lp:openbabel

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Branches

Name Last Modified Last Commit
master 2022-09-22 18:34:59 UTC
Fix 338 (#2537)

Author: Fredrik Wallner
Author Date: 2022-09-22 18:34:59 UTC

Fix 338 (#2537)

* Make sure charge is read as int8 as in spec
Will not handle files from ChemDraw >=8.0 <8.06

* Fix typo in test

smilesorder 2020-10-14 12:42:17 UTC
Ensure that specifying the output atom order in SMILES does not cause any hyd...

Author: baoilleach
Author Date: 2020-10-14 12:42:17 UTC

Ensure that specifying the output atom order in SMILES does not cause any hydrogens to be suppressed

javadoc 2020-05-25 08:39:00 UTC
Enable Javadoc for SWIG 4.0

Author: baoilleach
Author Date: 2020-05-25 08:39:00 UTC

Enable Javadoc for SWIG 4.0

enable_pydoc 2020-05-25 06:44:26 UTC
Ensure that the code works with both SWIG 3 and SWIG 4. Also avoid non-ascii ...

Author: baoilleach
Author Date: 2020-05-25 06:44:26 UTC

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.

appveyor 2020-05-24 09:21:56 UTC
Force build to test appveyor

Author: baoilleach
Author Date: 2020-05-24 09:21:56 UTC

Force build to test appveyor

py27_support 2020-05-23 09:25:01 UTC
Revert the slash n change

Author: baoilleach
Author Date: 2020-05-23 09:25:01 UTC

Revert the slash n change

msvc2015 2020-05-16 09:33:01 UTC
Add extra include for MSVC2015 support of back_inserter

Author: baoilleach
Author Date: 2020-05-16 09:33:01 UTC

Add extra include for MSVC2015 support of back_inserter

FixFunctorWarning 2020-05-08 14:20:11 UTC
Fix Functor warning

Author: baoilleach
Author Date: 2020-05-08 14:20:11 UTC

Fix Functor warning

FixCompileWarning 2020-05-08 13:35:31 UTC
Fix the compiler warning about large object size

Author: baoilleach
Author Date: 2020-05-08 13:35:31 UTC

Fix the compiler warning about large object size

workaroundswigjava 2020-05-02 11:41:42 UTC
Workaround a problem in SWIG 4.0.1 (at least) where the generated Java source...

Author: baoilleach
Author Date: 2020-05-02 11:41:42 UTC

Workaround a problem in SWIG 4.0.1 (at least) where the generated Java source relies on reserve being present

adalke_writestring 2020-04-13 10:51:55 UTC
Apply patch from @fredrikw to fix test failure. Also minor changes as recomme...

Author: baoilleach
Author Date: 2020-04-13 10:51:55 UTC

Apply patch from @fredrikw to fix test failure. Also minor changes as recommended by codacity code review.

smiles_charge 2020-02-20 21:33:22 UTC
Be more strict when parsing charges in SMILES

Author: baoilleach
Author Date: 2020-02-20 21:33:22 UTC

Be more strict when parsing charges in SMILES

CastStereoBase 2020-02-03 21:10:25 UTC
Add testcase

Author: baoilleach
Author Date: 2020-02-03 21:02:22 UTC

Add testcase

kekulizesulfoxide 2020-01-30 20:21:13 UTC
Support kekulization of aromatic sulfoxides, if such a thing would every occur.

Author: baoilleach
Author Date: 2020-01-30 20:21:13 UTC

Support kekulization of aromatic sulfoxides, if such a thing would every occur.

Fix2081 2020-01-20 20:46:21 UTC
Correct the path to the openbabel-python.cpp so that the Python bindings can ...

Author: baoilleach
Author Date: 2020-01-20 20:46:21 UTC

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).

suppreshydrogens 2020-01-03 23:10:19 UTC
Minor update

Author: baoilleach
Author Date: 2020-01-03 23:10:19 UTC

Minor update

nocharge 2020-01-03 23:05:45 UTC
Add call to suppress hydrogens. Also minor tweak to docstring.

