openbabel commits | Ecosyste.ms: OpenCollective

2010-02-19 Noel O'Boyle

* src/CMakeLists.txt: Create plugin OBFs on Windows
* tests/CMakeLists.txt: Rename test target...

github.com/openbabel/openbabel - 38cbafeac0b1e939c79a8ef2487329e0b2b72068 authored almost 15 years ago

* test/conversion.cpp: Remove former test 8 as it was failing on

Windows because of the open file handle.
* src/formats/CMakeLists.txt: Build shared_ptr depende...

github.com/openbabel/openbabel - ec70082701321a395b4ebf49d4845b449696f913 authored almost 15 years ago

2010-02-17 Noel O'Boyle

* tools/obabel.cpp: Include cstdlib header to enable compilation
on Linux (due to missing exit())

github.com/openbabel/openbabel - f11899199088a4290486fbe19c4b38642f14a8db authored almost 15 years ago

Add nulformat and tweak MSVC Cmake build.

github.com/openbabel/openbabel - 10cf8d5715712a1f45d41edec7520b572ef4726a authored almost 15 years ago

Revert one of my changes that got rid of warnings

github.com/openbabel/openbabel - f2c52613ec9ab3f1db828cf2a1022b3ade7f7108 authored almost 15 years ago

* src/formats/tinkerformat.cpp (OpenBabel): Add support for MMFF94

atom typing with "-xm" flag. Fix warning from previous revision.

github.com/openbabel/openbabel - 1d65c54d43e1d0dd362ea4f7accd2954385bb92e authored almost 15 years ago

2010-02-15 Noel O'Boyle

* scripts/openbabel-python.i: Get rid of warnings. Allow access to
rotors. Tidy up the interfa...

github.com/openbabel/openbabel - 17e00be9d1d8cd9db3822686a0165543940cad96 authored almost 15 years ago

Add option -xm to output MMFF94 atom types. Needs more testing.

github.com/openbabel/openbabel - 6c58901afdddc7e83e596308393995ec2dd27489 authored almost 15 years ago

2010-02-14 Noel O'Boyle

* src/formats/CMakeLists.txt: Tidy up, and ensure that formats that
formats with dependencies ...

github.com/openbabel/openbabel - 54578f96f98c069cc1d970045a3ddba6cbe534a8 authored almost 15 years ago

* src/formats/CMakeLists.txt: Group formats into four different OBF

files on Window

github.com/openbabel/openbabel - cfd09a09a5869d065db08292d12bfea8eb9af1c3 authored almost 15 years ago

2010-02-14 Noel O'Boyle

* test/*: Avoid SafeOpen warnings by including obutil.h
* src/stereo/perception.cpp: Added de...

github.com/openbabel/openbabel - 13fc1aefc8da37dd2c432252a7e865090e3b3f44 authored almost 15 years ago

* src/forcefieldgaff.cpp: Fix warnings

github.com/openbabel/openbabel - ad7f76289bcfed0ff84fc48944a16e977934a762 authored almost 15 years ago

* test/*: Avoid SafeOpen warnings by including obutil.h

* formats/gulpformat.cpp, inchiformat.cpp: Add some dynamic casts to
avoid warning

github.com/openbabel/openbabel - 1b35d89c517137ec2af575d26b97d44f50fa359b authored almost 15 years ago

* test/CMakeLists.txt: Add FORMATDIR to point tests at appropriate

format location.

* test/*: Use it.

github.com/openbabel/openbabel - 5593b7b297726ac0e25a5ee11e40d3ad5c3501b6 authored almost 15 years ago

* src/formats/CMakeLists.txt: On Windows, make sure that the XML

formats compile to the correct location. Also no need to have
XML_INCLUDE on Windows

github.com/openbabel/openbabel - 6636ad0ec1c692e1a305f87105988894b281d215 authored almost 15 years ago

test/CMakeLists.txt: On Windows, put the test executables along with the compiled DLLs

github.com/openbabel/openbabel - 4f85d41ef80c22a2d277764ea7e20d800dec8435 authored almost 15 years ago

MDLFormat: allow numbers to be left justified.

github.com/openbabel/openbabel - 5418424e5996e8490f1b04f64c987e6e52024173 authored almost 15 years ago

Enable testing by default.

github.com/openbabel/openbabel - c7cc74239f7e8f205f17515cca89c6e05b998267 authored almost 15 years ago

Remove "format loaded" debugging messages.

