[OpenBabel-Updates] SF.net SVN: openbabel:[4311] openbabel/branches/openbabel-2-3-x

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Revision: 4311
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4311&view=rev
Author:   ghutchis
Date:     2010-11-17 21:33:59 +0000 (Wed, 17 Nov 2010)

Log Message:
-----------
Merged revisions 4284-4297,4299-4310 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4284 | baoilleach | 2010-10-28 11:03:19 -0400 (Thu, 28 Oct 2010) | 1 line

  Commit of ancillary files to create the Python distribution(s) on Windows.
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  r4285 | annulen | 2010-10-29 09:46:48 -0400 (Fri, 29 Oct 2010) | 6 lines

  * scripts/CMakeLists.txt: added dependency 'openbabel' to target
  '_openbabel' (Python bindings)

  On non-Windows platfroms Python module is linked by custom script
  which is not aware of target dependencies. This change fixes parallel
  build
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  r4286 | annulen | 2010-10-29 12:38:19 -0400 (Fri, 29 Oct 2010) | 2 lines

  * scripts/CMakeLists.txt: fixed behavior of build system if some of
  JNI dependencies were not found
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  r4287 | timvdm | 2010-10-30 10:31:52 -0400 (Sat, 30 Oct 2010) | 1 line

  XML and InChI are now turned off for static builds. These will be enabled again once the win32 linking issues are resolved. Options are: WITH_STATIC_LIBXML and WITH_STATIC_INCHI
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  r4288 | mr_grieves | 2010-11-03 13:22:27 -0400 (Wed, 03 Nov 2010) | 1 line

  Allow GULP format reader to handle single point output, fix url.
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  r4289 | hansdewinter | 2010-11-03 18:50:13 -0400 (Wed, 03 Nov 2010) | 1 line

  Modified StripSalts() method to fix bug when followed by SmartsPattern::Match() method
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  r4290 | mr_grieves | 2010-11-04 08:14:05 -0400 (Thu, 04 Nov 2010) | 1 line

  Extract energies from GULP single point output.
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  r4291 | baoilleach | 2010-11-04 08:17:12 -0400 (Thu, 04 Nov 2010) | 1 line

  Add Python bindings for new canonical labelling, isomorphism, OBAlign and OBQuery classes.
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  r4292 | chrismorl | 2010-11-05 18:51:22 -0400 (Fri, 05 Nov 2010) | 3 lines

  Fix for bug 3102719: babel not reading the option parameters specifying the number of columns and rows. But it requires the use of --rows and --cols instead of xr and -xc (and --px instead of -xp). With babel the options are shared with other formats, which causes conflicts when they take different numbers of parameters (as here).  obabel, because it does not need to be told the number of parameters, works with both the old and new styles. 
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  r4293 | chrismorl | 2010-11-06 16:31:20 -0400 (Sat, 06 Nov 2010) | 1 line

  Updated MACCS.txt file. Fixes bug reported by Andrew Dalke on mailing list.
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  r4294 | chrismorl | 2010-11-06 17:33:24 -0400 (Sat, 06 Nov 2010) | 1 line

  obfit.cpp: catch some faulty input before seg fault, as reported by Jean-Paul Ebejer.
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  r4295 | chrismorl | 2010-11-07 04:22:07 -0500 (Sun, 07 Nov 2010) | 1 line

  Change error message to avoid compiler warning.
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  r4296 | chrismorl | 2010-11-09 15:14:56 -0500 (Tue, 09 Nov 2010) | 1 line

  Output number of bits and datafile version(if applicable) on second line of fingerprint descriptions.
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  r4297 | chrismorl | 2010-11-10 05:17:23 -0500 (Wed, 10 Nov 2010) | 1 line

  For patternFP fingerprints display the number of bits and version in Description() only if the fingerprint has already been used, to avoid unnecessary parsing of the datafiles.
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  r4299 | ghutchis | 2010-11-11 11:37:51 -0500 (Thu, 11 Nov 2010) | 2 lines

  Added a port of EEM methods from OBSpectrophore.
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  r4300 | ghutchis | 2010-11-11 15:02:48 -0500 (Thu, 11 Nov 2010) | 2 lines

  Add missing EEM method.
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  r4301 | baoilleach | 2010-11-12 05:26:57 -0500 (Fri, 12 Nov 2010) | 1 line

  3D Builder test case from Martin Guetlin. PR#3107218. Works fine for me under MSVC, but maybe there's a problem on Linux.
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  r4302 | hansdewinter | 2010-11-12 07:47:28 -0500 (Fri, 12 Nov 2010) | 1 line

  Made the test for Spectrophores a little stricter (Thx to Andrew Dalke)
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  r4303 | baoilleach | 2010-11-15 17:12:06 -0500 (Mon, 15 Nov 2010) | 1 line