Author: baoilleach
Author Date: 2020-01-03 23:05:45 UTC

Add call to suppress hydrogens. Also minor tweak to docstring.

wln 2019-11-16 12:58:54 UTC
Update test cases and docstring with info from NextMove Bio-IT poster

Author: baoilleach
Author Date: 2019-11-16 12:58:54 UTC

Update test cases and docstring with info from NextMove Bio-IT poster

smartshashzero 2019-11-08 18:11:42 UTC
Support #0 in SMARTS so that asterisks can be matched

Author: baoilleach
Author Date: 2019-11-08 18:11:42 UTC

Support #0 in SMARTS so that asterisks can be matched

updatedocstrings 2019-10-06 20:00:59 UTC
Fix file format docstrings that were causing problems with Sphinx or with the...

Author: baoilleach
Author Date: 2019-10-06 19:19:55 UTC

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

fix_compilation 2019-09-25 14:41:24 UTC
Fix compilation with GCC 4.8 (standard compiler on CentOS 7.5)

Author: baoilleach
Author Date: 2019-09-25 14:41:24 UTC

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

Bump30 2019-09-20 18:50:42 UTC
Remove minor version from some names

Author: baoilleach
Author Date: 2019-09-20 18:50:42 UTC

Remove minor version from some names

kekule_not_default 2019-09-20 14:10:17 UTC
Don't make kekule SMILES the default in the GUI

Author: baoilleach
Author Date: 2019-09-20 14:10:17 UTC

Don't make kekule SMILES the default in the GUI

remove_babel 2019-09-10 15:06:48 UTC
Change references to babel to obabel

Author: baoilleach
Author Date: 2019-04-23 19:49:50 UTC

Change references to babel to obabel

valencedegree 2019-04-22 15:41:42 UTC
Replace static methods, or in-place expressions, to calculate the total valen...

Author: baoilleach
Author Date: 2019-04-22 15:41:42 UTC

Replace static methods, or in-place expressions, to calculate the total valence or total degree with calls to the new OBAtom methods.

obrandom 2019-04-15 19:54:45 UTC
smilesformat.cpp doesn't actually use OBRandom. It just calls rand().

Author: baoilleach
Author Date: 2019-03-25 20:29:31 UTC

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

cmakewarnings 2019-03-19 13:53:58 UTC
Drive-by fix for Python tests on Windows

Author: baoilleach
Author Date: 2019-03-19 13:53:58 UTC

Drive-by fix for Python tests on Windows

flags 2019-03-19 07:30:45 UTC
Update one of the Python tests for the API changes

Author: baoilleach
Author Date: 2019-03-19 07:30:45 UTC

Update one of the Python tests for the API changes

Fix310 2019-02-28 21:36:14 UTC
Revert "CMakeLists.txt: Allow configuring BABEL_DATADIR"

Author: baoilleach
Author Date: 2019-02-28 21:36:14 UTC

Revert "CMakeLists.txt: Allow configuring BABEL_DATADIR"

This reverts commit 417361bb9f19c78434b067293980085464760c20.

PR1929 2019-02-26 21:35:23 UTC
Fix isomorphism mapper issue. PR1929

Author: baoilleach
Author Date: 2019-02-26 21:35:23 UTC

Fix isomorphism mapper issue. PR1929

phmodel 2018-11-26 21:30:11 UTC
Remove (almost) all patterns with #1. A change in 2007 ensured that all hydro...

Author: Noel O'Boyle
Author Date: 2018-11-26 21:30:11 UTC

Remove (almost) all patterns with #1. A change in 2007 ensured that all hydrogens were removed at the start of the function. Given that's the case these patterns will never fire.

Fix1830 2018-09-10 19:27:59 UTC
Support lone pair stereo on nitrogen as well as sulfur

Author: baoilleach
Author Date: 2018-09-10 19:27:59 UTC

Support lone pair stereo on nitrogen as well as sulfur

kekfailure 2018-08-08 15:35:45 UTC
Add an option to the SMILES reader to treat kekulization failure as an error....

