Merged revisions 4624,4626-4632,4636 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4624 | ghutchis | 2011-10-09 09:00:56 -0400 (Sun, 09 Oct 2011) | 2 lines
  
  Updated inchi to 1.0.4 release from September 2011.
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  r4626 | mbanck | 2011-10-09 14:05:48 -0400 (Sun, 09 Oct 2011) | 2 lines
  
  Add initial Aces (tested with AcesII for now) output parsing and trivial input file (ZMAT) output
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  r4627 | mbanck | 2011-10-10 10:43:55 -0400 (Mon, 10 Oct 2011) | 1 line
  
  Add Aces2 to outformat
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  r4628 | ghutchis | 2011-10-10 12:28:14 -0400 (Mon, 10 Oct 2011) | 3 lines
  
  Add support for using Eigen 3, if found.
  Default to using Eigen3 over Eigen2 if installed.
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  r4629 | jiahao | 2011-10-10 14:03:31 -0400 (Mon, 10 Oct 2011) | 3 lines
  
  Fixed aberrant closing brace in formats/outformat.cpp that broke compilation.
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  r4630 | baoilleach | 2011-10-10 14:34:40 -0400 (Mon, 10 Oct 2011) | 1 line
  
  Correction to r4628 to fix Eigen2 compilation.
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  r4631 | timvdm | 2011-10-11 17:44:39 -0400 (Tue, 11 Oct 2011) | 3 lines
  
  * include/openbabel/obiter.h: Add OpenBabel namespace to the iterator
    macro's to ensure they work when used outside OpenBabel scope (without
    using namespace OpenBabel). Fixes #3126901 reported by Igor Filippov.
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  r4632 | timvdm | 2011-10-11 17:50:09 -0400 (Tue, 11 Oct 2011) | 2 lines
  
  * src/obiter.cpp: Doc update to make code examples compile without
    errors.
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  r4636 | mr_grieves | 2011-10-13 11:05:16 -0400 (Thu, 13 Oct 2011) | 5 lines
  
  Set _current_conformer when only one conformer is predicted.
  
  Otherwise, this variable will be uninitialized when trying to generate
  later conformers in the "GetNext" functions, leading to array boundary
  issues.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4919 71e0b675-c112-0410-beda-96664073b5c2
Blocked revisions 4599-4600,4603 via svnmerge

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  r4599 | mr_grieves | 2011-09-20 10:22:47 -0400 (Tue, 20 Sep 2011) | 5 lines
  
  Fix bug PR#3411738 Restore ABI from break in r4401.
  
  Adding the const keyword broke binary compatibility in r4401. This patch
  adds the non-const overloads back. Thanks to Andrey Ponomarenko for
  pointing this out.
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  r4600 | mr_grieves | 2011-09-21 14:03:04 -0400 (Wed, 21 Sep 2011) | 1 line
  
  More binary compatibility fixes for OBUnitCell/OBPointGroup.
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  r4603 | mr_grieves | 2011-09-22 11:46:20 -0400 (Thu, 22 Sep 2011) | 3 lines
  
  Move definition of IdentifyPointGroup() to cpp file.
  
  This is to preserve binary compatibility.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4920 71e0b675-c112-0410-beda-96664073b5c2
Bump version number and library version for 2.3.2.


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4924 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4646-4655 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4646 | baoilleach | 2011-10-20 05:01:40 -0400 (Thu, 20 Oct 2011) | 1 line
  
  src/formats/inchiformat.cpp: Should fix segfault for InChI->InChIKey conversion on Linux. (PR#3425892, Adrià Cereto-Massagué)
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  r4647 | chrismorl | 2011-10-20 15:33:09 -0400 (Thu, 20 Oct 2011) | 1 line
  
  Add FPSFormat for writing Andrew Dalke's text fingerprint format
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  r4648 | chrismorl | 2011-10-20 15:40:30 -0400 (Thu, 20 Oct 2011) | 1 line
  
  Add InChI 1.04 header and 32-bit DLL. Only the licence has changed in the header. I can't find a lib file; the old one seems to still work. 
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  r4649 | chrismorl | 2011-10-21 09:04:28 -0400 (Fri, 21 Oct 2011) | 1 line
  
  Correct illegal use of Trim() causing failure in gcc (but not VS)
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  r4650 | chrismorl | 2011-10-22 05:59:00 -0400 (Sat, 22 Oct 2011) | 1 line
  
