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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

Fix #2071

github.com/openbabel/openbabel - d4a184e32db2c00fe8f57fffffac8e0de8318aa4 authored about 5 years ago by Eisuke Kawashima <[email protected]>
Merge pull request #2060 from e-kwsm/OB3

Update for Open Babel 3

github.com/openbabel/openbabel - f84536d804b4e2b530daf8831f264ea72a5cedf0 authored about 5 years ago by Geoff Hutchison <[email protected]>
only use boost threads if not static build

github.com/openbabel/openbabel - 9e093701df695a9d0983298eac3e255e255aba56 authored about 5 years ago by Ricardo R-S <[email protected]>
travis: install boost to enable maeparser & coordgen

github.com/openbabel/openbabel - 412b5be15e0fdf351819fe0704280ffbdc15a932 authored about 5 years ago by Ricardo R-S <[email protected]>
update maeparser include paths to use the same as coorden

github.com/openbabel/openbabel - 3809081838b673a9ab45f3e6061dc1a525eba4f3 authored about 5 years ago by Ricardo R-S <[email protected]>
update CMakelists

github.com/openbabel/openbabel - c4c6ef37d91c8b27e0b8af9f2e4772332caa7cf1 authored about 5 years ago by Ricardo R-S <[email protected]>
add Find modules for maeparser and coordgen

github.com/openbabel/openbabel - e259b6737787d2545f45b63c90f0f27a40e0179f authored about 5 years ago by Ricardo R-S <[email protected]>
Update scripts/python/setup.py

github.com/openbabel/openbabel - 7bf2ec203f297735f067c06d976577db92504e3b authored about 5 years ago by Eisuke Kawashima <[email protected]>
Update variables in CMake files to version 3

github.com/openbabel/openbabel - 8f24fa64606376e38180a455e7a60c71a23b2d71 authored about 5 years ago by Eisuke Kawashima <[email protected]>
Update version and release date of man [ci skip]

github.com/openbabel/openbabel - 5514d77c39c9270e79a72699937d5b514a33903d authored about 5 years ago by Eisuke Kawashima <[email protected]>
Update INSTALL and READMEs under scripts/ [ci skip]

- perl
- assume perl-binding version is different from Open Babel's
- python
- assume ta...

github.com/openbabel/openbabel - 8a8ede202b40a6dee06a2bcd78badc574f0c861c authored about 5 years ago by Eisuke Kawashima <[email protected]>
Merge pull request #2056 from dkoes/staticbuild_fix

Fix BUILD_SHARED=OFF

github.com/openbabel/openbabel - 6ef538d4ff2ce3b0810e70761ad069b00d02420b authored about 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2055 from e-kwsm/avoid-using-namespace-in-header

Avoid `using namespace` in headers

github.com/openbabel/openbabel - 00394707ecebbb5af959b4ecacebd88a15b75a27 authored about 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2059 from e-kwsm/OB_INCLUDE_DIRS

Do not hard-code Open Babel major version for include directory

github.com/openbabel/openbabel - 7989031a37172c045ec7b106d1a261df35957feb authored about 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2058 from e-kwsm/fix-import-openbabel

Fix import of openbabel

github.com/openbabel/openbabel - 1f63432aaf117304ec10b37301052b8c37a04b22 authored about 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2057 from e-kwsm/remove-babel-doc

Remove babel doc

github.com/openbabel/openbabel - 704623efc770c08293f0b9594c176eb1628f7557 authored about 5 years ago by Geoff Hutchison <[email protected]>
Do not hard-code Open Babel major version for include directory

github.com/openbabel/openbabel - 3f7a07f7e40afa3fcce3bf9014f3c3a8ceca0da5 authored over 5 years ago by Eisuke Kawashima <[email protected]>
Fix import of openbabel

github.com/openbabel/openbabel - b657ca216c2a21f5162cc595aac97cbffdcd23c9 authored over 5 years ago by Eisuke Kawashima <[email protected]>
Rename doc/{babel.html => obabel.html} (#1976) [ci skip]

github.com/openbabel/openbabel - 1351b77ad091aee8dace7eab17e2f659b5501d21 authored over 5 years ago by Eisuke Kawashima <[email protected]>
Rename doc/{babel.1 => obabel.1} (#1976) [ci skip]

github.com/openbabel/openbabel - 183cb58343ad28c60e0e587d99fbe495dd8d7276 authored over 5 years ago by Eisuke Kawashima <[email protected]>
Fix BUILD_SHARED=OFF

maeparser doesn't appear to support static builds out of the box, so
disable it in this case

github.com/openbabel/openbabel - 3455dbdc332959999c49ddf959d69b013396b7ed authored over 5 years ago by David Koes <[email protected]>
Avoid `using namespace` in headers

github.com/openbabel/openbabel - b269d81864aa786afda2f660cc07060a4aeaf4ec authored over 5 years ago by Eisuke Kawashima <[email protected]>
Merge pull request #2052 from ghutchis/mark-3.0-release

