe Antoine <[email protected]>
Update descriptions with the new obabel command (#2296)

github.com/openbabel/openbabel - 08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b authored almost 4 years ago by Yi-Shu Tu <[email protected]>
Initialize allocated memory to zero. (#2248)

It is arguable if this is strictly better (you won't see uninitialized
reads in valgrind when d...

github.com/openbabel/openbabel - 9a7bd9bc6ed32d035a77298bc7729740c7e3b6c7 authored almost 4 years ago by Geoff Hutchison <[email protected]>
make OBMol::NumHvyAtoms const (#2300)

github.com/openbabel/openbabel - bfdea1c95e5525964876ccbb09092e87ef51d600 authored almost 4 years ago by Rocco Meli <[email protected]>
Add GetNumHvyAtoms to OBResidue (#2299)

* add GetNumHvyAtoms to OBResidue

* add some sort of test

* add more atoms to test

github.com/openbabel/openbabel - 9111acd6584742d0fded4fe54eb870278b29f899 authored almost 4 years ago by Rocco Meli <[email protected]>
Merge pull request #2283 from dkoes/issue1999

Resolve Issue #1999

github.com/openbabel/openbabel - 8598a8115d86a8fa2023a5a8ab4c4834edfe6910 authored almost 4 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2297 from bsiegert/coordgen

Do not search for coordgen template files

github.com/openbabel/openbabel - ad91fc61a52ceff938b2c8528ba06e56fac3bbf6 authored almost 4 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2315 from pinotree/cmake-config-improvements

Improve the CMake config files

github.com/openbabel/openbabel - d30537b0ba2b50954f744363683f32665f258748 authored almost 4 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2328 from dkoes/updatedata

Update built-in data files.

github.com/openbabel/openbabel - 01c17a7b6430fc9e64cca4444ed8e2e54cf603c1 authored almost 4 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2293 from dkoes/pybelfix

Fix missing atom pybel properties.

github.com/openbabel/openbabel - a66ca6374ea7b9a3eb539de7dcade17b3ba21810 authored almost 4 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2324 from yishutu/set_env-fix

Replacing deprecated set-env and set-path commands

github.com/openbabel/openbabel - f1921eb4c9c4909809dd19435775dd7cfa7340a0 authored almost 4 years ago by Geoff Hutchison <[email protected]>
Update built-in data files.

If openbabel can't find the txt datafiles, for many datatypes there is a
built-in version that i...

github.com/openbabel/openbabel - d1fe1dac6ae58126e6ecf795be4afeb1795d4652 authored almost 4 years ago by dkoes <[email protected]>
Add space line between steps

github.com/openbabel/openbabel - 197b8763e6078afc08bdd927d994ecc40b07fac0 authored almost 4 years ago by Yi-Shu Tu <[email protected]>
change the redirect to windows style

(cherry picked from commit f750031a22670ae4127c76ef304d10b02b818e1f)

github.com/openbabel/openbabel - 4a9cc6a104b51cdbf41047c1066889118fc8412c authored almost 4 years ago by Yi-Shu Tu <[email protected]>
Update create-pull-request verstion

to 3.8.0 avoid set-env and add-path errors.

(cherry picked from commit 07a96214dfcf604af6736f7b...

github.com/openbabel/openbabel - c1f984d08a380af8ff48b2dce39eccac82259c69 authored almost 4 years ago by Yi-Shu Tu <[email protected]>
doc: improve documentation on cmake usage

Stop telling people to write their cmake find module, it is not useful
with the provided cmake c...

github.com/openbabel/openbabel - f18ad45750bdc7906bdf035e533a16756efa867b authored about 4 years ago by Pino Toscano <[email protected]>
cmake: use imported openbabel library

Switch the OpenBabel3_INCLUDE_DIRS & OpenBabel3_LIBRARIES variables
of the cmake config file to ...

github.com/openbabel/openbabel - 96b7a33b58e5496b6570aab5172cd6cb6ade7d15 authored about 4 years ago by Pino Toscano <[email protected]>
cmake: set public include dirs for openbabel library

Set the include directories as public include interfaces of the
openbabel library: this way they...

github.com/openbabel/openbabel - 01b472dba12175cfaca5d4fe34f012ba27967f89 authored about 4 years ago by Pino Toscano <[email protected]>
cmake: consider the openbabel dependencies as private

Mark all the library dependencies of the openbabel library as private:
this way, they will not b...

github.com/openbabel/openbabel - b4566b859d3e77d05f60a96c4047523f83b1584a authored about 4 years ago by Pino Toscano <[email protected]>
cmake: use CMakePackageConfigHelpers for config files

Make use of the CMakePackageConfigHelpers (available already in cmake
3.1) to generate the OpenB...

github.com/openbabel/openbabel - 7ec18edca2d749d29642261b5ad8578091f6e392 authored about 4 years ago by Pino Toscano <[email protected]>
Do not search for coordgen template files.

