Merged revisions 4416 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4416 | baoilleach | 2011-03-18 12:42:51 -0400 (Fri, 18 Mar 2011) | 3 lines
  
  src/mcdlutil.cpp: Reapply r4403 (reverted in r4410). Avoid stereo perception if Modify flag is set. The InChI tests now pass.
  test/testsym.py: Some basic gen2d tests for SMILES -> MDL
  src/formats/mdlformat.cpp: Invert the "w" option. Now the default is to recalculate wedge/hash and "w" forces reuse of existing wedge/hash bond designations.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4453 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4427-4432,4434-4440,4449,4451 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4427 | ghutchis | 2011-03-23 21:57:15 -0400 (Wed, 23 Mar 2011) | 2 lines
  
  CMake magic to handle Mac Python install paths -- update links to libopenbabel.dylib.
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  r4428 | baoilleach | 2011-03-24 15:24:25 -0400 (Thu, 24 Mar 2011) | 1 line
  
  src/CMakeLists.txt: Only include opalign if EIGEN2_FOUND
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  r4429 | ghutchis | 2011-03-31 14:52:37 -0400 (Thu, 31 Mar 2011) | 2 lines
  
  Fix messages from GUI, INCHI to allow use of ccmake tool. Thanks to Andrew Fant for the heads-up.
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  r4430 | ghutchis | 2011-03-31 14:53:45 -0400 (Thu, 31 Mar 2011) | 2 lines
  
  Cmake fixes to handle SWIG > 2.0 and various script binding installation issues.
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  r4431 | chrismorl | 2011-04-04 05:34:16 -0400 (Mon, 04 Apr 2011) | 1 line
  
  Correct bug #3273062, gaussformat seg faults with empty file, reported by Jiahao Chen
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  r4432 | vincefn | 2011-04-12 16:48:11 -0400 (Tue, 12 Apr 2011) | 1 line
  
  Update reference for cif -> cartesian conversion.
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  r4434 | baoilleach | 2011-04-14 15:09:27 -0400 (Thu, 14 Apr 2011) | 1 line
  
  mcdlutil.cpp: Bug fix from Sergey Trepalin. Fixes the problem with the 35 that were not converting (see http://forums.openbabel.org/Performance-of-gen2d-td3393389.html).
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  r4435 | cryosuk | 2011-04-14 23:07:23 -0400 (Thu, 14 Apr 2011) | 1 line
  
  Only set the output dirs if not already set.
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  r4436 | cryosuk | 2011-04-14 23:07:30 -0400 (Thu, 14 Apr 2011) | 3 lines
  
  Added an option (on Windows) to use prebuilt binaries.
  
  This defaults to ON in order to preserve existing behavior.
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  r4437 | cryosuk | 2011-04-14 23:07:38 -0400 (Thu, 14 Apr 2011) | 4 lines
  
  Only force Inchi off if using prebuilt binaries.
  
  The default behavior is still preserved, and the logic simplified. Inchi
  can now be build for MSVC too, if the user chooses to.
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  r4438 | baoilleach | 2011-04-15 03:57:42 -0400 (Fri, 15 Apr 2011) | 2 lines
  
  openbabel-csharp.i: Fix Downcast method (was already fixed in 2.2.x but was not merged to trunk)
  pybel.py: Updated to synch with Cinfony.
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  r4439 | baoilleach | 2011-04-15 05:06:24 -0400 (Fri, 15 Apr 2011) | 2 lines
  
  scripts/openbabel-perl.i: Fix warning
  src/ops/opisomorph.cpp: Fix warning
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  r4440 | baoilleach | 2011-04-16 08:55:45 -0400 (Sat, 16 Apr 2011) | 1 line
  
  a_obpython.bat: Minor correction to setup for generating of Python bindings on Windows.
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  r4449 | ghutchis | 2011-04-20 21:13:20 -0400 (Wed, 20 Apr 2011) | 2 lines
  
