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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 #2155 from e-kwsm/MAEPARSER_BUILD_SHARED_LIBS

Set MAEPARSER_BUILD_SHARED_LIBS (fix #2089)

github.com/openbabel/openbabel - 59ca340c3b9d0824432ffffbb047eb44f784d3a1 authored almost 5 years ago by Geoff Hutchison <[email protected]>
Set MAEPARSER_BUILD_SHARED_LIBS (fix #2089)

See https://github.com/schrodinger/maeparser/blob/v1.2.3/CMakeLists.txt#L8
for the option.
maepa...

github.com/openbabel/openbabel - f660e8431f0bff9c2da9857c0350122ce8968e7d authored almost 5 years ago by Eisuke Kawashima <[email protected]>
Improve tools/obenergy.cpp

- check if input file is passed to avoid SEGV
- remove unused variables
- clang-format

github.com/openbabel/openbabel - e06002d8c427d74e9ea92c275cde14f69a3f59e0 authored almost 5 years ago by Eisuke Kawashima <[email protected]>
Add unit test for #2144

Signed-off-by: Geoff Hutchison <[email protected]>

github.com/openbabel/openbabel - 095a5395f48bb75eed74ae5d4f801b2f3e2a8deb authored almost 5 years ago by Geoff Hutchison <[email protected]>
Minor cleanups in iterators - should fix codacy check

Signed-off-by: Geoff Hutchison <[email protected]>

github.com/openbabel/openbabel - b0aa9b2050e87797f5b781df16fd67fd13c074fc authored almost 5 years ago by Geoff Hutchison <[email protected]>
Remove fragments with zero coordinates - fixes #2144.

Rebuilt database from COD 'clean' subset from DataWarrior
and Platinum subset

Fix obfragment to...

github.com/openbabel/openbabel - 02fbe2d8a321f5966f632cb0e73431e47dd88861 authored almost 5 years ago by Geoff Hutchison <[email protected]>
OBBuilder: Add error message for ring/rigid fragments with all zero

coords.

github.com/openbabel/openbabel - c402bc2e15a86c4718284a1e84e04d0c1d52fb16 authored almost 5 years ago by timvdm <[email protected]>
Fix: #2125

github.com/openbabel/openbabel - fc667bcc161c84fc22f8151b9efc6534abf9990b authored almost 5 years ago by kirill <[email protected]>
Merge pull request #2124 from baoilleach/CastStereoBase

Enable casting to StereoBase in the Python bindings

github.com/openbabel/openbabel - 686ee22f21a1970b526b7882c2c23adc5357959c authored almost 5 years ago by Noel O'Boyle <[email protected]>
Be more strict when parsing charges in SMILES

github.com/openbabel/openbabel - 53d07eeb02ece49e3554ab8ee22a2e354dcb1592 authored almost 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2121 from baoilleach/kekulizesulfoxide

Support kekulization of aromatic sulfoxides

github.com/openbabel/openbabel - 6e80d6548e04af1dc13f9ff975f18714c7024617 authored almost 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2119 from baoilleach/Fix2081

Correct the path to the openbabel-python.cpp

github.com/openbabel/openbabel - 1aab8f208a1cd6ebc0e4e7f8160fcb19286799da authored almost 5 years ago by Noel O'Boyle <[email protected]>
Add testcase

github.com/openbabel/openbabel - 7e169c41c6c0e5dab85859e6ada9529a0b8bd8d8 authored almost 5 years ago by Noel O'Boyle <[email protected]>
Add cast to StereoBase

github.com/openbabel/openbabel - efaa11d91cdf4e6fc0e1d202c112b3c70dede518 authored almost 5 years ago by Noel O'Boyle <[email protected]>
Support kekulization of aromatic sulfoxides, if such a thing would every occur.

github.com/openbabel/openbabel - 1580c94e90b34ac850bc326c1487e5e7ca145417 authored almost 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #1853 from bbucior/periodic-boundaries