Mark 3.0 release

github.com/openbabel/openbabel - 49f9cfb32bd0bc6ea440639d338123eb27accbe2 authored over 5 years ago by Geoff Hutchison <[email protected]>
Remove the NEWS since that's covered in documentation, etc.

github.com/openbabel/openbabel - 6cd7780b09e3182aa20dc9937749b3021f5086be authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2054 from baoilleach/updatedocstrings

Fix file format docstrings that were causing problems with Sphinx or GUI

github.com/openbabel/openbabel - 691e2d660172106411bafc3e2c6938b299323509 authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2053 from openbabel/maestro-extensions

Rename MAESTRO extensions from uppercase to lowercase

github.com/openbabel/openbabel - 1f010c9b204fb9faf9c173dc5d321e94feaf40d5 authored over 5 years ago by Geoff Hutchison <[email protected]>
Fix file format docstrings that were causing problems with Sphinx or with the GUI

github.com/openbabel/openbabel - 710ad5222f4a8acf40f4b3c9afe6bcd179a84be1 authored over 5 years ago by Noel O'Boyle <[email protected]>
Rename extensions from uppercase to lowercase

The file extensions should be lowercase for .mae and .maegz. See discussion at #1993.

github.com/openbabel/openbabel - d49f98569177cb89de67f5cc4fd13af47b34b2ff authored over 5 years ago by Noel O'Boyle <[email protected]>
Mark 3.0 release.

github.com/openbabel/openbabel - cd05cb451e9c68639f92adff24ed6a37efbe59fe authored over 5 years ago by Geoff Hutchison <[email protected]>
Change the SO number to reflect different API break, changes, etc.

github.com/openbabel/openbabel - e039b440116a86e4fbef48b1857d15fbea72996d authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2051 from ghutchis/cmake-script-fixes

Fix CMake error with R and C# bindings

github.com/openbabel/openbabel - b287c9bbe8b735dfb56803cb138678572eb0b4eb authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2045 from e-kwsm/gas_constant

Update GAS CONSTANT to 2018 CODATA recommended value

github.com/openbabel/openbabel - 4d93662ab5fd301124a34e2338112a03fd6ad7f1 authored over 5 years ago by Geoff Hutchison <[email protected]>
Fix CMake error with R and C# bindings

github.com/openbabel/openbabel - 72e74f83245101a042c03dafc6424843b9c905b7 authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2008 from dkoes/some_tests

Added roundtrip tests using 14k non-redundant ligands from PDB

github.com/openbabel/openbabel - 88148eb2a0912a0cd15cbfabf913e0bbf9fc3276 authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2043 from e-kwsm/CMake3.1

Bump cmake_minimum_required to 3.1

github.com/openbabel/openbabel - 93a2b4cbbb0b142f492a174970c46a1a87800dbd authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2047 from baoilleach/fix_compilation

Fix compilation with GCC 4.8 (standard compiler on CentOS 7.5)

github.com/openbabel/openbabel - 2bfffa014f0b330657cb0d5610eec6b2b8f6c928 authored over 5 years ago by Geoff Hutchison <[email protected]>
Fix compilation with GCC 4.8 (standard compiler on CentOS 7.5)

github.com/openbabel/openbabel - a4f0f811481dc700fafd9d012bc830b3e5994b69 authored over 5 years ago by Noel O'Boyle <[email protected]>
Update GAS CONSTANT to 2018 CODATA recommended value

The variable was called as Boltzmann's constant but actually gas constant,
and the value was inc...

github.com/openbabel/openbabel - 08419cbe9eb47510b2d6766a5fb3bc8b691649ec authored over 5 years ago by Eisuke Kawashima <[email protected]>
Bump cmake_minimum_required to 3.1

github.com/openbabel/openbabel - b6b50ab7765ce325d7171c8052b5236e417dc308 authored over 5 years ago by Eisuke Kawashima <[email protected]>
Merge pull request #2042 from ghutchis/add-funding-link

Add a GitHub funding link to the open collective page.

github.com/openbabel/openbabel - 41730e2d82d01eb52cc5a58ed60000c533ee8ce9 authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2040 from baoilleach/Bump30

Remove minor version from some names

github.com/openbabel/openbabel - 3acb2dcca7b8b9674ab8c912da781a0a2ad99092 authored over 5 years ago by Geoff Hutchison <[email protected]>
Add a GitHub funding link to the open collective page.

