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[OpenBabel-Updates] SF.net SVN: openbabel:[4340] openbabel/trunk/src

From: <ghutchis@us...> - 2010-12-15 21:44

Revision: 4340
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4340&view=rev
Author:   ghutchis
Date:     2010-12-15 21:44:02 +0000 (Wed, 15 Dec 2010)

Log Message:
-----------
Incorporated MMFF94 changes from Paolo.

Modified Paths:
--------------
    openbabel/trunk/src/forcefields/forcefieldmmff94.cpp
    openbabel/trunk/src/formats/mol2format.cpp
    openbabel/trunk/src/mol.cpp


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Thread	Author	Date
[OpenBabel-Updates] SF.net SVN: openbabel:[2772] openbabel/trunk/src	<cjames53@us...>

[OpenBabel-Updates] SF.net SVN: openbabel:[2950] openbabel/trunk/src

From: <ghutchis@us...> - 2009-03-27 02:00

Revision: 2950
          http://openbabel.svn.sourceforge.net/openbabel/?rev=2950&view=rev
Author:   ghutchis
Date:     2009-03-27 01:51:04 +0000 (Fri, 27 Mar 2009)

Log Message:
-----------
Fix some minor merge issues.

Modified Paths:
--------------
    openbabel/trunk/src/formats/CMakeLists.txt
    openbabel/trunk/src/mol.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3251] openbabel/trunk/src

From: <timvdm@us...> - 2009-07-18 22:32

Revision: 3251
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3251&view=rev
Author:   timvdm
Date:     2009-07-18 22:32:25 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
src/builder.cpp: OBBuilder::GetNewBondVec(), compute 2D coordinates for
molecules where OBMol::GetDimensions() == 2. Also, check for
stereochemistry, if we find a hash or wedge make sure the new atom will
be placed next to the hash/wedge so the stereochemistry remains the
same.

src/mol.cpp: OBMol::AddHydrogens(), When adding hydrogens to a 2D
molecule, check if we need to set a hash/wedge flag for the bond to the
newly added hydrogen.

Conflicts:

	src/builder.cpp
	src/mol.cpp

Modified Paths:
--------------
    openbabel/trunk/src/builder.cpp
    openbabel/trunk/src/mol.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3297] openbabel/trunk/src

From: <timvdm@us...> - 2009-07-18 22:43

Revision: 3297
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3297&view=rev
Author:   timvdm
Date:     2009-07-18 22:43:56 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
remove some debug output

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp
    openbabel/trunk/src/stereo/perception.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3320] openbabel/trunk/src

From: <timvdm@us...> - 2009-07-18 22:51

Revision: 3320
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3320&view=rev
Author:   timvdm
Date:     2009-07-18 22:50:53 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
0D now working for inchi, smiles and mdl.

Modified Paths:
--------------
    openbabel/trunk/src/formats/inchiformat.cpp
    openbabel/trunk/src/formats/mdlformat.cpp
    openbabel/trunk/src/formats/smilesformat.cpp
    openbabel/trunk/src/stereo/perception.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3289] openbabel/trunk/src

From: <timvdm@us...> - 2009-07-19 00:17

Revision: 3289
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3289&view=rev
Author:   timvdm
Date:     2009-07-18 22:42:08 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Some improvements to 2D stereochemistry perception + handle '@?' smiles input

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp
    openbabel/trunk/src/stereo/perception.cpp
    openbabel/trunk/src/stereo/tetrahedral.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3226] openbabel/trunk/src

From: <timvdm@us...> - 2009-07-19 00:18

Revision: 3226
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3226&view=rev
Author:   timvdm
Date:     2009-07-18 22:19:48 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Use chiral_neighbors paramter in smiles writing...

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp
    openbabel/trunk/src/mol.cpp
    openbabel/trunk/src/stereo/tetrahedral.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3270] openbabel/trunk/src

From: <timvdm@us...> - 2009-07-19 00:19

Revision: 3270
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3270&view=rev
Author:   timvdm
Date:     2009-07-18 22:37:18 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
src/formats/smilesformat.cpp: delete objects in _tetrahedralMap after
parsing smiles. Correct an of-by-one error. Will add more checks to see
if we are "overwriting" a reference id.

src/graphsym.cpp: Some improvements to BreakChiralTies

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp
    openbabel/trunk/src/graphsym.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3413] openbabel/trunk/src

From: <baoilleach@us...> - 2009-09-19 16:43

Revision: 3413
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3413&view=rev
Author:   baoilleach
Date:     2009-09-19 16:43:44 +0000 (Sat, 19 Sep 2009)