  Generate non-standard InChI key if necessary (Bug #3426902)
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  r4651 | vincefn | 2011-10-22 08:05:43 -0400 (Sat, 22 Oct 2011) | 1 line
  
  Enable reading multiple structures from a CIF file
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  r4652 | chrismorl | 2011-10-25 12:07:32 -0400 (Tue, 25 Oct 2011) | 1 line
  
  In --append \t at start delimits list with tabs
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  r4653 | ghutchis | 2011-10-27 15:57:06 -0400 (Thu, 27 Oct 2011) | 3 lines
  
  Patches from Roger Sayle to remove all uses of a local stack
  and historically unused code.
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  r4654 | ghutchis | 2011-10-27 17:05:11 -0400 (Thu, 27 Oct 2011) | 2 lines
  
  First set of warnings from clang static analyzer -- possible unitialized variables.
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  r4655 | ghutchis | 2011-11-01 14:05:40 -0400 (Tue, 01 Nov 2011) | 3 lines
  
  Enhance formula test to operate on a specific file.
  Allows benchmark testing for generating formulas on every mol in a SDF.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4925 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4658-4661 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4658 | ghutchis | 2011-11-04 13:54:29 -0400 (Fri, 04 Nov 2011) | 4 lines
  
  Adjust trust radius for geometry optimization.
  Previous value (no moves more than 0.3A) is too
  pessamistic.
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  r4659 | mr_grieves | 2011-11-07 15:22:04 -0500 (Mon, 07 Nov 2011) | 1 line
  
  Fix MOPAC parser for periodic calculation output.
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  r4660 | mr_grieves | 2011-11-08 14:42:47 -0500 (Tue, 08 Nov 2011) | 1 line
  
  Fix some uninitialized pointers in MMFF94s forcefield.
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  r4661 | baoilleach | 2011-11-10 03:42:00 -0500 (Thu, 10 Nov 2011) | 1 line
  
  src/stereo/tetrahedral.cpp: Bugfix. Handle the case of comparison of two stereo Configs where the 'other' Config has an implicitRef in the 'from' position.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4926 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4664-4672 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4664 | mr_grieves | 2011-11-10 17:44:41 -0500 (Thu, 10 Nov 2011) | 1 line
  
  Speedup MMFF94s setup by reducing time spent checking for masked interactions.
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  r4665 | mr_grieves | 2011-11-10 17:44:45 -0500 (Thu, 10 Nov 2011) | 1 line
  
  Fix MMFF94s to both allow custom interaction groups and respect cutoffs.
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  r4666 | baoilleach | 2011-11-11 07:34:57 -0500 (Fri, 11 Nov 2011) | 1 line
  
  smilesformat.cpp: Fix PR#3428432. Memory leak from evil SMILES from the mind of Andrew Dalke.
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  r4667 | mr_grieves | 2011-11-11 16:56:51 -0500 (Fri, 11 Nov 2011) | 3 lines
  
  Add selective dynamics and file writing to VASP.
  
  Thanks to Jiri Klimes for the original patch, PR#3436235.
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  r4668 | mr_grieves | 2011-11-14 15:07:36 -0500 (Mon, 14 Nov 2011) | 1 line
  
  Preserve atomic order in POSCAR generation by default.
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  r4669 | baoilleach | 2011-11-15 14:55:45 -0500 (Tue, 15 Nov 2011) | 1 line
  
  scripts/CMakeLists.txt: Add new Python bindings enabled by -DNEW_PYTHON_BINDINGS=ON which use CMake's own build system to avoid future problems. The side-effect is that the Python libraries are installed with the Open Babel library rather than in site-packages or so.
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  r4670 | chrismorl | 2011-11-17 08:29:31 -0500 (Thu, 17 Nov 2011) | 1 line
  
  Correct erroneous charge on an alias atom made from nitro or isocyanide group, visible in mol or svg. 
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  r4671 | chrismorl | 2011-11-18 08:30:17 -0500 (Fri, 18 Nov 2011) | 2 lines
  
  Correct the parameters of a virtual function in some descriptors, which compiled ok but the wrong function was being called. The new C++11 keyword override would have caught this.
  Improve the Description of compound filters.
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  r4672 | chrismorl | 2011-11-19 06:43:29 -0500 (Sat, 19 Nov 2011) | 1 line
  