Closes #1536: implement periodic boundary conditions

github.com/openbabel/openbabel - 3d6384b50152d9096594bd5de1435b44f49161a6 authored almost 5 years ago by Geoff Hutchison <[email protected]>
Specify includes for the periodicity tests

github.com/openbabel/openbabel - 884b1640984b56c3a80dd24a137a3adc735dd1fc authored almost 5 years ago by Ben Bucior <[email protected]>
Include OBUnitCell in stereo perception

github.com/openbabel/openbabel - 76e77a6be6120a09586e1fd5d8a05a7d5198c9c4 authored almost 5 years ago by Ben Bucior <[email protected]>
Include OBUnitCell symbol for atom/bond periodicity

github.com/openbabel/openbabel - d84b3c356449b33fe702f797964ac3c21f6282c8 authored almost 5 years ago by Ben Bucior <[email protected]>
Apply conventions from #1951 to SetPeriodicMol

github.com/openbabel/openbabel - e4c0d4aea2553a12b8ea53833a50ffa4051df970 authored almost 5 years ago by Ben Bucior <[email protected]>
Merge branch 'master' into periodic-boundaries

# Resolved Conflicts:
# test/CMakeLists.txt

github.com/openbabel/openbabel - 27e081721f7489f653be15781e3e88e44d00f6db authored almost 5 years ago by Ben Bucior <[email protected]>
Correct the path to the openbabel-python.cpp so that the Python bindings can be built directly from the source release (i.e. without SWIG).

github.com/openbabel/openbabel - cd07cc06803031302210b214b85a969128066cfa authored almost 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2115 from timvdm/issue2111

Fix segfault on SMI to InChI conversion when using "-d"

github.com/openbabel/openbabel - e030d2ed5c8572c48cf41527dc0967bf5c994a7f authored almost 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2114 from timvdm/issue1794

Fix issue #1794, UFF atom typing for deuterium

github.com/openbabel/openbabel - 66027f04c6e27aaa936bcb86b8261195dc2fc7f4 authored almost 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2109 from baoilleach/nocharge

Add the --neutralize operation to convert charged atoms to neutral

github.com/openbabel/openbabel - eca90f28f114a2dbe75c376c79868fa51e3133b9 authored about 5 years ago by Geoff Hutchison <[email protected]>
Fix issue #2111, Segfault on SMI to InChI conversion when using "-d"

- src/formats/inchiformat.cpp: Improve handling of implicit stereo refs.
- src/regressiontest.cp...

github.com/openbabel/openbabel - 66164012c26309895d99097f9539aee3554b8a3e authored about 5 years ago by timvdm <[email protected]>
Merge pull request #2110 from baoilleach/suppreshydrogens

Change docstrings of add/delete hydrogens

github.com/openbabel/openbabel - 6160fe856e5be99b22b4e3027c034a832d1b6d39 authored about 5 years ago by Geoff Hutchison <[email protected]>
Fix issue #1794, UFF atom typing for deuterium

- data/UFF.prm: Add line for atom type 'D'.
- src/forcefields/forcefielduff.cpp: Add checks to p...

github.com/openbabel/openbabel - 083cff8c50b9f59c82c9d96ce6078bb3e4bd3095 authored about 5 years ago by timvdm <[email protected]>
Minor update

github.com/openbabel/openbabel - 8566e9ea3c2305c003562e5f736925c9b00842a8 authored about 5 years ago by Noel O'Boyle <[email protected]>
Change docstrings of add/delete hydrogens to refer to conversion from explicit<->implicit rather than adding or deleting hydrogens (because that's not what they do).

github.com/openbabel/openbabel - 46fe6d872c8201d0a4087d6e1b7e08dfb7e6c744 authored about 5 years ago by Noel O'Boyle <[email protected]>
Add call to suppress hydrogens. Also minor tweak to docstring.

github.com/openbabel/openbabel - 3144eab329be06b7ea01b90a091ab66244a40e7c authored about 5 years ago by Noel O'Boyle <[email protected]>
Add test for --neutralize

github.com/openbabel/openbabel - a41738a6002978aa4170c893868e88e50bb14e30 authored about 5 years ago by Noel O'Boyle <[email protected]>
Add --neutralize

github.com/openbabel/openbabel - 195cbd7e860e714116118049b7a8000c5ae209b8 authored about 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2102 from au1985/issue_2095