  Fix bug with sp3 atoms -- now properly defines 109.47 degrees for NH3, CH3, etc.
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  r4451 | ghutchis | 2011-04-21 15:39:43 -0400 (Thu, 21 Apr 2011) | 2 lines
  
  Add AliasData cast for Igor.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4454 71e0b675-c112-0410-beda-96664073b5c2
Blocked revisions 4433,4450 via svnmerge

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  r4433 | ghutchis | 2011-04-14 13:14:24 -0400 (Thu, 14 Apr 2011) | 3 lines
  
  Update pointgroup perception with better tolerances and a fallback tree to
  assign an enum symbol. (e.g., not-quite symmetric benzene = C6h)
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  r4450 | ghutchis | 2011-04-20 21:14:04 -0400 (Wed, 20 Apr 2011) | 2 lines
  
  Add improved symmetry detection and Symmetrize() function.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4581 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4441-4448,4452 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4441 | timvdm | 2011-04-16 13:28:20 -0400 (Sat, 16 Apr 2011) | 2 lines
  
  OBGroupContrib: Ensure all exported API cpp code is inside the openbabel
  library.
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  r4442 | timvdm | 2011-04-16 13:28:34 -0400 (Sat, 16 Apr 2011) | 1 line
  
  Add unit test for writing stereo bond flags.
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  r4443 | ghutchis | 2011-04-16 21:12:13 -0400 (Sat, 16 Apr 2011) | 2 lines
  
  Ignore compiled subdirectories.
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  r4444 | timvdm | 2011-04-17 06:41:02 -0400 (Sun, 17 Apr 2011) | 1 line
  
  SVG format: Use thicker lines
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  r4445 | timvdm | 2011-04-17 06:41:23 -0400 (Sun, 17 Apr 2011) | 2 lines
  
  SVGFormat: Add -xs option to enable asymmetric double bonds. This option
  is not enabled by default.
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  r4446 | timvdm | 2011-04-17 06:41:38 -0400 (Sun, 17 Apr 2011) | 2 lines
  
  SVGFormat: Make thicker lines optional with -xt option. This options is
  not enabled by default.
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  r4447 | timvdm | 2011-04-17 09:51:35 -0400 (Sun, 17 Apr 2011) | 1 line
  
  Remove invalid stereo bond unit test
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  r4448 | timvdm | 2011-04-18 06:34:42 -0400 (Mon, 18 Apr 2011) | 3 lines
  
  Revert "OBGroupContrib: Ensure all exported API cpp code is inside the openbabel"
  
  This reverts commit affc33b86be0a50a0d1c8b80a1b1c3f2b7000108.
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  r4452 | ghutchis | 2011-04-21 15:40:21 -0400 (Thu, 21 Apr 2011) | 2 lines
  
  Fix warning from clang-analyzer (i.e., use "count" instead of discarding.)
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4582 71e0b675-c112-0410-beda-96664073b5c2
Blocked revisions 4574,4576 via svnmerge

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  r4574 | chrismorl | 2011-09-14 15:50:23 -0400 (Wed, 14 Sep 2011) | 1 line
  
  Define a new flag for OBMol and use it in SetSpinMultiplicityAssigned() and HasSpinMultiplicityAssigned() instead of OB_TSPIN_MOL. Specifying total spin for a molecule no longer prevents the hydrogen deficiencies of individual atoms being assigned.
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  r4576 | ghutchis | 2011-09-15 12:49:52 -0400 (Thu, 15 Sep 2011) | 2 lines
  
  Patch contributed by Magnus Lundborg, PR#3155737.
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git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4583 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4455-4535 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

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  r4455 | timvdm | 2011-04-25 13:55:28 -0400 (Mon, 25 Apr 2011) | 1 line
  
  SVGPainter & SVGFormat: Enable black background again.
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  r4456 | chrismorl | 2011-04-26 05:26:56 -0400 (Tue, 26 Apr 2011) | 1 line
  