Log Message:
-----------
More miscellaneous static_casts added and unused variables removed to get rid of warnings under MSVC

Modified Paths:
--------------
    openbabel/trunk/src/forcefields/forcefieldgaff.cpp
    openbabel/trunk/src/formats/mopacformat.cpp
    openbabel/trunk/src/formats/qchemformat.cpp
    openbabel/trunk/src/formats/smilesformat.cpp
    openbabel/trunk/src/formats/vaspformat.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3548] openbabel/trunk/src

From: <ghutchis@us...> - 2010-02-23 03:56

Revision: 3548
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3548&view=rev
Author:   ghutchis
Date:     2010-02-23 03:56:31 +0000 (Tue, 23 Feb 2010)

Log Message:
-----------
Fix minor 32-bit conversion warnings with GCC (mostly truncated float/double).

Modified Paths:
--------------
    openbabel/trunk/src/canon.cpp
    openbabel/trunk/src/formats/cifformat.cpp
    openbabel/trunk/src/graphsym.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3569] openbabel/trunk/src

From: <baoilleach@us...> - 2010-02-28 13:33

Revision: 3569
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3569&view=rev
Author:   baoilleach
Date:     2010-02-28 13:33:22 +0000 (Sun, 28 Feb 2010)

Log Message:
-----------
Revert 3566, 3567

Modified Paths:
--------------
    openbabel/trunk/src/CMakeLists.txt
    openbabel/trunk/src/formats/CMakeLists.txt


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[OpenBabel-Updates] SF.net SVN: openbabel:[3664] openbabel/trunk/src

From: <annulen@us...> - 2010-04-01 13:09

Revision: 3664
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3664&view=rev
Author:   annulen
Date:     2010-04-01 12:58:32 +0000 (Thu, 01 Apr 2010)

Log Message:
-----------
Added 'formats' target to prevent race condition on parallel build

Modified Paths:
--------------
    openbabel/trunk/src/CMakeLists.txt
    openbabel/trunk/src/formats/CMakeLists.txt


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[OpenBabel-Updates] SF.net SVN: openbabel:[3753] openbabel/trunk/src

From: <baoilleach@us...> - 2010-05-25 20:32

Revision: 3753
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3753&view=rev
Author:   baoilleach
Date:     2010-05-25 20:31:49 +0000 (Tue, 25 May 2010)

Log Message:
-----------
Minor fixes for warnings. Set some eol:style to native to avoid inconsistent line-endings in svgformat.cpp.

Modified Paths:
--------------
    openbabel/trunk/src/descriptors/cansmidescriptor.cpp
    openbabel/trunk/src/formats/CMakeLists.txt
    openbabel/trunk/src/formats/pwscfformat.cpp
    openbabel/trunk/src/formats/svgformat.cpp
    openbabel/trunk/src/mol.cpp

Property Changed:
----------------
    openbabel/trunk/src/formats/genbankformat.cpp
    openbabel/trunk/src/formats/gulpformat.cpp
    openbabel/trunk/src/formats/molproformat.cpp
    openbabel/trunk/src/formats/outformat.cpp
    openbabel/trunk/src/formats/pwscfformat.cpp
    openbabel/trunk/src/formats/svgformat.cpp
    openbabel/trunk/src/formats/vaspformat.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3864] openbabel/trunk/src

From: <timvdm@us...> - 2010-07-12 12:23

Revision: 3864
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3864&view=rev
Author:   timvdm
Date:     2010-07-12 12:23:19 +0000 (Mon, 12 Jul 2010)

Log Message:
-----------
(o)babel: Add --write-conformers option to write all conformers to a file.

Modified Paths:
--------------
    openbabel/trunk/src/obmolecformat.cpp
    openbabel/trunk/src/transform.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3865] openbabel/trunk/src

From: <timvdm@us...> - 2010-07-12 12:23

Revision: 3865
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3865&view=rev
Author:   timvdm
Date:     2010-07-12 12:23:34 +0000 (Mon, 12 Jul 2010)

Log Message:
-----------
src/ops/conformer.cpp: Operations for conformer generation (--conformer options)

Modified Paths:
--------------
    openbabel/trunk/src/CMakeLists.txt

Added Paths:
-----------
    openbabel/trunk/src/ops/conformer.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3869] openbabel/trunk/src

From: <timvdm@us...> - 2010-07-12 14:36

Revision: 3869
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3869&view=rev
Author:   timvdm
Date:     2010-07-12 14:36:27 +0000 (Mon, 12 Jul 2010)

Log Message:
-----------
OBConformerSearch: Some changes from testing for robustness (testes 25000 molecules)

Modified Paths:
--------------
    openbabel/trunk/src/conformersearch.cpp
    openbabel/trunk/src/ops/conformer.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3879] openbabel/trunk/src

From: <timvdm@us...> - 2010-07-12 22:52

Revision: 3879
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3879&view=rev
Author:   timvdm
Date:     2010-07-12 22:52:10 +0000 (Mon, 12 Jul 2010)

Log Message:
-----------
OBConversion: Add --read-conformers option.