github.com/openbabel/openbabel - d7bcbc9800cc4ff6904c10a4990b209db35387c3 authored almost 15 years ago

2010-02-08 Noel O'Boyle

* src/formats/inchiformat.cpp, smilesformat.cpp, xml/cmlformat.cpp and include/openbabel/atomcl...

github.com/openbabel/openbabel - f9859a457a9446d67d8f73de700cf3b83048cf34 authored almost 15 years ago

2010-02-07 Noel O'Boyle

* src/builder.h, cpp: Make things easier by referring to unsigned long
instead of OBStereo::Re...

github.com/openbabel/openbabel - ed372d83eda5c6f3d7a7b3e3d0d516d68255b099 authored almost 15 years ago

src/builder.cpp: IsSpiroAtom assumed that Ids were preserved on copying a molecule. Not true.

github.com/openbabel/openbabel - b704da69ad1eeba44c9a0301caae86903de4b701 authored almost 15 years ago

Fix for the new OBElementTable::GetAtomicNum(string,int&) to properly overload the old function.

github.com/openbabel/openbabel - 761b869191ac05512057860ddf90b724e81af7f8 authored almost 15 years ago

Improvements to OBUnitCell -- forgot a file from last commit.

github.com/openbabel/openbabel - 6f0b7af6b4ce4e1e932aa6807ff3ecb7fd47d617 authored almost 15 years ago

Improvements to OBUnitCell.

github.com/openbabel/openbabel - b4ed1d1f04e899444de0afec7af5e4246f76cdd5 authored almost 15 years ago

Added GetAtomicNum accepting IUPAC name

github.com/openbabel/openbabel - 2d80706000ce36934775d6b23342497a96575332 authored almost 15 years ago

Changed identification of Gaussian (current doesn't recognize all files)

github.com/openbabel/openbabel - d9db31687f4ddb8134616b22da6f241ea4978051 authored almost 15 years ago

Remove atoms from pmol before adding more in the gulp format reader.

github.com/openbabel/openbabel - fe40614c07ae81fb52f512e4ca7905e18c97fe4a authored almost 15 years ago

Correction to invalid SMARTS in example.

github.com/openbabel/openbabel - 706fe22b8b203b52d631f45ae425b92be0c199e4 authored almost 15 years ago

Change include file logic for shared_ptr in GCC, as suggested by Konstantin Tokarev

github.com/openbabel/openbabel - 9f32f0e53cadfe736d68b57b91928c3e9e529ece authored almost 15 years ago

Correct fastsearchformat description which misled Noel.

github.com/openbabel/openbabel - 83f7131e88e3e675b120842bacd0241f6ede930c authored almost 15 years ago

Added MNA format

github.com/openbabel/openbabel - 00410bbf6c34213bd792dc4ec9882eb9c01ca733 authored about 15 years ago

Set vectors in OBUnitCell when lengths/angles are specified.

github.com/openbabel/openbabel - b5dbecb09227704e23660ceded768f69b7257a08 authored about 15 years ago

Raman activities

github.com/openbabel/openbabel - 7f3452062dab1c5d35f054e841cd197b0ff66867 authored about 15 years ago

Some more fixes to make finding the path of the binaries easier.

github.com/openbabel/openbabel - 9418ef0039ce1f4bd4c2af20736532a328f5146b authored about 15 years ago

Some updates to the build system and the dashboard config.

github.com/openbabel/openbabel - e084d5c2fa5e6dda2c85b03de2c3990ca8fcd668 authored about 15 years ago

2009-12-15 Noel O'Boyle

* src/formats/smilesformat.cpp: Create OBPairData of "SMILES Atom
Order" whenever creating a S...

github.com/openbabel/openbabel - 6e4d9a1f32b1959b64c6ab94ae238e861feb9c9e authored about 15 years ago

Improve the handling of dative bonds in Fastsearch.

github.com/openbabel/openbabel - 4be4e41c89b6a390f0d605d20b4037cded348e3f authored about 15 years ago

2009-12-14 Noel O'Boyle

* src/GUI/OBGUI.cpp: Fix compilation on Linux.

github.com/openbabel/openbabel - 4f4db438da934e25ec4ef567bbe98820ece6fa79 authored about 15 years ago

Get description of any plugin class from commandline -L option of GUI.

github.com/openbabel/openbabel - b99b5e74807ef66431aec08c16e63af150c15c20 authored about 15 years ago