This is used to enable open financial contributions
(e.g., meetings at ACS, etc.)

github.com/openbabel/openbabel - e2b65cc2b0693d94dfb3c87f9837253bef573af0 authored over 5 years ago by Geoff Hutchison <[email protected]>
Remove minor version from some names

github.com/openbabel/openbabel - c49c4442f7ac162f351f7aa598de379d31cd9e35 authored over 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #1979 from e-kwsm/update-man

Update doc [skip ci]

github.com/openbabel/openbabel - 24b3e797594f94c371f1f64bc2971698394984d8 authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2035 from fredrikw/cdx_multialias_fix

Fixed alias expansion for files with multiple aliases

github.com/openbabel/openbabel - aa594ab87236a49d2979b746c3a3a978086be023 authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2038 from dkoes/valgrind_error_fix

Fix reading of uninitialized data.

github.com/openbabel/openbabel - 8a3e2bc6a0b220ce046e4478dc7e618eca28a535 authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2039 from baoilleach/kekule_not_default

Don't make kekule SMILES the default in the GUI [skip ci]

github.com/openbabel/openbabel - be2d61b1f55bce1601a2f47ac80c7e02dedfe8dc authored over 5 years ago by Geoff Hutchison <[email protected]>
Extra safety on get residue

Make sure that if GetResidue does trigger a perception, the perception
will be run on the molecu...

github.com/openbabel/openbabel - 98b46c677777643fe7b8e9e695f7b77dc595abcb authored over 5 years ago by David Koes <[email protected]>
Only update residues if they already exist

I did not process the fact that GetResidue does perception.
Avoid this expensive operation if no...

github.com/openbabel/openbabel - d65bb0ed7e107b0082c7d14da320616b6b3ee796 authored over 5 years ago by David Koes <[email protected]>
Don't make kekule SMILES the default in the GUI

github.com/openbabel/openbabel - fee94bf21dd05b791a562ec469b5fb22f9714f99 authored over 5 years ago by Noel O'Boyle <[email protected]>
Remove redundant call to SetResidue

This is done inside OBResidue::AddAtom

github.com/openbabel/openbabel - 8d84f95e0debca04541d93f8ed2e1041ad93c9a7 authored over 5 years ago by David Koes <[email protected]>
Merge pull request #2036 from baoilleach/MajorVersion

Bumping the major version requires more changes throughout the library.

github.com/openbabel/openbabel - 57ad592524951c3c005e977c7053e7436d1cb13c authored over 5 years ago by Noel O'Boyle <[email protected]>
Merge branch 'some_tests' of github.com:dkoes/openbabel into some_tests

github.com/openbabel/openbabel - e05b1542ccdae594c7c6d3d10ebfcd542570a070 authored over 5 years ago by David Koes <[email protected]>
Fix reading of uninitialized data.

Valgrind was reporting Conditional jump or move depends on uninitialised value(s)
I am pretty su...

github.com/openbabel/openbabel - fd258cecd55d3a6213ca096ce5f7960b8865c796 authored over 5 years ago by David Koes <[email protected]>
Fixed alias expansion for files with multiple aliases

github.com/openbabel/openbabel - 7bac4a81bd9f648f022211c5ea6d5d2d221936e1 authored over 5 years ago by Fredrik Wallner <[email protected]>
Squashed commit of the following:

commit ba62bcfcb8e9c494c51e0e8a2b3b83885b764a55
Author: David Koes <[email protected]>
Date: Thu ...

github.com/openbabel/openbabel - 7cd802b15d428fa006023ae9afc603d8850f59df authored over 5 years ago by David Koes <[email protected]>
Merging with master

github.com/openbabel/openbabel - ba62bcfcb8e9c494c51e0e8a2b3b83885b764a55 authored over 5 years ago by David Koes <[email protected]>
Merge remote-tracking branch 'openbabel/master' into some_tests

github.com/openbabel/openbabel - 9dc34000282304918555a257c0e0d04d694513ea authored over 5 years ago by David Koes <[email protected]>
Make test work with Python2

github.com/openbabel/openbabel - 03b8f44d99a05c14e0ae5fe37d350e253f8b91b3 authored over 5 years ago by David Koes <[email protected]>
Merge branch 'some_tests' of github.com:dkoes/openbabel into some_tests

github.com/openbabel/openbabel - 1b48bc0fe4dee02ed7ef62150e4d1e5832ffcbaf authored over 5 years ago by David Koes <[email protected]>
Add hydrogen adding tests

github.com/openbabel/openbabel - 4fc2544af3a3709195ec4a64c5102c28dca0e302 authored over 5 years ago by David Koes <[email protected]>
Bumping the major version requires more changes throughout the library.