Modified Paths:
--------------
    openbabel/trunk/src/obconversion.cpp
    openbabel/trunk/src/transform.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[3921] openbabel/trunk/src

From: <timvdm@us...> - 2010-07-31 14:20

Revision: 3921
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3921&view=rev
Author:   timvdm
Date:     2010-07-31 14:19:57 +0000 (Sat, 31 Jul 2010)

Log Message:
-----------
Documentation:
* external projects using CMake page
* generic data page (work in progress)

Modified Paths:
--------------
    openbabel/trunk/src/base.cpp

Added Paths:
-----------
    openbabel/trunk/src/doxygen_pages.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4084] openbabel/trunk/src

From: <timvdm@us...> - 2010-09-23 23:04

Revision: 4084
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4084&view=rev
Author:   timvdm
Date:     2010-09-23 23:04:34 +0000 (Thu, 23 Sep 2010)

Log Message:
-----------
src/graphsym.cpp: Precompute stereo descriptors for canonical labeling.

Modified Paths:
--------------
    openbabel/trunk/src/graphsym.cpp
    openbabel/trunk/src/stereo/stereoutil.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4111] openbabel/trunk/src

From: <chrismorl@us...> - 2010-09-27 13:32

Revision: 4111
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4111&view=rev
Author:   chrismorl
Date:     2010-09-27 13:32:14 +0000 (Mon, 27 Sep 2010)

Log Message:
-----------
Correct some typos; minor changes to Descriptions to improve GUI appearance

Modified Paths:
--------------
    openbabel/trunk/src/formats/fastsearchformat.cpp
    openbabel/trunk/src/formats/mmcifformat.cpp
    openbabel/trunk/src/formats/pdbqtformat.cpp
    openbabel/trunk/src/ops/partialcharges.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4126] openbabel/trunk/src

From: <chrismorl@us...> - 2010-10-01 08:47

Revision: 4126
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4126&view=rev
Author:   chrismorl
Date:     2010-10-01 08:47:12 +0000 (Fri, 01 Oct 2010)

Log Message:
-----------
In OBMol::operator+= remove atom and bond IDs of molecule being added to ensure their uniqueness in the combined molecule.

Modified Paths:
--------------
    openbabel/trunk/src/alias.cpp
    openbabel/trunk/src/mol.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4160] openbabel/trunk/src

From: <ghutchis@us...> - 2010-10-09 13:47

Revision: 4160
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4160&view=rev
Author:   ghutchis
Date:     2010-10-09 13:47:30 +0000 (Sat, 09 Oct 2010)

Log Message:
-----------
Fix some errors from cppcheck.

Modified Paths:
--------------
    openbabel/trunk/src/formats/mdlformat.cpp
    openbabel/trunk/src/formats/xtcformat.cpp
    openbabel/trunk/src/mcdlutil.cpp
    openbabel/trunk/src/parsmart.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4165] openbabel/trunk/src

From: <cryosuk@us...> - 2010-10-10 18:57

Revision: 4165
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4165&view=rev
Author:   cryosuk
Date:     2010-10-10 18:57:11 +0000 (Sun, 10 Oct 2010)

Log Message:
-----------
Fixed a few more compiler warnings.

Modified Paths:
--------------
    openbabel/trunk/src/atom.cpp
    openbabel/trunk/src/chiral.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4166] openbabel/trunk/src

From: <ghutchis@us...> - 2010-10-10 23:15

Revision: 4166
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4166&view=rev
Author:   ghutchis
Date:     2010-10-10 23:15:06 +0000 (Sun, 10 Oct 2010)

Log Message:
-----------
Improvement on some kekulize errors -- make sure to note explicit c=c double bonds.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp
    openbabel/trunk/src/kekulize.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4170] openbabel/trunk/src

From: <baoilleach@us...> - 2010-10-11 18:52

Revision: 4170
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4170&view=rev
Author:   baoilleach
Date:     2010-10-11 18:52:10 +0000 (Mon, 11 Oct 2010)

Log Message:
-----------
Replace several uses of TriangleSign with the more robust AngleOrder, which should catch some corner cases that TriangleSign may miss.