Fixes to the VASP format reader.

github.com/openbabel/openbabel - 0a2069b14b8e8634661d10d63ad2474ce1df9ef4 authored about 15 years ago

Don't build wxWidgets GUI on Mac -- there are strange build problems. (Apple/wxWidgets bug, not ours.)

github.com/openbabel/openbabel - de796c812ecda0afe7b5002b5c290d212bcef766 authored about 15 years ago

Fix ghemcial vdw term (including analytical gradients)

github.com/openbabel/openbabel - d78dbb0e0c1a2f4c6c49b3c361a3f0315c238590 authored about 15 years ago

Update CMake files for OBDepict and svgformat

github.com/openbabel/openbabel - 54b7c41a72c7efa808e9ed44c590c61ab7251bd2 authored about 15 years ago

Fix rotational constants in GaussFormat and atom display in OBDepict

github.com/openbabel/openbabel - 1107a6f4023d3148a710467a4aceab4178dd1c3f authored about 15 years ago

Add names to methods in generic.h

github.com/openbabel/openbabel - d0ee06502012e293209a4e2ff6f267309b9e6ed5 authored about 15 years ago

Make gulp format handle the conv output.

github.com/openbabel/openbabel - 9cdbfe0c9b987d6e572b8415cda483a4a904f379 authored about 15 years ago

Temporarily disable SVGformat until I have time to debug the link errors with GCC on Mac.

github.com/openbabel/openbabel - aa5bebafcd4bbc59df2788c624aae354a3487c6f authored about 15 years ago

Closer to compiling on gcc?

github.com/openbabel/openbabel - 252608c79135a70e2744bd9c44c9e51f7d6662d3 authored about 15 years ago

Remove "OpenBabel Symmetry Classes" from sdf and cml output.

github.com/openbabel/openbabel - 6e82c139a9b126221c1ab93fa8448f1fa6102db4 authored about 15 years ago

Fixes to gulp format reader

github.com/openbabel/openbabel - 0c839b2dcc94739de0a6fc874f3d589dea7417d1 authored about 15 years ago

FastSearch: can simultaneously match aromatic and aliphatic atoms and bonds

github.com/openbabel/openbabel - 8ee09895cdcb7741307d8ba1063b92d8d8c558f2 authored about 15 years ago

Quadruple bond in smilesformat

github.com/openbabel/openbabel - 6e7c3bece4daad1a51b1211febe026fca90c9403 authored about 15 years ago

Avoid leading separators with --append

github.com/openbabel/openbabel - 2b550b917d16e32a1066fd8823d5481217150842 authored about 15 years ago

Added svgdepict program and renamed nbabel as obabel.

github.com/openbabel/openbabel - 7686f522b3fae6417dfcec0501bc019e74c2ac01 authored about 15 years ago

New classes SVGPainter and SVGFormat for 2D depiction

github.com/openbabel/openbabel - 25eeec97394f8d57ef00c8c75145d56ecb50f26f authored about 15 years ago

Add coordinates when expanding aliases. mdlformat writes alias form.

github.com/openbabel/openbabel - 54e831f0e97ded47911bb12bb8ca60072b38a585 authored about 15 years ago

Added a format parser for the GULP package.

github.com/openbabel/openbabel - 2bc325fac04cd01b618e9b4bb2d882d4e1cbc168 authored about 15 years ago

Trivial change to copyright header.

github.com/openbabel/openbabel - d2fedd697f10377e6a57c3e8ce6921d187a6afee authored about 15 years ago

Converting a reaction to most molecule formats (not CML) outputs molecules

github.com/openbabel/openbabel - 96022a895dcb7697e9cfacd4be58a44d0c27288e authored about 15 years ago

OBMol::Has3D easier to use; other precautionary and cosmetic mods

github.com/openbabel/openbabel - 15284a92bd059c3336d2ea17ae6074c039296209 authored about 15 years ago

Minor build-related mods (Windows mainly)

github.com/openbabel/openbabel - e864965a7184e17fdefc5b44fde8a232c2b045b5 authored about 15 years ago

Fix compile error.

github.com/openbabel/openbabel - 1c35c8ced5117e0a16246864fcd952edbe52fe76 authored about 15 years ago

Fix tetrahedral stereocenter detection for cases where there are two duplicated symmetry classes not in a ring.

github.com/openbabel/openbabel - b2aee5a671b2822099c811cef89c4c87f70aaef6 authored about 15 years ago