  Read and write valence field in MDL atom block when it is 15 (no attachments)
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  r4457 | chrismorl | 2011-04-26 05:29:56 -0400 (Tue, 26 Apr 2011) | 1 line
  
  Do not process the output mol vector in deferredformat if it is empty
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  r4458 | chrismorl | 2011-04-26 05:33:05 -0400 (Tue, 26 Apr 2011) | 1 line
  
  Left justify the title of a single mol in svgformat
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  r4459 | chrismorl | 2011-04-26 06:14:21 -0400 (Tue, 26 Apr 2011) | 1 line
  
  Add CSharpBindings to Windows Installer
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  r4460 | jbrefort | 2011-05-04 10:54:09 -0400 (Wed, 04 May 2011) | 2 lines
  
  Fixed space group P -2yac
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  r4461 | chrismorl | 2011-05-09 08:45:45 -0400 (Mon, 09 May 2011) | 1 line
  
  Generate wedge/hash bonds in OBDepict and svgFormat by default. Replace enum item genWedgeHash by noWedgeHashGen
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  r4462 | mr_grieves | 2011-05-10 13:47:10 -0400 (Tue, 10 May 2011) | 7 lines
  
  Fix enthalpy parsing in the VASP input reader.
  
  OBMol::SetData() does not overwrite existing entries as assumed
  previously, causing the reported enthalpy to match the first enthalpy
  printed in the OUTCAR, not the last (final) enthalpy.
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  r4463 | chrismorl | 2011-05-11 09:15:25 -0400 (Wed, 11 May 2011) | 1 line
  
  Ensure binary reading in ReadFile(). Hopefully will allow gzipped files to be read from Python in Windows, although not tested yet. 
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  r4464 | baoilleach | 2011-05-14 05:18:33 -0400 (Sat, 14 May 2011) | 1 line
  
  scripts/CMakeLists.txt: Minor change that I never committed. Places openbabel.py in the windows-vc2008/build/bin/Release folder instead of build/Release.
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  r4465 | baoilleach | 2011-05-14 05:28:32 -0400 (Sat, 14 May 2011) | 1 line
  
  windows-vc2008/default_build.bat: Trivial fix for compile fail on Windows after recent changes to handling of InChI by Marcus.
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  r4466 | baoilleach | 2011-05-14 12:25:16 -0400 (Sat, 14 May 2011) | 1 line
  
  scripts/openbabel-python.i: Add support for toAliasData in Python bindings.
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  r4467 | baoilleach | 2011-05-14 13:04:31 -0400 (Sat, 14 May 2011) | 1 line
  
  obconversion.h, .cpp: Some extra doxygen docs on Read and ReadFile showing typical use through bindings. Fixes PR#3158080.
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  r4468 | baoilleach | 2011-05-15 08:07:19 -0400 (Sun, 15 May 2011) | 1 line
  
  scripts/CMakeLists.txt: Fix Ruby bindings as reported by Christoph Helma on openbabel-scripting on 11 May
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  r4469 | baoilleach | 2011-05-15 08:49:37 -0400 (Sun, 15 May 2011) | 1 line
  
  src/ops/opisomorph.h: Fix trivial warning.
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  r4470 | chrismorl | 2011-05-15 11:57:06 -0400 (Sun, 15 May 2011) | 1 line
  
  Allow image size to be specified in SVGFormat with multiple mols
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  r4471 | baoilleach | 2011-05-16 16:14:36 -0400 (Mon, 16 May 2011) | 1 line
  
  Update the draw method of Pybel so that it uses our own depiction and 2D layout. I've removed the dependency on OASA (but added optional dependencies on cairo and pyrsvg). Once we have direct depiction on PNG I'll be able to drop the pyrsvg one.
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  r4472 | mr_grieves | 2011-05-17 12:47:17 -0400 (Tue, 17 May 2011) | 1 line
  