Modified Paths:
--------------
    openbabel/trunk/src/formats/mdlformat.cpp
    openbabel/trunk/src/stereo/perception.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4178] openbabel/trunk/src

From: <timvdm@us...> - 2010-10-12 17:23

Revision: 4178
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4178&view=rev
Author:   timvdm
Date:     2010-10-12 17:23:00 +0000 (Tue, 12 Oct 2010)

Log Message:
-----------
src/canon.cpp: Ignore metallocene bonds. The result is still canonical and the molecule is not modified in any way.

Modified Paths:
--------------
    openbabel/trunk/src/canon.cpp
    openbabel/trunk/src/isomorphism.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4214] openbabel/trunk/src

From: <timvdm@us...> - 2010-10-17 01:14

Revision: 4214
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4214&view=rev
Author:   timvdm
Date:     2010-10-17 01:14:35 +0000 (Sun, 17 Oct 2010)

Log Message:
-----------
src/stereo/stereoutil.cpp: Remove unused code

Modified Paths:
--------------
    openbabel/trunk/src/CMakeLists.txt

Removed Paths:
-------------
    openbabel/trunk/src/stereo/stereoutil.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4217] openbabel/trunk/src

From: <chrismorl@us...> - 2010-10-17 14:50

Revision: 4217
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4217&view=rev
Author:   chrismorl
Date:     2010-10-17 14:50:17 +0000 (Sun, 17 Oct 2010)

Log Message:
-----------
Fix in isomorphism.cpp to allow MSVC build.
Defensive NULL in xml.cpp

Modified Paths:
--------------
    openbabel/trunk/src/formats/xml/xml.cpp
    openbabel/trunk/src/isomorphism.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4245] openbabel/trunk/src

From: <timvdm@us...> - 2010-10-22 12:48

Revision: 4245
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4245&view=rev
Author:   timvdm
Date:     2010-10-22 12:48:29 +0000 (Fri, 22 Oct 2010)

Log Message:
-----------
src/depict/svgpainter.cpp, src/formats/svgformat.cpp

Modified Paths:
--------------
    openbabel/trunk/src/depict/svgpainter.cpp
    openbabel/trunk/src/formats/svgformat.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4253] openbabel/trunk/src

From: <timvdm@us...> - 2010-10-23 12:31

Revision: 4253
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4253&view=rev
Author:   timvdm
Date:     2010-10-23 12:30:59 +0000 (Sat, 23 Oct 2010)

Log Message:
-----------
Enable implicit cis bonds for small rings again. Now correctly used by smiles format & canonicalization.

Modified Paths:
--------------
    openbabel/trunk/src/canon.cpp
    openbabel/trunk/src/formats/smilesformat.cpp
    openbabel/trunk/src/stereo/perception.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4304] openbabel/trunk/src

From: <baoilleach@us...> - 2010-11-16 14:42

Revision: 4304
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4304&view=rev
Author:   baoilleach
Date:     2010-11-16 14:42:13 +0000 (Tue, 16 Nov 2010)

Log Message:
-----------
Additional partial fixes for reported problem with chirality. These fixes target OBMol::AddHydrogens() and OBBuilder::Build(). The test cases now pass, but I need to add more tests.

Modified Paths:
--------------
    openbabel/trunk/src/builder.cpp
    openbabel/trunk/src/mol.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4340] openbabel/trunk/src

From: <ghutchis@us...> - 2010-12-15 21:44

Revision: 4340
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4340&view=rev
Author:   ghutchis
Date:     2010-12-15 21:44:02 +0000 (Wed, 15 Dec 2010)

Log Message:
-----------
Incorporated MMFF94 changes from Paolo.

Modified Paths:
--------------
    openbabel/trunk/src/forcefields/forcefieldmmff94.cpp
    openbabel/trunk/src/formats/mol2format.cpp
    openbabel/trunk/src/mol.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4344] openbabel/trunk/src

From: <chrismorl@us...> - 2010-12-22 15:15

Revision: 4344
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4344&view=rev
Author:   chrismorl
Date:     2010-12-22 15:15:08 +0000 (Wed, 22 Dec 2010)

Log Message:
-----------
Fix problem with 0xout when given untrimmed strings. 
Make OBConversion::SetOptions("") clear all the options.