Author: baoilleach
Author Date: 2018-08-08 15:35:45 UTC

Add an option to the SMILES reader to treat kekulization failure as an error. Without this, it cannot be caught.

snaps 2018-07-21 09:12:14 UTC
Merge branch 'snaps' of https://github.com/baoilleach/openbabel into snaps

Author: baoilleach
Author Date: 2018-07-21 09:12:14 UTC

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

smilesrxn 2018-07-18 21:01:18 UTC
Merge branch 'master' into smilesrxn

Author: baoilleach
Author Date: 2018-07-18 21:01:18 UTC

Merge branch 'master' into smilesrxn

FirstLast 2018-07-05 07:21:11 UTC
On second thoughts - don't add 'm' option - it doesn't make any sense. Also a...

Author: baoilleach
Author Date: 2018-07-05 07:21:11 UTC

On second thoughts - don't add 'm' option - it doesn't make any sense. Also add tests

reducelinking 2018-02-18 10:56:28 UTC
WIP - Initial changes

Author: baoilleach
Author Date: 2018-02-18 10:56:28 UTC

WIP - Initial changes

FixWarnings 2018-01-11 08:03:25 UTC
Use a portable way to mark variables as unused. Hopefully fix MSVC build.

Author: baoilleach
Author Date: 2018-01-11 08:03:25 UTC

Use a portable way to mark variables as unused. Hopefully fix MSVC build.

MoveAtomClass 2017-12-30 20:30:47 UTC
Add missing include to fix Linux build

Author: baoilleach
Author Date: 2017-12-30 20:30:47 UTC

Add missing include to fix Linux build

SwitchStatement 2017-12-28 20:54:18 UTC
A test was failing due to Windows line-endings. Added code to explicitly hand...

Author: baoilleach
Author Date: 2017-12-14 20:36:03 UTC

A test was failing due to Windows line-endings. Added code to explicitly handle the \r.

SwigIterators 2017-12-16 21:31:37 UTC
Reduce Python bindings by 20% by avoiding adding methods from the iterated ob...

Author: baoilleach
Author Date: 2017-12-16 21:31:37 UTC

Reduce Python bindings by 20% by avoiding adding methods from the iterated object to the iterator

AvoidStringCopy 2017-12-14 21:10:02 UTC
In the SMILES reader, avoid the allocation of the BUFSIZE buffer, and the ass...

Author: baoilleach
Author Date: 2017-12-14 21:10:02 UTC

In the SMILES reader, avoid the allocation of the BUFSIZE buffer, and the associated string copy.

SmilesSpeedImprov 2017-12-14 20:08:12 UTC
Add some std::vector reserves to speed things up

Author: baoilleach
Author Date: 2017-12-12 20:44:13 UTC

Add some std::vector reserves to speed things up

AvoidSSSR 2017-12-14 07:46:57 UTC
Correct the comparison. I was stripping the stereo from the wrong double bonds.

Author: baoilleach
Author Date: 2017-12-14 07:46:57 UTC

Correct the comparison. I was stripping the stereo from the wrong double bonds.

IsInRing 2017-12-08 13:54:36 UTC
Make sure that OBAtom::IsInRing always triggers ring perception if not set as...

Author: baoilleach
Author Date: 2017-12-08 13:54:36 UTC

Make sure that OBAtom::IsInRing always triggers ring perception if not set as perceived

FixGraphSymMemleak 2017-11-27 09:17:11 UTC
Only ABCs should have a virtual dtor

Author: baoilleach
Author Date: 2017-11-27 09:17:11 UTC

Only ABCs should have a virtual dtor

rsmi_missing_comps 2017-10-09 20:33:21 UTC
Merge branch 'rsmi_missing_comps' of https://github.com/baoilleach/openbabel ...

Author: baoilleach
Author Date: 2017-10-09 20:33:21 UTC

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

moreagents 2017-09-15 07:30:16 UTC
Remove final reference to original _agent

Author: baoilleach
Author Date: 2017-09-15 07:30:16 UTC

Remove final reference to original _agent

rinchi 2017-08-31 06:10:59 UTC
Change OBReaction to support multiple agents instead of just one

Author: baoilleach
Author Date: 2017-08-31 06:10:59 UTC

Change OBReaction to support multiple agents instead of just one

radicals 2017-08-14 07:27:55 UTC
Remove not-longer-needed comment, and some blank lines.