  Fix copyright info in castepformat.cpp
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  r4473 | mr_grieves | 2011-05-17 12:47:51 -0400 (Tue, 17 May 2011) | 1 line
  
  Fix enthalpy storage in the GULP format reader.
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  r4474 | mr_grieves | 2011-05-17 12:48:06 -0400 (Tue, 17 May 2011) | 1 line
  
  Fix enthalpy storage in the PWscf format reader.
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  r4475 | chrismorl | 2011-05-18 06:43:52 -0400 (Wed, 18 May 2011) | 1 line
  
  SVGFormat, called from OBConversion::Write(), makes a fixed size window, sizable with the P option. 
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  r4476 | chrismorl | 2011-05-18 12:58:25 -0400 (Wed, 18 May 2011) | 1 line
  
  In TetStereoToWedgeHash swap atoms in bond so stereo center comes first, so that OBDepiction renders wedge and hash with pointy end at the center.
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  r4477 | ghutchis | 2011-05-19 12:48:57 -0400 (Thu, 19 May 2011) | 4 lines
  
  Improve options in reading FASTA files:
  generate single-stranded DNA and change # of base pairs per turn
  (Now suitable for a DNA/RNA builder in Avogadro.)
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  r4478 | ghutchis | 2011-05-19 12:50:02 -0400 (Thu, 19 May 2011) | 2 lines
  
  Add support for reading alpha/beta orbital eigenvalues (e.g., open shell calcs)
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  r4479 | ghutchis | 2011-05-19 12:51:42 -0400 (Thu, 19 May 2011) | 3 lines
  
  Add support for reading/writing unit cell from BGF.
  (Examples of space group info would be welcome.)
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  r4480 | ghutchis | 2011-05-19 12:52:21 -0400 (Thu, 19 May 2011) | 2 lines
  
  Generate a tag file for incorporation into Doxygen sub-projects (e.g., Avogadro).
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  r4481 | ghutchis | 2011-05-19 13:17:05 -0400 (Thu, 19 May 2011) | 2 lines
  
  Add support for "organometallic" phosphorous atom type -- look for bonded metals.
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  r4482 | ghutchis | 2011-05-19 14:32:05 -0400 (Thu, 19 May 2011) | 2 lines
  
  Ignore openbabel-ruby.txt file.
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  r4483 | ghutchis | 2011-05-19 14:34:45 -0400 (Thu, 19 May 2011) | 2 lines
  
  Initial changes to support Eigen3
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  r4484 | chrismorl | 2011-05-21 08:28:18 -0400 (Sat, 21 May 2011) | 3 lines
  
  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.
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  r4485 | baoilleach | 2011-05-25 15:17:10 -0400 (Wed, 25 May 2011) | 1 line
  
  svgpainter.cpp: Make SVG file slightly more verbose than necessary due to apparent limitations of rsvg used in Pybel (the lines are not drawn otherwise). Once Open Babel can generate PNGs itself, this line can be brought back.
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  r4486 | chrismorl | 2011-05-26 03:39:54 -0400 (Thu, 26 May 2011) | 1 line
  
  Revert the writing of the atom valence field in MDLFormat.
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  r4487 | baoilleach | 2011-05-26 15:34:09 -0400 (Thu, 26 May 2011) | 1 line
  
  Pybel Python files: Updates on the drawing code using Chris's "P" option for SVG.
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  r4488 | chrismorl | 2011-05-28 10:45:26 -0400 (Sat, 28 May 2011) | 1 line
  
  Note that a datafile cannot be larger than 4GB in FastSeachFormat and a check on the size when preparing a large index.
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  r4489 | baoilleach | 2011-05-28 16:19:02 -0400 (Sat, 28 May 2011) | 1 line
  
  cairopainter.cpp, .h, png2format.cpp, and src/formats/CMakeLists.txt: Add support for PNG depiction. This support is currently protected by "-DWITH_PNG=ON" to prevent build problems (the current code works only on Windows and has hardcoded library locations). The PNG2 format also needs to be merged with PNG format.
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  r4490 | baoilleach | 2011-05-29 12:05:51 -0400 (Sun, 29 May 2011) | 1 line
  