The coordgen upstream does not install the template file. It is
also not required at runtime, si...

github.com/openbabel/openbabel - b6887a8a82162278983a8489e365e61a0372b1b8 authored about 4 years ago by Benny Siegert <[email protected]>
Merge pull request #2295 from dkoes/ringiterfix

Fix ring iterations w/no rings

github.com/openbabel/openbabel - 9c001b5aeb8b985f26d111d811673150607662fa authored about 4 years ago by Geoff Hutchison <[email protected]>
Fix ring iterations w/no rings

The constructor was not initializing _ptr to null, and this is what was
used to test the validit...

github.com/openbabel/openbabel - 584f560be000a3ade45ef7edf02fe66b128a2c3d authored about 4 years ago by dkoes <[email protected]>
Fix missing atom pybel properties.

Some properties (e.g. implicitvalence) are no longer available.
Also added index as a property a...

github.com/openbabel/openbabel - f68dbd4a7f51d8ab4a9d6b27fc9ddf71d2258d55 authored about 4 years ago by dkoes <[email protected]>
Merge pull request #2292 from cygwin-lem/pr_fix-typo-HAVE_RAPIDJSON

Fix a typo to '-DHAVE_RAPIDJSON'

github.com/openbabel/openbabel - 945b8d0731d91600e23e652ca51dc23d4db824d6 authored about 4 years ago by Geoff Hutchison <[email protected]>
Fix a typo to '-DHAVE_RAPIDJSON'

github.com/openbabel/openbabel - f9724a8089512f11715b66c58ab75edae32cc4a1 authored about 4 years ago by Lemures Lemniscati <[email protected]>
Make PHP_INSTDIR configurable

github.com/openbabel/openbabel - 234e6f769bb71c52a20ee0cbf4271bd997d76a64 authored about 4 years ago by Lemures Lemniscati <[email protected]>
Make CSHARP_INSTDIR configurable

github.com/openbabel/openbabel - 5a8423e5d7b7e4d7ee2f110a0b73d15ced027b84 authored about 4 years ago by Lemures Lemniscati <[email protected]>
Make RUBY_INSTDIR configurable

github.com/openbabel/openbabel - ea693e7475a1321d1bd8ad2b9b181b949c00ed51 authored about 4 years ago by Lemures Lemniscati <[email protected]>
Make PERL_INSTDIR configurable

github.com/openbabel/openbabel - 8d4ce03a2cf9a58789b78a0739083c52bb63b826 authored about 4 years ago by Lemures Lemniscati <[email protected]>
Make R_INSTDIR configurable

github.com/openbabel/openbabel - 0d554f91e4b6d4d9b6d301c1cdd1fea5b982704b authored about 4 years ago by Lemures Lemniscati <[email protected]>
Make JAVA_INSTDIR configurable

github.com/openbabel/openbabel - 78599c56021aa0c9464366d0f066ba782ec08ce7 authored about 4 years ago by Lemures Lemniscati <[email protected]>
Make PYTHON_INSTDIR configurable

github.com/openbabel/openbabel - f7910915c904a18ac1bdc209b2dc9deeb92f7db3 authored about 4 years ago by Lemures Lemniscati <[email protected]>
Merge pull request #2285 from dspoel/fix-obthermo

Fixed crash in obthermo due to pointgroup code.

github.com/openbabel/openbabel - 43fffbd2afe04128fbfdfe701a13584ad93fecfe authored about 4 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2287 from baoilleach/smilesorder

Fix hydrogen suppression when specifying SMILES atom order

github.com/openbabel/openbabel - e14ef6e45ebd276e398e39ed7e3ea657e038fc18 authored about 4 years ago by Geoff Hutchison <[email protected]>
Ensure that specifying the output atom order in SMILES does not cause any hydrogens to be suppressed

github.com/openbabel/openbabel - b9d3110f23f24381e3288c227643fcbbebcdc609 authored about 4 years ago by Noel O'Boyle <[email protected]>
Fixed crash in obthermo due to pointgroup code.