Fix issue #2095, caused by incorrect application of protonated SMARTS

github.com/openbabel/openbabel - 5d1f087d48110324ed29dd3aff02e93e1993399c authored about 5 years ago by Noel O'Boyle <[email protected]>
Merge branch 'master' into periodic-boundaries

github.com/openbabel/openbabel - 25c5a71c13f3db31d81bcd910ea8b28e2cbd868f authored about 5 years ago by Geoff Hutchison <[email protected]>
removed some code left after previous commit by mistake

github.com/openbabel/openbabel - a14c9d232bd97f2585abb76bafd481431ef27137 authored about 5 years ago by Alex Ustinov <[email protected]>
Fix alias test to set BABEL_LIBDIR

github.com/openbabel/openbabel - c243d6fd933d0364b90bb04387621d6cd3764f66 authored about 5 years ago by Alex Ustinov <[email protected]>
Alias generation does not require copy construction of OBMol; added unit test for alias feature

github.com/openbabel/openbabel - 97f5bec788bfd1938e35be97a7c573f93a524b85 authored about 5 years ago by Alex Ustinov <[email protected]>
Alias generation does not require copy construction of OBMol; added unit test for alias feature

github.com/openbabel/openbabel - 837e060361493936750b7f706507356238c44316 authored about 5 years ago by Alex Ustinov <[email protected]>
Install LBFGS headers

github.com/openbabel/openbabel - a298255ef8b2ca6d8a2868960817c4a9a498421e authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Fix issue #2095, caused by incorrect application of protonated SMARTS from superatom.txt to non-protonated molecules

github.com/openbabel/openbabel - ddfe87e97bbbbcf83b49d9d197229e1ed1648a08 authored about 5 years ago by Alex Ustinov <[email protected]>
Merge pull request #2100 from baoilleach/lowercase_elements

Bring back support for lowercase elements and D/T in GetAtomicNum().

github.com/openbabel/openbabel - aa951cbe6edd5538406d26ef4898f09347983fa5 authored about 5 years ago by Geoff Hutchison <[email protected]>
Add direct test for Issue #2063. Also minor tidy to earlier test.

github.com/openbabel/openbabel - bf91aec513d5879a11be9f60ed30714f6f2ee67d authored about 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2086 from dkoes/cmake_lib_fix

Define OpenBabel3_LIBRARIES for use by other CMake projects

github.com/openbabel/openbabel - c6b00dce3fe38205a2f8850a81e2fe8196448474 authored about 5 years ago by Noel O'Boyle <[email protected]>
Support D/T in GetAtomicNum()

github.com/openbabel/openbabel - 45da0860fb1cf33982d013fca91719706be32bc9 authored about 5 years ago by Noel O'Boyle <[email protected]>
Support lowercase versions of atomic symbols

github.com/openbabel/openbabel - 9d2966e73126a6db43d64e07bf3aabe982d1886a authored about 5 years ago by Noel O'Boyle <[email protected]>
LIBRARIES instead of LIBRARY

Also removed python.i change

github.com/openbabel/openbabel - d387295788c4a7cfbafaca12ec5d555660245056 authored about 5 years ago by David Koes <[email protected]>
merge from upstream

github.com/openbabel/openbabel - d62ebce437110fb5ee08535545e2a2fa4851100f authored about 5 years ago by David Koes <[email protected]>
Merge remote-tracking branch 'openbabel/master' into cmake_lib_fix

github.com/openbabel/openbabel - ace6d0bc14d2098d4f7cb45345bd3dd8ebd07989 authored about 5 years ago by David Koes <[email protected]>
Merge pull request #2094 from njzjz/patch-1

update download link

github.com/openbabel/openbabel - 6d774e8d152b7e252420e07c047eebb88d8c242c authored about 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2093 from voidpin/master

patched to build on NetBSD

github.com/openbabel/openbabel - 59dff1b4568b752b5a93b9f0c81bc4c7105ce1af authored about 5 years ago by Geoff Hutchison <[email protected]>
update download link

I don't know why, but obviously the sourceforge does not have the latest version (3.0.0).

github.com/openbabel/openbabel - 6a1c26ab58a12a668d0607ddbd63dab0989cba17 authored about 5 years ago by Jinzhe Zeng <[email protected]>
Correction

github.com/openbabel/openbabel - 5dd6ad8ff2894ff1563029821fbedc4f13fe0092 authored about 5 years ago by voidpin <[email protected]>
patched to build on NetBSD

github.com/openbabel/openbabel - f9dc85ce0b5fea05a43f88f1c5b1e2d82f12893f authored about 5 years ago by voidpin <[email protected]>
Merge pull request #1875 from n-yoshikawa/distance-geometry