  CMakeLists.txt, formats/CMakeLists.txt, FindCairo.cmake: Add Cmake build support for PNG depiction on Linux. On Ubuntu, install libcairo2-dev if you want PNG depiction.
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  r4491 | baoilleach | 2011-05-29 12:55:04 -0400 (Sun, 29 May 2011) | 1 line
  
  Add Cairo dependencies and include files for Windows build.
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  r4492 | baoilleach | 2011-05-29 13:35:27 -0400 (Sun, 29 May 2011) | 1 line
  
  cairopainter.cpp: Correct bug in translating the image to the center. Draw filled polygon for wedge.
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  r4493 | baoilleach | 2011-05-29 15:15:05 -0400 (Sun, 29 May 2011) | 1 line
  
  chemdrawcdx.cpp: Fix compilation on Cygwin reported (with fix) by Dmitry Katsubo (PR#3308500).
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  r4494 | baoilleach | 2011-05-29 15:30:33 -0400 (Sun, 29 May 2011) | 1 line
  
  obutil.cpp: Fixed problem deleting dummy atoms in InternalToCartesian reported by My Th, Patch PR#3196285.
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  r4495 | baoilleach | 2011-05-29 16:26:57 -0400 (Sun, 29 May 2011) | 1 line
  
  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.
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  r4496 | baoilleach | 2011-05-30 04:30:23 -0400 (Mon, 30 May 2011) | 1 line
  
  fastsearchformat.cpp: Minor fix to r4488 for non-MSVC builds.
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  r4497 | mr_grieves | 2011-05-30 09:04:13 -0400 (Mon, 30 May 2011) | 1 line
  
  Fixed compiler warnings in gulp, vasp, castep, and pwscf parsers.
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  r4498 | baoilleach | 2011-05-30 14:52:48 -0400 (Mon, 30 May 2011) | 2 lines
  
  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.
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  r4499 | chrismorl | 2011-05-31 03:30:17 -0400 (Tue, 31 May 2011) | 1 line
  
  Add destructor for OBDepict to delete the private class instance
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  r4500 | baoilleach | 2011-05-31 12:40:37 -0400 (Tue, 31 May 2011) | 3 lines
  
  depict.h: Minor fix to destructor for Linux systems.
  cairopainter.cpp: Fix memory leak. I forgot to destroy the new surface.
  mcdlutil.cpp: Fix memory leak. Uncomment the destructor.
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  r4501 | baoilleach | 2011-05-31 13:53:44 -0400 (Tue, 31 May 2011) | 2 lines
  
  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.
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  r4502 | baoilleach | 2011-05-31 16:15:19 -0400 (Tue, 31 May 2011) | 1 line
  
  mcdlutil.cpp: Revert of edit in r4500.
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  r4503 | baoilleach | 2011-05-31 16:55:19 -0400 (Tue, 31 May 2011) | 1 line
  
  depict.cpp: Restore setting wedges+hashes.
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  r4504 | baoilleach | 2011-06-01 16:14:35 -0400 (Wed, 01 Jun 2011) | 1 line
  
  depict.cpp, svgpainter.cpp: Sort out placing labels for implicit hydrogens in PNG (and SVG).
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  r4505 | baoilleach | 2011-06-02 04:22:46 -0400 (Thu, 02 Jun 2011) | 1 line
  
  depict.cpp: Correct the length of hashes. Should be the same as wedges.
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  r4506 | baoilleach | 2011-06-02 16:54:56 -0400 (Thu, 02 Jun 2011) | 2 lines
  
  depict.cpp: Improve placement of + and - signs.
  svgformat.cpp: In the JavaScript, don't scroll when zooming.
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  r4507 | baoilleach | 2011-06-02 17:00:59 -0400 (Thu, 02 Jun 2011) | 1 line
  