github.com/openbabel/openbabel - 130ebe8cc64fba3cd8db20a4ce5296928597887d authored over 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2034 from baoilleach/bumpversion

Bump version to 3.0.0a2

github.com/openbabel/openbabel - be7cc84eacb99a77a728e44b0ffa4b71c6590e2e authored over 5 years ago by Noel O'Boyle <[email protected]>
Bump version to 3.0.0a2

github.com/openbabel/openbabel - 4947447992f74ef28e948f413e35c350710f0aee authored over 5 years ago by Noel O'Boyle <[email protected]>
Merge branch 'master' into periodic-boundaries

github.com/openbabel/openbabel - 805cbd5854385b2216a8637d85081e13ec20223b authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2022 from ghutchis/ff-dielectric-const

Add force field support for dielectric constants in charge terms.

github.com/openbabel/openbabel - c1957136675ca366054c5cf7aabbb51763c115eb authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2032 from baoilleach/UpdateCSharp

Update the CSharp bindings

github.com/openbabel/openbabel - 62bc9b4defdae99342e0994769f811bbfd7896a8 authored over 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #1976 from baoilleach/remove_babel

"Bye bye babel" - remove the babel binary

github.com/openbabel/openbabel - 4f1c718ff531e762adea7a25c09e8df71e7ffa0e authored over 5 years ago by Noel O'Boyle <[email protected]>
Update the CSharp bindings

github.com/openbabel/openbabel - c9daca8f2a917864e3c06d0a97c2f81fe184251a authored over 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2031 from yishutu/ph_option

Add a warning message when both -p and -h options are set

github.com/openbabel/openbabel - 30a365ef0baa4eb6abae6190b85a7024df9d0129 authored over 5 years ago by Geoff Hutchison <[email protected]>
Add a warning message when both -p and -h options are set

github.com/openbabel/openbabel - e310901424519dc0f469d60443edfc2ecc0b30a9 authored over 5 years ago by Yi-Shu Tu <[email protected]>
Change references to babel to obabel

github.com/openbabel/openbabel - 97f722a751b55acead04f8f3d914eab1c7b66ea5 authored over 5 years ago by Noel O'Boyle <[email protected]>
Remove babel.cpp.

github.com/openbabel/openbabel - 819fb2414fd085b2be1c0b0099649f9561480be2 authored over 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2027 from RMeli/enhancements/cmake

Ignore in-source installation

github.com/openbabel/openbabel - d44cb70a2644fd1922cc864124c74be1f95d9141 authored over 5 years ago by Noel O'Boyle <[email protected]>
add build-static back

github.com/openbabel/openbabel - b611d0badb619c178adc41331d11ab4dbdb644b0 authored over 5 years ago by Rocco Meli <[email protected]>
Merge pull request #2028 from baoilleach/bumpversion

Bump version to 3.0.0a1

github.com/openbabel/openbabel - 5f249f9200a74a7b78d7f332fd3d1f50399ffe12 authored over 5 years ago by Noel O'Boyle <[email protected]>
Bump version to 3.0.0a1

github.com/openbabel/openbabel - a44fe81be23165371c2a7ff2c4f563f5708e7c39 authored over 5 years ago by Noel O'Boyle <[email protected]>
ignore in-source installation

github.com/openbabel/openbabel - eaf93b3fb9501e0c1e39f675b55c0e9f02eb24c7 authored over 5 years ago by Rocco Meli <[email protected]>
Merge remote-tracking branch 'upstream/master'

github.com/openbabel/openbabel - 4431d6a4da2d541044926196e76b0c68d4b27346 authored over 5 years ago by Rocco Meli <[email protected]>
Merge remote-tracking branch 'upstream/master' into some_tests

github.com/openbabel/openbabel - 2694e44605a01769df0595f6d15b48e15936e497 authored over 5 years ago by David Koes <[email protected]>
Merge pull request #2026 from n-yoshikawa/fix-obabel-fast

Update coordinates in the fast option of obabel

github.com/openbabel/openbabel - bc6e5a23c4fabab45df06fb341fed01afb391101 authored over 5 years ago by Geoff Hutchison <[email protected]>
Update coordinates in fast option of obabel

github.com/openbabel/openbabel - ac9ccd392fd4ca6c60a11a08350d8b0ee7b9c0bd authored over 5 years ago by Naruki Yoshikawa <[email protected]>
Add MMFF94s tests and MMFF94 + dielectric constant unit tests.

github.com/openbabel/openbabel - 166b7bdedb2fd85f3900db23e546886c6bb22cd6 authored over 5 years ago by Geoff Hutchison <[email protected]>
Add force field support for dielectric constants in charge terms.