Distance geometry method

github.com/openbabel/openbabel - c25172429fe8f0e074efae77380b5ba76b08f1a6 authored about 5 years ago by Geoff Hutchison <[email protected]>
Merge pull request #2084 from baoilleach/wln

Wiswesser Line Notation reader

github.com/openbabel/openbabel - 202550a6ee4aa16ce10243a1ea1f41a70fe108a4 authored about 5 years ago by Geoff Hutchison <[email protected]>
Use easy test

github.com/openbabel/openbabel - c154a720917d322eb632d423395db687dec86de3 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Fix tests

github.com/openbabel/openbabel - b0473c4820ad5133601c59cb1604337c3219b206 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Force to update stereo from 3D

github.com/openbabel/openbabel - 2f51910df2aebbfd1258a2c1100d50a3e1ec7d9e authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Fix conflict

github.com/openbabel/openbabel - a47e7835ecd22c36c7257b230453b2514485bdd4 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Definie OpenBabel3_LIBRARY

Every cmake package I've used exports the location of the library as a
variable. Perhaps this i...

github.com/openbabel/openbabel - cd5f7fa6b00bce871a2a8109e030aae5dd35e990 authored about 5 years ago by David Koes <[email protected]>
Update test cases and docstring with info from NextMove Bio-IT poster

github.com/openbabel/openbabel - c0fc6a3f4a7e71c3b585c489376f4b68d9e8ed25 authored about 5 years ago by Noel O'Boyle <[email protected]>
Spell Wiswesser correctly

github.com/openbabel/openbabel - fe18800bab7f5bfe5d028f7e3f75e46e92486369 authored about 5 years ago by Noel O'Boyle <[email protected]>
Add test cases

github.com/openbabel/openbabel - 0eaa18e97195ff3db0eb4803f540297edf510dcc authored about 5 years ago by Noel O'Boyle <[email protected]>
Refactor a bit and update for current

github.com/openbabel/openbabel - 0f6cff082be446a42cba68f7a8d7ba3c9f632f38 authored about 5 years ago by Noel O'Boyle <[email protected]>
WLN from NextMove

github.com/openbabel/openbabel - 672621292fdf50576b1aa8c7d56dd3617ff49067 authored about 5 years ago by Noel O'Boyle <[email protected]>
fix issue template bug (#2082)

github.com/openbabel/openbabel - ac33dc43fd6cd964864a2b561ec8894468de35a0 authored about 5 years ago by Rocco Meli <[email protected]>
Merge pull request #2064 from ricrogz/find_or_build_maeparser_coordgen

Find or build maeparser & coordgen libraries

github.com/openbabel/openbabel - 8500f8a98caa4306816b5f39c7ce0215f7b330e9 authored about 5 years ago by Geoff Hutchison <[email protected]>
restore master as fallback; remove leftover debug msgs

github.com/openbabel/openbabel - a97306e9a32ee210701ae20d3073dd1d384dd68d authored about 5 years ago by Ricardo R-S <[email protected]>
set fixed versions; handle github dirs

github.com/openbabel/openbabel - 9d79d1358cfce4cf977629ffb638fbf659fc6573 authored about 5 years ago by Ricardo R-S <[email protected]>
Merge pull request #2079 from baoilleach/smartshashzero

Support #0 in SMARTS so that asterisks can be matched

github.com/openbabel/openbabel - 49a4179f6ff93b148e2581ae57745f0aadda0e55 authored about 5 years ago by Geoff Hutchison <[email protected]>
Support #0 in SMARTS so that asterisks can be matched

github.com/openbabel/openbabel - 92e924feb57b10ea486fe1052a24e83377cef683 authored about 5 years ago by Noel O'Boyle <[email protected]>
Merge pull request #2076 from fredrikw/maecompileerror

Fix maeparser compile error with some Boost configs

github.com/openbabel/openbabel - 904a50d96a119cb88179ee8d86b057fefa48cb1f authored about 5 years ago by Geoff Hutchison <[email protected]>
Made check for Boost look for the same component as in https://github.com/schrodinger/maeparser/blob/master/CMakeLists.txt.