The pointgroup code has been disabled in obthermo because a
crash was introduced relating to th...

github.com/openbabel/openbabel - 7c05e0b035698dcef228a1c11ffeca5583229b73 authored over 4 years ago by David van der Spoel <[email protected]>
Resolve Issue #1999

Include kekulize.h in bindings so you can run OBKekulize.

github.com/openbabel/openbabel - bb7b0fc71ecf25f8f8393086bde802c524000381 authored over 4 years ago by dkoes <[email protected]>
Enable Javadoc for SWIG 4.0

github.com/openbabel/openbabel - d4eae670e93fa21ee11aebb5e3a285ef30a938ed authored over 4 years ago by Noel O'Boyle <[email protected]>
Ensure that the code works with both SWIG 3 and SWIG 4. Also avoid non-ascii symbols in Doxygen as it can break some Python processing downstream.

github.com/openbabel/openbabel - ae7c86c2437311cdd279bede74b031be2899c397 authored over 4 years ago by Noel O'Boyle <[email protected]>
For SWIG 4.0, enable doxygen comments in Python bindings

github.com/openbabel/openbabel - ecd2a49d98f9d97d5636a87976116ff507f6ccc4 authored over 4 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2239 from baoilleach/py27_support

Support Python 2.7 in setup.py

github.com/openbabel/openbabel - 4709b0752109db593f1bee6298ef3bfa718d260d authored over 4 years ago by Geoff Hutchison <[email protected]>
Revert the slash n change

github.com/openbabel/openbabel - d927b6e21a39e81307136031449bc9411f46980a authored over 4 years ago by Noel O'Boyle <[email protected]>
Support Python 2.7. Also Python 3.8.

github.com/openbabel/openbabel - 732444b1765d52138bdf86d69e940ecbc1871c11 authored over 4 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2232 from afonari/patch-20

Fix memory leaks in parsmart.cpp and smartstest.cpp

github.com/openbabel/openbabel - 38c33acd8c2f46b6716ec03e3e8854acd5748bab authored over 4 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2235 from jcbollinger/examples_build

Fix examples failing to build with GCC / libstdc++ v8.3

github.com/openbabel/openbabel - e8ca4ff069a5c57fc6017db65cf114daaefedcc3 authored over 4 years ago by Geoff Hutchison <[email protected]>
Fix examples build failure with GCC / libstdc++ v8.3

The example program obconformersearch_default does not build
successfully with GCC 8.3.1 and its...

github.com/openbabel/openbabel - faba3b7959182bbb7f2b026a0a33cd6530a71314 authored over 4 years ago by John Bollinger <[email protected]>
Update groupcontrib.h

github.com/openbabel/openbabel - c9721a5470ad8b6c737b86deac6cbb5887cbc554 authored over 4 years ago by Alexandr Fonari <[email protected]>
Add destructor to groupcontrib (fix memory leak)

github.com/openbabel/openbabel - d494a401ac034691b6e623563708b6da97d673a5 authored over 4 years ago by Alexandr Fonari <[email protected]>
Fix memory leak in parsmart.cpp

github.com/openbabel/openbabel - 202624756253f94a7bd4e1b07eceb11324831fa3 authored over 4 years ago by Alexandr Fonari <[email protected]>
Fix memory leak in smartstest.cpp

github.com/openbabel/openbabel - 11fcb7698cfa400879807f728a2e58afe561284c authored over 4 years ago by Alexandr Fonari <[email protected]>
Merge pull request #2227 from jcbollinger/catch_by_reference

Fixes catching polymorphic exceptions by value

github.com/openbabel/openbabel - 303fc607187a7b7560b87c52f46c93b8c0f4598c authored over 4 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2220 from afonari/patch-17

Fix memory leak in mol.cpp

github.com/openbabel/openbabel - 4e212e3bf95ae2ace7e686001ffe0039a888e374 authored over 4 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2225 from afonari/patch-18

Fix memory leaks in spacegroup.cpp and cifspacegrouptest.cpp

github.com/openbabel/openbabel - 14368bb8c98d04c4c492fb29d619869982127d62 authored over 4 years ago by Geoff Hutchison <[email protected]>