Modified Paths:
--------------
    openbabel/trunk/src/GUI/OBGUI.cpp
    openbabel/trunk/src/obconversion.cpp
    openbabel/trunk/src/ops/xout.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4345] openbabel/trunk/src

From: <chrismorl@us...> - 2010-12-22 15:22

Revision: 4345
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4345&view=rev
Author:   chrismorl
Date:     2010-12-22 15:22:15 +0000 (Wed, 22 Dec 2010)

Log Message:
-----------
Make mdlformat and OBDepict read and write * atoms with atomclass as an RGroup. These are already read and written in SMILES as, e.g. [*:2] . See
http://blueobelisk.shapado.com/questions/how-r-group-atoms-should-be-represented-in-smiles

Modified Paths:
--------------
    openbabel/trunk/src/alias.cpp
    openbabel/trunk/src/depict/depict.cpp
    openbabel/trunk/src/formats/mdlformat.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4364] openbabel/trunk/src

From: <ghutchis@us...> - 2011-01-14 20:56

Revision: 4364
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4364&view=rev
Author:   ghutchis
Date:     2011-01-14 20:56:05 +0000 (Fri, 14 Jan 2011)

Log Message:
-----------
Added "none" charge model as suggested by Scott Brozell.

Modified Paths:
--------------
    openbabel/trunk/src/CMakeLists.txt

Added Paths:
-----------
    openbabel/trunk/src/charges/none.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4421] openbabel/trunk/src

From: <chrismorl@us...> - 2011-03-21 09:09

Revision: 4421
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4421&view=rev
Author:   chrismorl
Date:     2011-03-21 09:09:17 +0000 (Mon, 21 Mar 2011)

Log Message:
-----------
TextFormat writes OBText objects

Modified Paths:
--------------
    openbabel/trunk/src/CMakeLists.txt
    openbabel/trunk/src/formats/textformat.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4441] openbabel/trunk/src

From: <timvdm@us...> - 2011-04-16 17:28

Revision: 4441
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4441&view=rev
Author:   timvdm
Date:     2011-04-16 17:28:20 +0000 (Sat, 16 Apr 2011)

Log Message:
-----------
OBGroupContrib: Ensure all exported API cpp code is inside the openbabel
library.

Modified Paths:
--------------
    openbabel/trunk/src/CMakeLists.txt
    openbabel/trunk/src/descriptors/groupcontrib.cpp

Added Paths:
-----------
    openbabel/trunk/src/groupcontrib.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4446] openbabel/trunk/src

From: <timvdm@us...> - 2011-04-17 10:41

Revision: 4446
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4446&view=rev
Author:   timvdm
Date:     2011-04-17 10:41:38 +0000 (Sun, 17 Apr 2011)

Log Message:
-----------
SVGFormat: Make thicker lines optional with -xt option. This options is
not enabled by default.

Modified Paths:
--------------
    openbabel/trunk/src/depict/svgpainter.cpp
    openbabel/trunk/src/formats/svgformat.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4448] openbabel/trunk/src

From: <timvdm@us...> - 2011-04-18 10:34

Revision: 4448
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4448&view=rev
Author:   timvdm
Date:     2011-04-18 10:34:42 +0000 (Mon, 18 Apr 2011)

Log Message:
-----------
Revert "OBGroupContrib: Ensure all exported API cpp code is inside the openbabel"

This reverts commit affc33b86be0a50a0d1c8b80a1b1c3f2b7000108.

Modified Paths:
--------------
    openbabel/trunk/src/CMakeLists.txt
    openbabel/trunk/src/descriptors/groupcontrib.cpp

Removed Paths:
-------------
    openbabel/trunk/src/groupcontrib.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4455] openbabel/trunk/src

From: <timvdm@us...> - 2011-04-25 17:55

Revision: 4455
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4455&view=rev
Author:   timvdm
Date:     2011-04-25 17:55:28 +0000 (Mon, 25 Apr 2011)

Log Message:
-----------
SVGPainter & SVGFormat: Enable black background again.

Modified Paths:
--------------
    openbabel/trunk/src/depict/svgpainter.cpp
    openbabel/trunk/src/formats/svgformat.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4484] openbabel/trunk/src

From: <chrismorl@us...> - 2011-05-21 12:28

Revision: 4484
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4484&view=rev
Author:   chrismorl
Date:     2011-05-21 12:28:18 +0000 (Sat, 21 May 2011)

Log Message:
-----------
Do wedge and hash bonds without using begin and end atoms on the bond, at Noel's insistence.
Remove W option - stereo perception is always done anyway.
Consolidate stroke-linecap attributes.