Add OBAPI

github.com/openbabel/openbabel - e3295a1a0da7f3ec0e713444701c00d9e5eaa2fb authored about 15 years ago

Correct error. Wrong method name.

github.com/openbabel/openbabel - 8075ee68789564e5153406ba18270e30e783ee0f authored about 15 years ago

* src/formats/inchiformat.cpp (WriteMolecule): Don't create

stereo objects to pass to the InChI code if the stereo is unspecified.
This avoids an InChI war...

github.com/openbabel/openbabel - 6ad59392accade908352695c05ee4ceb33b03695 authored about 15 years ago

2009-10-29 Michael Banck <[email protected]>

* src/formats/molproformat.cpp (ReadMolecule): Applied patch #2893477
by Konstan...

github.com/openbabel/openbabel - 572ac6620b5c531a77ab976015582a26001da5b8 authored about 15 years ago

* src/formats/xml/xml.cpp (OpenBabel): Defensive programming for

issue reported by Matt Sprague -- access violation when
reading/writing xml formats.

github.com/openbabel/openbabel - 06562b7e6e32b8ac613b6dc81d7b81989c3217e5 authored about 15 years ago

Updated with latest version from OB-2-2-x branch.

github.com/openbabel/openbabel - 7619663431c3916148438a540cf2159672dc8ac0 authored about 15 years ago

2009-10-29 Michael Banck <[email protected]>

* src/formats/outformat.cpp: Applied patch #2888693 to add support for
PC-GAMES...

github.com/openbabel/openbabel - 4e86dbb3c020bb0c4e02b3cd850289375f76c25d authored about 15 years ago

* builder.h, .cpp: Add code to fix ring stereochemistry if possible by inverting the coordinates of a ring system

github.com/openbabel/openbabel - 8c1b5f4e794e8c3d04760c8796a304f6ccd79177 authored over 15 years ago

Add warning that AliasData::Expand() currently does not add atom coordinates.

github.com/openbabel/openbabel - b2ea180f78fe1504061c4196e6e13a79a696f434 authored over 15 years ago

Improved support for aliases (superatoms)

github.com/openbabel/openbabel - ac41e164bbe1e36167ebfe9923d2d0ae3ad8b68b authored over 15 years ago

* src/parsmart.cpp, include/openbabel/parsmart.h: Make bond_parse_order an instance variable rather than a class variable. Fixes bug where multiple SMARTS patterns are parsed before being used to Match.

github.com/openbabel/openbabel - 79c4d657cdb22c432aa6158a0739fed4d992ab9a authored over 15 years ago

Correct small memory leak

github.com/openbabel/openbabel - b2fa6b917f7f3df8771649b257a6e4b646061ee6 authored over 15 years ago

* src/builder.h,.cpp: Handle ring template matches that overlap at spiro atoms, and correct spiro stereochemistry. Minor fix to Swap to correct bond lengths.

github.com/openbabel/openbabel - e7fb7badaa49231ae4293dde60c5b6380d2c9feb authored over 15 years ago

Doc fix for StripSalts: "Delete any fragments with fewer than @p threshold atoms"

github.com/openbabel/openbabel - 4131d39d080951249d328ed952547ac52d132667 authored over 15 years ago

* src/builder.cpp: Don't attempt to fix stereochemistry if unspecified.

github.com/openbabel/openbabel - 3f026c81ffcd60bd18edd7eb5470b331341b74a9 authored over 15 years ago

* src/forcefield.cpp: Correctly handle SteepestDescent and Conjugate Gradients where nsteps is 0 or 1

github.com/openbabel/openbabel - 46d424147f94f4b703de536041f4c7066886db79 authored over 15 years ago

* src/forcefield.cpp: In ff.GetConformers(mol) if only a single conformer was generated it was not being copied.

github.com/openbabel/openbabel - b943699318f5c22e20c7a8721be3804bfc5aaf17 authored over 15 years ago

Rename test/data.cpp to test/datatest.cpp (conflicted with data directory)

github.com/openbabel/openbabel - f4f76681b88457b0382ab5d0253232eb12984da1 authored over 15 years ago

minor change to previous commit

github.com/openbabel/openbabel - 69190ff44cdd501eaf8cb0d12257f42e87b784f1 authored over 15 years ago

Some updates for the MinGW (GCC 4.4) build.