Author: baoilleach
Author Date: 2017-08-14 07:27:55 UTC

Remove not-longer-needed comment, and some blank lines.

updatedocs 2016-06-02 21:40:16 UTC
Docstring updates to fix formatting

Author: baoilleach
Author Date: 2016-06-02 21:40:16 UTC

Docstring updates to fix formatting

align_permutations 2014-02-10 21:07:04 UTC
Use PermutationWrapper to permute rows instead of doing it manually.

Author: baoilleach
Author Date: 2014-02-10 21:07:04 UTC

Use PermutationWrapper to permute rows instead of doing it manually.

confab 2013-04-28 11:55:42 UTC
Add confabreport output format used to replace 'calcrmsd' executable in origi...

Author: baoilleach
Author Date: 2013-04-28 11:55:42 UTC

Add confabreport output format used to replace 'calcrmsd' executable in original Confab. Tidy up opconfab code, and suppress writing out of the original molecule.

openbabel-2-3-x 2012-10-06 16:01:56 UTC
Add splash.png to /data.

Author: Chris Morley
Author Date: 2012-10-06 16:01:56 UTC

Add splash.png to /data.

openbabel-2-2-x 2010-05-13 13:25:10 UTC
CMakeLists.txt: Backported output directories

Author: Konstantin Tokarev
Author Date: 2010-05-13 13:25:10 UTC

CMakeLists.txt: Backported output directories

experimental 2008-09-12 17:06:40 UTC
* CMakeLists.txt, src/config.h.cmake: apply patch from Christian

Author: timvdm
Author Date: 2008-09-12 17:06:40 UTC

       * CMakeLists.txt, src/config.h.cmake: apply patch from Christian
        Ehrlicher to fix cmake MSVC compilation.

openbabel-2-1-x 2008-01-20 16:42:25 UTC
Added inchi.sym, missing from last commit

Author: Michael Banck
Author Date: 2008-01-20 16:42:25 UTC

Added inchi.sym, missing from last commit

openbabel-2-0-x 2006-10-17 16:09:04 UTC
* configure, configure.in, */Makefile.*: Updated with latest

Author: Geoff Hutchison
Author Date: 2006-10-17 16:09:04 UTC

  * configure, configure.in, */Makefile.*: Updated with latest
  autoconf, automake, etc.

openbabel-new-framework 2005-11-24 12:27:01 UTC
*** empty log message ***

Author: Chris Morley
Author Date: 2005-11-24 12:27:01 UTC

*** empty log message ***

ob-newf 2004-10-20 02:53:12 UTC
This commit was manufactured by cvs2svn to create branch 'ob-newf'.

Author: No Author
Author Date: 2004-10-20 02:53:12 UTC

This commit was manufactured by cvs2svn to create branch 'ob-newf'.

openbabel-1-100-x 2004-10-04 09:21:53 UTC
2004-10-04 Michael Banck <mbanck@gmx.net>

Author: Michael Banck
Author Date: 2004-10-04 09:21:53 UTC

2004-10-04 Michael Banck <mbanck@gmx.net>

        * src/crk.cpp: Use sstream if present and strstream if not.

openbabel-1-100 2002-12-07 01:55:59 UTC
This commit was manufactured by cvs2svn to create branch

Author: No Author
Author Date: 2002-12-07 01:55:59 UTC

This commit was manufactured by cvs2svn to create branch
'openbabel-1-100'.

macos 2002-07-28 01:41:38 UTC
This commit was manufactured by cvs2svn to create branch 'macos'.

Author: No Author
Author Date: 2002-07-28 01:41:38 UTC

This commit was manufactured by cvs2svn to create branch 'macos'.

openeye 2001-11-27 18:50:36 UTC
This commit was manufactured by cvs2svn to create branch 'openeye'.

Author: No Author
Author Date: 2001-11-27 18:50:36 UTC

This commit was manufactured by cvs2svn to create branch 'openeye'.

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