Modified Paths:
--------------
    openbabel/trunk/src/depict/depict.cpp
    openbabel/trunk/src/depict/svgpainter.cpp
    openbabel/trunk/src/formats/svgformat.cpp
    openbabel/trunk/src/stereo/perception.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4495] openbabel/trunk/src

From: <baoilleach@us...> - 2011-05-29 20:27

Revision: 4495
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4495&view=rev
Author:   baoilleach
Date:     2011-05-29 20:26:57 +0000 (Sun, 29 May 2011)

Log Message:
-----------
depict.cpp, mcdlutil.cpp: Apply Sergei's patch that ensures that MCDL generates coordinates with increasing Y going up. Invert the Y coordinate in the depiction correspondingly. Now that we know which way is up, the next step is to track down errors in tet stereochemistry. Note to self: the depictor appears to be modifying the molecules coordinates - I don't think it should be, and it certainly shouldn't be now, given the y coordinate inversion.

Modified Paths:
--------------
    openbabel/trunk/src/depict/depict.cpp
    openbabel/trunk/src/mcdlutil.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4498] openbabel/trunk/src

From: <baoilleach@us...> - 2011-05-30 18:52

Revision: 4498
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4498&view=rev
Author:   baoilleach
Date:     2011-05-30 18:52:48 +0000 (Mon, 30 May 2011)

Log Message:
-----------
png2format.cpp: Remove commented out code
depict.cpp: Call TetStereoToWedgeHash *before* inverting the y coordinates. Now finally the correct stereochemistry is depicted! Time to test for segfaults on a large dataset.

Modified Paths:
--------------
    openbabel/trunk/src/depict/depict.cpp
    openbabel/trunk/src/formats/png2format.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4501] openbabel/trunk/src

From: <baoilleach@us...> - 2011-05-31 17:53

Revision: 4501
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4501&view=rev
Author:   baoilleach
Date:     2011-05-31 17:53:44 +0000 (Tue, 31 May 2011)

Log Message:
-----------
depict.cpp: Have OBDepict work off a copy of the molecule, to avoid altering the original coordinates.
png2format.cpp: Work off a copy of the molecule, so that generation of 2D coordinates will not affect the original molecule.

Modified Paths:
--------------
    openbabel/trunk/src/depict/depict.cpp
    openbabel/trunk/src/formats/png2format.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4506] openbabel/trunk/src

From: <baoilleach@us...> - 2011-06-02 20:55

Revision: 4506
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4506&view=rev
Author:   baoilleach
Date:     2011-06-02 20:54:56 +0000 (Thu, 02 Jun 2011)

Log Message:
-----------
depict.cpp: Improve placement of + and - signs.
svgformat.cpp: In the JavaScript, don't scroll when zooming.

Modified Paths:
--------------
    openbabel/trunk/src/depict/depict.cpp
    openbabel/trunk/src/formats/svgformat.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4520] openbabel/trunk/src

From: <jiahao@us...> - 2011-07-05 23:47

Revision: 4520
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4520&view=rev
Author:   jiahao
Date:     2011-07-05 23:47:34 +0000 (Tue, 05 Jul 2011)

Log Message:
-----------
Preliminary support for periodic cells in MOPAC 2007/9 input.

Also fixed tokenize(,,) as per Noel's suggestion.

Modified Paths:
--------------
    openbabel/trunk/src/formats/mopacformat.cpp
    openbabel/trunk/src/tokenst.cpp


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[OpenBabel-Updates] SF.net SVN: openbabel:[4552] openbabel/trunk/src

From: <baoilleach@us...> - 2011-09-03 19:39

Revision: 4552
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4552&view=rev
Author:   baoilleach
Date:     2011-09-03 19:39:34 +0000 (Sat, 03 Sep 2011)
Log Message:
-----------
NEW_ENUM_VALUE: Add support for reading "Unknown" stereo for MDL, and writing it for SMILES.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp
    openbabel/trunk/src/stereo/perception.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4597] openbabel/trunk/src

From: <chrismorl@us...> - 2011-09-18 10:01

Revision: 4597
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4597&view=rev
Author:   chrismorl
Date:     2011-09-18 10:01:12 +0000 (Sun, 18 Sep 2011)
Log Message:
-----------
Add op --addfilename

Modified Paths:
--------------
    openbabel/trunk/src/CMakeLists.txt

Added Paths:
-----------
    openbabel/trunk/src/ops/addfilename.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4614] openbabel/trunk/src

From: <chrismorl@us...> - 2011-10-02 15:06

Revision: 4614
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4614&view=rev
Author:   chrismorl
Date:     2011-10-02 15:06:07 +0000 (Sun, 02 Oct 2011)
Log Message:
-----------
When copying an OBMol, ensure that the generic data on the bonds is copied. (Coloring a substructure in SVGFormat was not working.)
In SVGFormat, ensure that a wedge bond is filled with bond color.