Needs unit tests, but supported for MMFF94, GAFF, and Ghemical
force fields. Enables minimizatio...

github.com/openbabel/openbabel - 3a8126f0c3ec84eb9892853d500f09e5b3f757fe authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2012 from Artoria2e5/patch-1

Do not stoke around the (svg) text

github.com/openbabel/openbabel - 9c36d87f89c4e2c320d59bca9f5d5f79a331c894 authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #1980 from e-kwsm/update-mol-url

Update URL of specification of MDL MOL [skip ci]

github.com/openbabel/openbabel - 6ba014ed52a775b8582157e53e8c32d265caef82 authored over 5 years ago by Geoff Hutchison <[email protected]>
add quotes (#1988)

github.com/openbabel/openbabel - a0795dac0d9391975a32e23bb60e845d9b8f072b authored over 5 years ago by Rocco Meli <[email protected]>
PDB and PDBQT Insertion Code Fixes (#1998)

* add quotes
* fix icode copy
* ignore static build dir
* indentation
* fix icode in PDBQT
...

github.com/openbabel/openbabel - aff4330d1c8593fbe40204280f4fa720b6291bd6 authored over 5 years ago by Rocco Meli <[email protected]>
Merge remote-tracking branch 'upstream/master'

github.com/openbabel/openbabel - 10e1b579f5183ab2a6608461f094e0bd6ef159ce authored over 5 years ago by Rocco Meli <[email protected]>
Merge pull request #2017 from PeaWagon/master

change forcefield.cpp so that steepest descent and conjugate gradient…

github.com/openbabel/openbabel - 413a5a8289df5e143bd8931fff499bae93405feb authored over 5 years ago by Geoff Hutchison <[email protected]>
change forcefield.cpp so that steepest descent and conjugate gradients update maxgrad; proposed fix for github issue 1366

github.com/openbabel/openbabel - 76b7e242cd54be8caaf804b76b5a326935919f4e authored over 5 years ago by Jen Garner <[email protected]>
Merge remote-tracking branch 'upstream/master'

github.com/openbabel/openbabel - b7f21a8211a4017ddbbf19eff7f8939488cd99c5 authored over 5 years ago by Rocco Meli <[email protected]>
Use bold text for svg

github.com/openbabel/openbabel - 508720367e217acdf7b3fb86b8eccded8120fb5c authored over 5 years ago by Mingye Wang <[email protected]>
Merge pull request #1993 from schrodinger/master

Add maeparser support to openbabel

github.com/openbabel/openbabel - 8ef49540d506612037530400b912a5d05552a3a8 authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2010 from dkoes/h_vector_fix

H vector fix

github.com/openbabel/openbabel - 4ae308ff8e4f9b166193486459f7df8d56cf2082 authored over 5 years ago by Geoff Hutchison <[email protected]>
Merge remote-tracking branch 'upstream/master'

github.com/openbabel/openbabel - da3c02bb02da429c89beee5a677b5d291f7b83f1 authored over 5 years ago by Rocco Meli <[email protected]>
Fix windows compile error

github.com/openbabel/openbabel - b0afbe3cffba209ba74b06905a4cc59ce59dd940 authored over 5 years ago by David Koes <[email protected]>
Do not stoke around the text

The current version of OpenBabel adds a stroke around the text, creating an awkward "rounded bol...

github.com/openbabel/openbabel - 23911b079a10890eb5baf387e59ad33f4aebeb17 authored over 5 years ago by Mingye Wang <[email protected]>
Merge pull request #2005 from yishutu/pybel

Make pybel compatible with #1975

github.com/openbabel/openbabel - 7cfe44859a492b6eb5df00a2ef663afedce1357b authored over 5 years ago by Noel O'Boyle <[email protected]>
Merge remote-tracking branch 'upstream/master' into h_vector_fix

github.com/openbabel/openbabel - 28a436ade5ff72695cf2b89251d061341a51e1a1 authored over 5 years ago by David Koes <[email protected]>