github.com/openbabel/openbabel - ed08a34ce0a91e3b523c8f707432325fabf4a9f6 authored about 5 years ago by Fredrik Wallner <[email protected]>
Add include

github.com/openbabel/openbabel - cf56677166667557ecf0715bb4c544581c5b0030 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Convert atom id to atom index

github.com/openbabel/openbabel - f3e491c82197189b9bd0a11a4a5a0c305829efd1 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Move BFGS library

github.com/openbabel/openbabel - 554facee4461079a3783841c660fd11086b4f1e9 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Use canonical SMILES to check stereochemistry

github.com/openbabel/openbabel - 86f919638e5e956aef0d6acfd32c21b6b3718648 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Replace BFGS library

github.com/openbabel/openbabel - 015257831299ca12e039028361d0b3c9515ac431 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Move definition of TetrahedralInfo

github.com/openbabel/openbabel - a73f02543160dd43bbf59f31847772e7568159ec authored about 5 years ago by Naruki Yoshikawa <[email protected]>
old C++ compatible + run mmff after dg

github.com/openbabel/openbabel - 4a7ce9234965a929ddb6a4ecc157568432c930fd authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Make dimension independent

github.com/openbabel/openbabel - 8ac3cd1125331a45b63b0fe121bd702db4ec9718 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Refactor functions

github.com/openbabel/openbabel - b2cde06cf8ead8a0501caf3e99d5dc5b37f70515 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Add planar constraint for aromatic ring

github.com/openbabel/openbabel - 9a45fd73bdcadc7ab69f01188cc7b3ff0de8e2d2 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Use current canonical SMILES for stereochemistry evaluation

github.com/openbabel/openbabel - db29fb4965c3761edde2a42e16e0ee5b6866822d authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Display current canonical SMILES

github.com/openbabel/openbabel - ead85bba14ec4d4a3ad72b4b8ad4ec96f3808a7c authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Add corruption check

github.com/openbabel/openbabel - 0b0472645504586cf9d859edf234979ae90a01ae authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Fix argument of IsTrans

github.com/openbabel/openbabel - 092f86f0a00949f5dd2e908a649965fea2e6f9bd authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Change error function and optimization method

github.com/openbabel/openbabel - 8cec3d2875489cf1fb1c2d80c152eda9b599765d authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Add distance geometry test with some initial cases

github.com/openbabel/openbabel - 332820918abfd0ebd2f28897403095c5cedd6a17 authored about 5 years ago by Geoff Hutchison <[email protected]>
More changes.

github.com/openbabel/openbabel - 33ff59dc00ff3646a520ac7cbd888baeb82bbcf8 authored about 5 years ago by Geoff Hutchison <[email protected]>
Implement gradient

github.com/openbabel/openbabel - 413847500f78a8bc93c8395a6d27839f1d7938f9 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Updated, working version

github.com/openbabel/openbabel - 727968130c79328aaf08621b150aaab57268f51c authored about 5 years ago by Geoff Hutchison <[email protected]>
Fix compiler warnings

github.com/openbabel/openbabel - edfae0e0db06ea55c88711c4a3c66592bc5251f1 authored about 5 years ago by Geoff Hutchison <[email protected]>
Fix argument of IsCis/IsTrans

github.com/openbabel/openbabel - 4519e5a5d9c464e0d3f5773fe84783d76cd995b1 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Normalize gradient

github.com/openbabel/openbabel - cfb79d5bd0196fb9ecb8af847cf425e2776ec07d authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Add debugging

github.com/openbabel/openbabel - 4e8fc069e94408c8909e979be3cc462debd3f72f authored about 5 years ago by Geoff Hutchison <[email protected]>
Fix unit test to actually fail with incorrect stereo

github.com/openbabel/openbabel - 894ea6d255b8d25f7fc7dc460e5b170109fdf355 authored about 5 years ago by Geoff Hutchison <[email protected]>
Always use initial stereo data

github.com/openbabel/openbabel - f250bf137f4a31a9d71e5b1fc68391b54949dc37 authored about 5 years ago by Naruki Yoshikawa <[email protected]>
Updates to improve distance geometry generation

github.com/openbabel/openbabel - a7dd2e1cd29fb80815fbdc6e3c1e96c1bf0a97be authored about 5 years ago by Geoff Hutchison <[email protected]>