github.com/openbabel/openbabel - f1a68cf89c305a639668e6418ca2ea23cf53bc44 authored over 15 years ago

* For Windows build, enable tests to be run in either Debug or Release

build. Make the default solution file include the tests. Add a target

github.com/openbabel/openbabel - f395e2bd11301eed8a20c979ed4654114fe0176e authored over 15 years ago

* Update Windows build to use the InChI dll, and to build everything

to the same folder (e.g. Release or Debug). Tests can be run in Debug
build

github.com/openbabel/openbabel - 740c83f765d7beea697b4e4f980b789c3e354d98 authored over 15 years ago

* src/builder.cpp: Update handling of stereochemistry to use new

stereochemistry objects. For tetrahedral centres, stereochemistry is
currently not corrected if...

github.com/openbabel/openbabel - 153ec1430dec2fc2b84b6e368dc69e94ddef7504 authored over 15 years ago

Merged revisions 3341-3344 via svnmerge from

https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-2-x

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github.com/openbabel/openbabel - 64221a418404df01b5f0e7fbfdfa877f48ce716d authored over 15 years ago

Merged revisions 3339 via svnmerge from

https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-2-x

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github.com/openbabel/openbabel - 0e941f00b97765cbf621d45b9fef7108b1e50164 authored over 15 years ago

For some reason, two files were missed in the previous merge.

github.com/openbabel/openbabel - 2ad9a657ee1833695ce48e0545246848dc722031 authored over 15 years ago

Merged revisions 3335-3337 via svnmerge from

https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-2-x

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github.com/openbabel/openbabel - 1e44e0fc7dee70f2905bdb529433b5c54f7f03ce authored over 15 years ago

Blocked revisions 3367,3370 via svnmerge

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r3367 | mr_grieves | 2009-08-18 15:50:59 +0100 (Tue, 18 Aug 2009) | 1 line

Fix c...

github.com/openbabel/openbabel - d85df2318c19f888b8b1e9cf06f158b4a20cc78e authored over 15 years ago

Blocked revisions 3340,3346,3349,3360,3366,3381 via svnmerge

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r3340 | ghutchis | 2009-07-29 01:27:09 +0100 (Wed, 29 Jul 2009) | 2 lines

Bump b...

github.com/openbabel/openbabel - 94ba3a0b4a8e3f6871b82c0d5b6b826a60886637 authored over 15 years ago

Blocked revisions 3132,3136-3139,3148,3195,3221 via svnmerge

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r3132 | timvdm | 2009-07-08 07:46:45 +0100 (Wed, 08 Jul 2009) | 5 lines

* src/fo...

github.com/openbabel/openbabel - c2b6a6ad9922b3d4629ffe6f3ea7aea0c5c28849 authored over 15 years ago

Recorded merge of revisions 3131,3133-3134,3140-3142,3144-3147,3149-3152 via svnmerge from

https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-2-x

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github.com/openbabel/openbabel - fea35dd315521d136bd8b71bf82f6a72a23ca49f authored over 15 years ago

Merged revisions 3369 via svnmerge from

https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-2-x

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github.com/openbabel/openbabel - 452813d1f77b483c61fd0a29ad8f2b6caf4a29b1 authored over 15 years ago

Blocked revisions 3135,3143,3371 via svnmerge

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r3135 | baoilleach | 2009-07-08 15:55:42 +0100 (Wed, 08 Jul 2009) | 4 lines

2009...

github.com/openbabel/openbabel - be9eb803f8b23d4feed44b0cbdb9175275c2ff67 authored over 15 years ago

2009-09-30 Noel O'Boyle <[email protected]>

* src/builder.cpp: Reapplied Geoff's fix from r3028 (undone in r3251)
to enable 0D molecules t...

github.com/openbabel/openbabel - 1fc45b4aa85e154af625164bba1d46036f6f4adc authored over 15 years ago

2009-09-27 Noel O'Boyle <[email protected]>

* src/GUI/OBGUI.cpp: GUI now compiles and runs successfully on MacOSX.

github.com/openbabel/openbabel - ec4ff0cf8ecf4d41301f6111aa5b896c78d3f24c authored over 15 years ago

2009-09-27 Noel O'Boyle <[email protected]>

* include/openbabel/graphsym.h, src/graphsym.cpp: Changed how static
const unsigned int was de...

github.com/openbabel/openbabel - 54fc42d052f7c920a39f89026330ea6577967f58 authored over 15 years ago