  Partial fix to bug reported on openbabel-discuss by Miguel Olazabal. Formats that require stereochemical information on writing should call PerceiveStereo, rather than relying on it already being perceived. The problem is exposed when converting formats that do not require stereo perception to one that does, e.g. xyz to SMILES. This needs further testing to ensure that it working correctly. For example, xyz --> CML and xyz --> InChI still need looking at (and presumably MOL2 will also need some work...).
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  r4304 | baoilleach | 2010-11-16 09:42:13 -0500 (Tue, 16 Nov 2010) | 1 line

  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.
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  r4305 | baoilleach | 2010-11-16 10:17:56 -0500 (Tue, 16 Nov 2010) | 1 line

  Add XYZ test cases for chirality. No new failures here.
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  r4306 | baoilleach | 2010-11-16 12:03:11 -0500 (Tue, 16 Nov 2010) | 1 line

  Final part of chirality bug fix. The shuffle test now passes. The problem is that EndModify wipes all flags, so it's necessary to keep restoring the chirality flag or all the carefully conserved stereo data will be lost.
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  r4307 | baoilleach | 2010-11-16 12:08:11 -0500 (Tue, 16 Nov 2010) | 1 line

  Revert debug code mistakenly committed in r4305.
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  r4308 | cryosuk | 2010-11-16 22:08:45 -0500 (Tue, 16 Nov 2010) | 1 line

  Removed all of the extra semicolons from the static macros - compiler warnings.
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  r4309 | cryosuk | 2010-11-16 22:11:13 -0500 (Tue, 16 Nov 2010) | 1 line

  Added back in missing semicolon - got carried away at the end.
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  r4310 | baoilleach | 2010-11-17 04:50:10 -0500 (Wed, 17 Nov 2010) | 1 line

  scripts/openbabel-python.i: I recently added support for align.h. This is dependent on Eigen and needed another "if" statement added to the interface.
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Modified Paths:
--------------
    openbabel/branches/openbabel-2-3-x/CMakeLists.txt
    openbabel/branches/openbabel-2-3-x/ChangeLog
    openbabel/branches/openbabel-2-3-x/data/MACCS.txt
    openbabel/branches/openbabel-2-3-x/include/openbabel/plugin.h
    openbabel/branches/openbabel-2-3-x/scripts/CMakeLists.txt
    openbabel/branches/openbabel-2-3-x/scripts/openbabel-python.i
    openbabel/branches/openbabel-2-3-x/src/CMakeLists.txt
    openbabel/branches/openbabel-2-3-x/src/builder.cpp
    openbabel/branches/openbabel-2-3-x/src/fingerprints/finger2.cpp
    openbabel/branches/openbabel-2-3-x/src/fingerprints/finger3.cpp
    openbabel/branches/openbabel-2-3-x/src/formats/formats.cmake
    openbabel/branches/openbabel-2-3-x/src/formats/gulpformat.cpp
    openbabel/branches/openbabel-2-3-x/src/formats/mdlformat.cpp
    openbabel/branches/openbabel-2-3-x/src/formats/smilesformat.cpp
    openbabel/branches/openbabel-2-3-x/src/formats/svgformat.cpp
    openbabel/branches/openbabel-2-3-x/src/mol.cpp
    openbabel/branches/openbabel-2-3-x/src/plugin.cpp
    openbabel/branches/openbabel-2-3-x/test/CMakeLists.txt
    openbabel/branches/openbabel-2-3-x/test/buildertest.cpp
    openbabel/branches/openbabel-2-3-x/test/spectrophoretest.cpp
    openbabel/branches/openbabel-2-3-x/test/testsym.py
    openbabel/branches/openbabel-2-3-x/tools/CMakeLists.txt
    openbabel/branches/openbabel-2-3-x/tools/obfit.cpp

Added Paths:
-----------
    openbabel/branches/openbabel-2-3-x/src/charges/eem.cpp
    openbabel/branches/openbabel-2-3-x/windows-vc2008/Distribution/Python/
    openbabel/branches/openbabel-2-3-x/windows-vc2008/Distribution/Python/a_obpython.bat
    openbabel/branches/openbabel-2-3-x/windows-vc2008/Distribution/Python/b_obpython.bat
    openbabel/branches/openbabel-2-3-x/windows-vc2008/Distribution/Python/logo.bmp
    openbabel/branches/openbabel-2-3-x/windows-vc2008/Distribution/Python/setup.py

Removed Paths:
-------------
    openbabel/branches/openbabel-2-3-x/windows-vc2008/Distribution/Python/a_obpython.bat
    openbabel/branches/openbabel-2-3-x/windows-vc2008/Distribution/Python/b_obpython.bat
    openbabel/branches/openbabel-2-3-x/windows-vc2008/Distribution/Python/logo.bmp
    openbabel/branches/openbabel-2-3-x/windows-vc2008/Distribution/Python/setup.py

Property Changed:
----------------
    openbabel/branches/openbabel-2-3-x/
    openbabel/branches/openbabel-2-3-x/scripts/openbabel-mono.i

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