Modified Paths:
--------------
    openbabel/trunk/src/depict/svgpainter.cpp
    openbabel/trunk/src/mol.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4654] openbabel/trunk/src

From: <ghutchis@us...> - 2011-10-27 21:05

Revision: 4654
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4654&view=rev
Author:   ghutchis
Date:     2011-10-27 21:05:11 +0000 (Thu, 27 Oct 2011)
Log Message:
-----------
First set of warnings from clang static analyzer -- possible unitialized variables.

Modified Paths:
--------------
    openbabel/trunk/src/alias.cpp
    openbabel/trunk/src/chains.cpp
    openbabel/trunk/src/formats/mdlformat.cpp
    openbabel/trunk/src/mcdlutil.cpp
    openbabel/trunk/src/ops/opisomorph.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4665] openbabel/trunk/src

From: <mr_grieves@us...> - 2011-11-10 22:44

Revision: 4665
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4665&view=rev
Author:   mr_grieves
Date:     2011-11-10 22:44:45 +0000 (Thu, 10 Nov 2011)
Log Message:
-----------
Fix MMFF94s to both allow custom interaction groups and respect cutoffs.

Modified Paths:
--------------
    openbabel/trunk/src/forcefield.cpp
    openbabel/trunk/src/forcefields/forcefieldmmff94.cpp
    openbabel/trunk/src/forcefields/forcefieldmmff94.h

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[OpenBabel-Updates] SF.net SVN: openbabel:[4682] openbabel/trunk/src

From: <mr_grieves@us...> - 2011-12-06 16:53

Revision: 4682
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4682&view=rev
Author:   mr_grieves
Date:     2011-12-06 16:53:07 +0000 (Tue, 06 Dec 2011)
Log Message:
-----------
Merge branch 'patch_3452482'

Modified Paths:
--------------
    openbabel/trunk/src/generic.cpp
    openbabel/trunk/src/ops/fillUC.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4718] openbabel/trunk/src

From: <baoilleach@us...> - 2012-03-04 14:09

Revision: 4718
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4718&view=rev
Author:   baoilleach
Date:     2012-03-04 14:09:42 +0000 (Sun, 04 Mar 2012)
Log Message:
-----------
ophighlight.cpp, src/CMakeLists.txt: Add a new op to highlight substructures in 2D depictions. Based on opisomorph.cpp. Suggested by Chris Swain's comment at http://baoilleach.blogspot.com/2012/02/portrait-of-molecule-as-green.html

Modified Paths:
--------------
    openbabel/trunk/src/CMakeLists.txt

Added Paths:
-----------
    openbabel/trunk/src/ops/ophighlight.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4727] openbabel/trunk/src

From: <baoilleach@us...> - 2012-03-13 13:23

Revision: 4727
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4727&view=rev
Author:   baoilleach
Date:     2012-03-13 13:23:03 +0000 (Tue, 13 Mar 2012)
Log Message:
-----------
mol.cpp, obutil.cpp: Fix trivial compilation error with MSVC++ 2010.

Modified Paths:
--------------
    openbabel/trunk/src/mol.cpp
    openbabel/trunk/src/obutil.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4730] openbabel/trunk/src

From: <baoilleach@us...> - 2012-03-15 18:55

Revision: 4730
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4730&view=rev
Author:   baoilleach
Date:     2012-03-15 18:55:41 +0000 (Thu, 15 Mar 2012)
Log Message:
-----------
alias.cpp, formats/mdlformat.cpp: Fix PR#3481603 - alias on stereo bond loses tet stereo when reading MOL file.

Modified Paths:
--------------
    openbabel/trunk/src/alias.cpp
    openbabel/trunk/src/formats/mdlformat.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4752] openbabel/trunk/src

From: <ghutchis@us...> - 2012-05-13 19:25

Revision: 4752
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4752&view=rev
Author:   ghutchis
Date:     2012-05-13 19:25:30 +0000 (Sun, 13 May 2012)
Log Message:
-----------
Added initial fixes found through clang static analyzer.