  svgformat.cpp: In the JavaScript, don't scroll when zooming.
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  r4508 | baoilleach | 2011-06-04 16:54:44 -0400 (Sat, 04 Jun 2011) | 1 line
  
  mdlformat.cpp: Expand option "-as" to allow determination of chirality from atom parities for 2D also. Correct handling of atom parities for cases where implicit refs or hydrogens are involved.
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  r4509 | baoilleach | 2011-06-05 14:40:28 -0400 (Sun, 05 Jun 2011) | 1 line
  
  pybel.py: Update pybel versions to draw using the PNG2 format.
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  r4510 | chrismorl | 2011-06-05 16:38:52 -0400 (Sun, 05 Jun 2011) | 1 line
  
  Integrated PNGFormat with PNG2Format. PNGFormat writes PNG files (by calling PNG2Format) and can embed and extract chemical structure data in them or external PNG files. Added option for changing (square) image size to cairopainter. Tidied up PNG2Format.cpp  
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  r4511 | ghutchis | 2011-06-05 23:17:47 -0400 (Sun, 05 Jun 2011) | 2 lines
  
  Add flag for OBMol::IsChiral() as pointed out by Dave Nunn.
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  r4512 | baoilleach | 2011-06-08 10:43:46 -0400 (Wed, 08 Jun 2011) | 1 line
  
  reportformat.cpp: Fix for r3313786.
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  r4513 | baoilleach | 2011-06-10 04:39:44 -0400 (Fri, 10 Jun 2011) | 1 line
  
  openbabel-java.i, openbabel-python.i: Synch the Python and Java interface files.
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  r4514 | baoilleach | 2011-06-10 06:34:35 -0400 (Fri, 10 Jun 2011) | 1 line
  
  scripts/CMakeLists.txt: Add EIGEN2 protection for building Java bindings
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  r4515 | baoilleach | 2011-06-24 06:39:35 -0400 (Fri, 24 Jun 2011) | 1 line
  
  scripts/CMakeLists.txt: Ruby code. Work around a bug in Cmake 2.6.0 PR#3314603
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  r4516 | chrismorl | 2011-06-26 16:16:02 -0400 (Sun, 26 Jun 2011) | 2 lines
  
  Extend --property option to handle multiple properties with spaces in attribute and value, e.g.
  --property attribute1=value1; multi word attribute2 = multi word value2
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  r4517 | baoilleach | 2011-06-27 04:36:52 -0400 (Mon, 27 Jun 2011) | 1 line
  
  Update draw method pybel to remove explicit Hs before calling gen2d.
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  r4518 | ghutchis | 2011-06-28 14:24:37 -0400 (Tue, 28 Jun 2011) | 2 lines
  
  Add initial support for ABINIT files.
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  r4519 | baoilleach | 2011-06-29 15:31:52 -0400 (Wed, 29 Jun 2011) | 1 line
  
  6 format files: Update Description strings for docs.
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  r4520 | jiahao | 2011-07-05 19:47:34 -0400 (Tue, 05 Jul 2011) | 5 lines
  
  Preliminary support for periodic cells in MOPAC 2007/9 input.
  
  Also fixed tokenize(,,) as per Noel's suggestion.
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  r4521 | baoilleach | 2011-07-06 05:10:59 -0400 (Wed, 06 Jul 2011) | 1 line
  
  Rename OBGUI to obgui in keeping with the other executables.
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  r4522 | baoilleach | 2011-07-06 15:11:22 -0400 (Wed, 06 Jul 2011) | 1 line
  
  smilesformat.cpp: Add output option "l <atomno>" to enable the user to specify the 'last atom'; really it's the atom to which any additional SMILES atoms should attach. I just need to implement "f" for first atom (by analogy with the -f and -l global options), which is much easier, and it will be good to go. "-xl" tested on all available connection points in the first 1000 members of PubChem... 100% success.
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  r4523 | jiahao | 2011-07-07 09:14:52 -0400 (Thu, 07 Jul 2011) | 2 lines
  