  Allow background and bond colors to be specified in SVGFormat. Add highlight facility. Javascript to zoom and pan now works in Firefox, Opera, Chrome and IE9.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4927 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4674-4676 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4674 | baoilleach | 2011-11-23 08:45:17 -0500 (Wed, 23 Nov 2011) | 1 line
  
  scripts/CMakeLists.txt: Fix Java bindings (tested on Linux).
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  r4675 | baoilleach | 2011-11-24 05:41:11 -0500 (Thu, 24 Nov 2011) | 1 line
  
  scripts/CMakeLists.txt: Update bindings to use new Python bindings.
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  r4676 | mr_grieves | 2011-11-28 12:21:46 -0500 (Mon, 28 Nov 2011) | 1 line
  
  Skip shell positions in GULP output, only use atom cores.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4928 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4643-4644 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4643 | chrismorl | 2011-10-16 15:23:08 -0400 (Sun, 16 Oct 2011) | 1 line
  
  Apply patch 3424378 by My Th formating the macro code in plugin.h
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  r4644 | chrismorl | 2011-10-16 15:41:32 -0400 (Sun, 16 Oct 2011) | 2 lines
  
  Apply patch 3424380 by My Th preventing the last instance of a plugin being deleted
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4929 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4681-4682,4684-4689 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4681 | jbrefort | 2011-12-06 10:17:06 -0500 (Tue, 06 Dec 2011) | 2 lines
  
  Avoid the generation of duplicate nodes.
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  r4682 | mr_grieves | 2011-12-06 11:53:07 -0500 (Tue, 06 Dec 2011) | 1 line
  
  Merge branch 'patch_3452482'
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  r4684 | ghutchis | 2011-12-07 15:17:58 -0500 (Wed, 07 Dec 2011) | 3 lines
  
  Alternate fix to address patch #3452697 by FX Coudert.
  Wrap atoms in unit cell using some fuzziness.
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  r4685 | ghutchis | 2011-12-07 15:31:37 -0500 (Wed, 07 Dec 2011) | 6 lines
  
  Patch from Roger Sayle to fix SMARTS [v2] against C[H]C.
  
  GetImplicitValence should never return a value less than GetValence,
  i.e. implicit hydrogens or radicals may be present, but the explicit
  bonds can never be ignored.
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  r4686 | ghutchis | 2011-12-07 15:52:49 -0500 (Wed, 07 Dec 2011) | 2 lines
  
  Forgot to commit other test updates after smarts test update.
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  r4687 | ghutchis | 2011-12-07 15:53:52 -0500 (Wed, 07 Dec 2011) | 6 lines
  
  Patch (and further updates) from Roger Sayle.
  
  Avoid idiom of testing stl::vector empty() and size()
  at the same time. Slight performance improvements,
  but also improved readability.
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  r4688 | ghutchis | 2011-12-08 12:26:41 -0500 (Thu, 08 Dec 2011) | 2 lines
  
  Fix double-counting OOP terms for MMFF94s, thanks to Chong Hak Chae.
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  r4689 | vincefn | 2011-12-08 15:51:56 -0500 (Thu, 08 Dec 2011) | 1 line
  
  Add handling of DDL2 tag _space_group.IT_coordinate_system_code, when this tag is used to designate origin choice 1 or 2
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4930 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4691-4694,4696-4698 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4691 | jbrefort | 2011-12-10 07:24:51 -0500 (Sat, 10 Dec 2011) | 2 lines
  
  Fixed two groups identifiers.
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  r4692 | vincefn | 2011-12-10 07:55:55 -0500 (Sat, 10 Dec 2011) | 1 line
  
  Make sure we do not write the origin choice in the HM name when writing files
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  r4693 | ghutchis | 2011-12-17 10:57:32 -0500 (Sat, 17 Dec 2011) | 4 lines
  
      // Make sure we keep the bond indexes the same
      // so we'll delete the bonds again and copy them
      // Fixes PR#3448379 (and likely other topology issues)
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  r4694 | ghutchis | 2011-12-22 13:17:49 -0500 (Thu, 22 Dec 2011) | 3 lines
  
  Fix for bug on C#O, reported via Avogadro. Any oxygen with a triple bond
  should only have 1 valence, regardless of charge.
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  r4696 | mr_grieves | 2012-01-03 14:41:00 -0500 (Tue, 03 Jan 2012) | 3 lines
  