Modified Paths:
--------------
    openbabel/trunk/src/chains.cpp
    openbabel/trunk/src/pointgroup.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4845] openbabel/trunk/src

From: <baoilleach@us...> - 2012-06-01 08:31

Revision: 4845
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4845&view=rev
Author:   baoilleach
Date:     2012-06-01 08:31:24 +0000 (Fri, 01 Jun 2012)
Log Message:
-----------
src/formats/smilesformat.cpp, src/stereo/perception.cpp: Change IMPLICIT_CIS_RING_SIZE from 12 to 8. There is an example of a trans bond in a ring of size 9 in ChEMBL.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp
    openbabel/trunk/src/stereo/perception.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4863] openbabel/trunk/src

From: <baoilleach@us...> - 2012-06-08 09:11

Revision: 4863
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4863&view=rev
Author:   baoilleach
Date:     2012-06-08 09:10:56 +0000 (Fri, 08 Jun 2012)
Log Message:
-----------
src/canon.cpp, src/formats/smilesformat.cpp: Fix some of the problems introduced by r4763 ("removal of molecule copy in SMILES output"). I removed don't add hydrogens to chiral centers in the SMILES writer and fixed the testcase failures introduced. Tautomer test still fails though.

Revision Links:
--------------
    http://openbabel.svn.sourceforge.net/openbabel/?rev=4763&view=rev

Modified Paths:
--------------
    openbabel/trunk/src/canon.cpp
    openbabel/trunk/src/formats/smilesformat.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4894] openbabel/trunk/src

From: <chrismorl@us...> - 2012-06-21 10:31

Revision: 4894
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4894&view=rev
Author:   chrismorl
Date:     2012-06-21 10:31:02 +0000 (Thu, 21 Jun 2012)
Log Message:
-----------
Remove erroneous test for UNICODE character in alias.cpp, which may be responsible for some build problems.
Improved error message in mdlformat.
Add DEPICTION2D flag to pngformat.

Modified Paths:
--------------
    openbabel/trunk/src/alias.cpp
    openbabel/trunk/src/formats/mdlformat.cpp
    openbabel/trunk/src/formats/pngformat.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4898] openbabel/trunk/src

From: <baoilleach@us...> - 2012-06-22 10:57

Revision: 4898
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4898&view=rev
Author:   baoilleach
Date:     2012-06-22 10:57:10 +0000 (Fri, 22 Jun 2012)
Log Message:
-----------
mdlformat.cpp: Support reading and writing CT and tet stereo in 0D MOL files. The "S" option was added to turn off this behaviour.
perception.cpp: Correction to CisTransFrom0D for subtle problem exposed by roundtripping CAN->0D SDF->CAN.

All current tests pass, but I should add specific tests for this functionality. Roundtripping 100K molecules from ChEMBL gives 20 failures, which all seem to be due to conjugated cis/trans in a ring (c.f. the well-known failure of SMILES in this area). Maybe something more can be done about this, but that's enough for now.

Modified Paths:
--------------
    openbabel/trunk/src/formats/mdlformat.cpp
    openbabel/trunk/src/stereo/perception.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[4964] openbabel/trunk/src

From: <chrismorl@us...> - 2012-07-23 14:06

Revision: 4964
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4964&view=rev
Author:   chrismorl
Date:     2012-07-23 14:06:06 +0000 (Mon, 23 Jul 2012)
Log Message:
-----------
Change comment on FPT_UNIQUEBITS and do not let it prevent a full isomorphism test in fastsearch. Pointed out by Tim.

Modified Paths:
--------------
    openbabel/trunk/src/fingerprints/finger3.cpp
    openbabel/trunk/src/formats/fastsearchformat.cpp

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[OpenBabel-Updates] SF.net SVN: openbabel:[5012] openbabel/trunk/src

From: <baoilleach@us...> - 2012-09-16 21:03

Revision: 5012
          http://openbabel.svn.sourceforge.net/openbabel/?rev=5012&view=rev
Author:   baoilleach
Date:     2012-09-16 21:03:35 +0000 (Sun, 16 Sep 2012)
Log Message:
-----------
src/bitvec.cpp: Correct OBBitVec::FromString to handle "1 2" correctly (was missing the 2).
src/formats/smilesformat.cpp: Add output option "F" to specify fragment numbers. Doesn't interfere with current fragment functionality used by Craig (an OBPairData called SMILES_Fragment).

Modified Paths:
--------------
    openbabel/trunk/src/bitvec.cpp
    openbabel/trunk/src/formats/smilesformat.cpp

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