  Changed 'and' to '&&' 
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  r4524 | baoilleach | 2011-07-07 09:20:51 -0400 (Thu, 07 Jul 2011) | 1 line
  
  Fix to previous commit "Rename OBGUI to obgui in keeping with the other executables"
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  r4525 | baoilleach | 2011-07-07 15:01:12 -0400 (Thu, 07 Jul 2011) | 1 line
  
  smilesformat.cpp: Add output option "f <atomno>" to enable the user to specify the 'first atom' of the SMILES string. Note to self: one corner case to handle for "l" option still.
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  r4526 | baoilleach | 2011-07-07 16:38:59 -0400 (Thu, 07 Jul 2011) | 1 line
  
  povrayformat.cpp: Fix bug reported by Steve Wathen. Don't quite understand why, but on Linux my clever use of STL generic erase and remove_if caused a segfault
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  r4527 | baoilleach | 2011-07-08 04:30:50 -0400 (Fri, 08 Jul 2011) | 1 line
  
  data/CMakeLists.txt: Install babel_povray3.inc
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  r4528 | baoilleach | 2011-07-09 08:22:00 -0400 (Sat, 09 Jul 2011) | 1 line
  
  smilesformat.cpp: Finish off "f" and "l" options: (1) Add docs, (2) Handle corner cases of "l" specified for [nH] and [C@@H], (3) Avoid rearranging the canonical tree after we've already dealt with _endatom as there's no need at that point.
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  r4529 | baoilleach | 2011-07-12 14:08:08 -0400 (Tue, 12 Jul 2011) | 1 line
  
  smilesformat.cpp: Finish off "f" options: Handle corner cases of "f" specified for [nH] and [C@@H]
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  r4530 | baoilleach | 2011-07-12 15:18:08 -0400 (Tue, 12 Jul 2011) | 1 line
  
  povrayformat.cpp: Update Description
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  r4531 | vincefn | 2011-07-19 18:09:32 -0400 (Tue, 19 Jul 2011) | 1 line
  
  Handle missing values for lattice parameters, or a missing spacegroup description
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  r4532 | vincefn | 2011-07-20 07:38:02 -0400 (Wed, 20 Jul 2011) | 1 line
  
  Add missing BeginModify()
........
  r4533 | baoilleach | 2011-07-31 09:48:21 -0400 (Sun, 31 Jul 2011) | 1 line
  
  depict/depict.cpp: Fix bug with premature truncation of bonds when bonds are stretched longer than normal. Test case is  c1ccc(cc1)[Si]2(O[Si](O[Si](O[Si](O2)(c3ccccc3)c4ccccc4)(c5ccccc5)c6ccccc6)(c7ccccc7)c8ccccc8)c9ccccc9
........
  r4534 | baoilleach | 2011-08-01 14:54:40 -0400 (Mon, 01 Aug 2011) | 1 line
  
  mcdlutil.cpp: Speed up structure layout in the general case, by carrying out systematic search on the inner N=10 rotbonds, and greedily searching the remainder. (The original code carried out systematic search on the 'first' N=20 rotbonds leaving the others unchanged.)
........
  r4535 | baoilleach | 2011-08-15 12:41:05 -0400 (Mon, 15 Aug 2011) | 1 line
  
  perception.cpp: Fix two stereo problems reported on openbabel-discuss by Robert Kiss (Aug 9th 2011). Loss of stereo from "C[P@](=O)(Br)Cl" and "C[N@+](I)(Br)Cl".
........


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4584 71e0b675-c112-0410-beda-96664073b5c2
Manual adaptation of r4536 from trunk, without adding API: OBAtom::IsMetal().


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4585 71e0b675-c112-0410-beda-96664073b5c2
Blocked revisions 4536 via svnmerge

........
  r4536 | chrismorl | 2011-08-21 15:50:45 -0400 (Sun, 21 Aug 2011) | 1 line
  
  Mods to MDLFormat, IMPVALs, inchiformat and metal atom detection to reduce the discrepancies reported by Robert Kiss 
........