  Fix bug in forcefield.cpp that reset the gradient after each step when
  using conjugate gradients for energy optimization. Trivial
  optimizations to the simple line search method added as well.
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  r4697 | mr_grieves | 2012-01-04 08:02:27 -0500 (Wed, 04 Jan 2012) | 1 line
  
  Use the Newton2Num linesearch method by default for geo opts.
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  r4698 | mr_grieves | 2012-01-04 08:29:17 -0500 (Wed, 04 Jan 2012) | 1 line
  
  Update docs to reflect the last commit.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4931 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4701-4707,4711-4714 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4701 | ghutchis | 2012-01-06 12:44:31 -0500 (Fri, 06 Jan 2012) | 3 lines
  
  Initial support for writing LAMMPS input files,
  contributed by Albert DeFusco.
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  r4702 | ghutchis | 2012-01-09 13:38:52 -0500 (Mon, 09 Jan 2012) | 2 lines
  
  Fix compile issue with unordered_map.
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  r4703 | mr_grieves | 2012-01-21 10:46:16 -0500 (Sat, 21 Jan 2012) | 1 line
  
  Make CML write all non-zero energies, even if positive.
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  r4704 | mr_grieves | 2012-01-24 19:12:24 -0500 (Tue, 24 Jan 2012) | 1 line
  
  Plug memory leak in OBForceField::Newton2LineSearch.
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  r4705 | chrismorl | 2012-01-27 10:39:26 -0500 (Fri, 27 Jan 2012) | 1 line
  
  Make wildcard * in --filter comparisons find contained strings 
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  r4706 | baoilleach | 2012-02-01 06:08:57 -0500 (Wed, 01 Feb 2012) | 1 line
  
  x64_default_build.bat: Update to compile cleanly. Disabled InChI as the 64-bit library is not available.
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  r4707 | mr_grieves | 2012-02-01 14:19:08 -0500 (Wed, 01 Feb 2012) | 1 line
  
  Plug memory leak in forcefielduff.cpp
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  r4711 | ghutchis | 2012-02-21 22:14:57 -0500 (Tue, 21 Feb 2012) | 2 lines
  
  Remove flag for lammps format.
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  r4712 | ghutchis | 2012-02-21 22:19:50 -0500 (Tue, 21 Feb 2012) | 2 lines
  
  Fix regression in MMFF94, from Paolo Tosco.
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  r4713 | ghutchis | 2012-02-23 22:11:02 -0500 (Thu, 23 Feb 2012) | 2 lines
  
  Final patch from Paolo for MMFF regression due to formal charge assignment.
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  r4714 | baoilleach | 2012-02-24 10:32:26 -0500 (Fri, 24 Feb 2012) | 1 line
  
  align.cpp, opalign.cpp, aligntest.cpp: Fix a bug when aligning objects in 3D. This would only have been observed if you used the rotation matrix returned by GetRotMatrix(). (1) GetRotMatrix() should have returned the transpose. (2) In opalign, the coords of the ref and target need to be adjusted by the centroid before applying the RotMatrix.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4932 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4716 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4716 | baoilleach | 2012-03-01 05:21:37 -0500 (Thu, 01 Mar 2012) | 1 line
  
  perception.cpp: Fixes #3423013. Now, aromatic bonds in rings do not give rise to cis/trans stereo objects.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4933 71e0b675-c112-0410-beda-96664073b5c2
Migrated merge tools to native "svn merge" rather than old python.


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4934 71e0b675-c112-0410-beda-96664073b5c2
Merge r4720:4723 from trunk

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4935 71e0b675-c112-0410-beda-96664073b5c2
Merge r4726:4727 from trunk

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4936 71e0b675-c112-0410-beda-96664073b5c2
Merge 4730:4731 from trunk.

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4937 71e0b675-c112-0410-beda-96664073b5c2
Merge 4734:4738 from trunk.

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4938 71e0b675-c112-0410-beda-96664073b5c2
Merge r4743:4752 from trunk

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4939 71e0b675-c112-0410-beda-96664073b5c2
Merge r4754:4765 from trunk

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4940 71e0b675-c112-0410-beda-96664073b5c2
Merge r4768:4838 from trunk

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4941 71e0b675-c112-0410-beda-96664073b5c2