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4586 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4537-4550,4552-4573,4575 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

........
  r4537 | ghutchis | 2011-08-22 14:42:39 -0400 (Mon, 22 Aug 2011) | 2 lines
  
  By default, set the spacegroup -- causes crashes in Avogadro 1.1.
........
  r4538 | ghutchis | 2011-08-22 14:46:29 -0400 (Mon, 22 Aug 2011) | 3 lines
  
  Add support for connecting fragments with dummy atoms (e.g., Cp rings).
  Simplify rotation code.
........
  r4539 | ghutchis | 2011-08-23 10:57:22 -0400 (Tue, 23 Aug 2011) | 3 lines
  
  Update torsion library to look for CIS arrangement of esters.
  Fixes Avogadro bug report PR#3307357.
........
  r4540 | ghutchis | 2011-08-28 15:33:27 -0400 (Sun, 28 Aug 2011) | 2 lines
  
  Fix reading MOPAC files with translation vectors.
........
  r4541 | chrismorl | 2011-08-29 04:32:53 -0400 (Mon, 29 Aug 2011) | 1 line
  
  mdlformat: ignore A line if alias is blank. Fixes bug #3400061 from Chong Hak Chae
........
  r4542 | baoilleach | 2011-08-29 10:30:34 -0400 (Mon, 29 Aug 2011) | 1 line
  
  stereo/perception.cpp: (a) Rewrite TetStereoToWedgeHash() to use a scoring system to choose the best bond (simpler code). (b) Give a high score to bonds that are within DELTA_ANGLE_FOR_OVERLAPPING_BONDS of each other. This fixes some of the problems with Robert Kiss' test set (down from 146 failures to 120) as the InChI code regards such close bonds as ambiguous if using them to determine the stereo.
........
  r4543 | baoilleach | 2011-08-29 16:27:28 -0400 (Mon, 29 Aug 2011) | 1 line
  
  src/stereo/perception.cpp: Correction to r4542 supplied by My Th. Fixes PR#3400330.
........
  r4544 | baoilleach | 2011-08-30 10:41:27 -0400 (Tue, 30 Aug 2011) | 1 line
  
  src/formats/cifformat.cpp: Change 'ERROR' to 'Error' in the error messages generated by the CIF code. This prevents unintended ctest failures in the test suite.
........
  r4545 | baoilleach | 2011-08-30 11:28:17 -0400 (Tue, 30 Aug 2011) | 1 line
  
  test/testbindings.py,testsym.py,testbabel.py: Applied patch PR#3399369 from My Th for Python 3 support running the tests.
........
  r4546 | ghutchis | 2011-08-30 12:21:00 -0400 (Tue, 30 Aug 2011) | 2 lines
  
  Remove un-needed space group definition. The bug is really in the client code.
........
  r4547 | vincefn | 2011-09-01 15:59:15 -0400 (Thu, 01 Sep 2011) | 1 line
  
  Better error/warning messages. Handle special case for empty data_global CIF data block
........
  r4548 | baoilleach | 2011-09-02 12:28:09 -0400 (Fri, 02 Sep 2011) | 1 line
  
  NEW_ENUM_VALUE: Add support for MOL file unknown stereochemistry. Needs to be pushed out to other formats now, and tests updated.
........
  r4549 | mbanck | 2011-09-02 12:33:00 -0400 (Fri, 02 Sep 2011) | 1 line
  
  Add initial support for frequencies to vaspformat
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  r4550 | vincefn | 2011-09-02 16:56:46 -0400 (Fri, 02 Sep 2011) | 1 line
  
  Better handling of missing unit cell data using space group information. Be more forgiving when determining space group.
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  r4552 | baoilleach | 2011-09-03 15:39:34 -0400 (Sat, 03 Sep 2011) | 1 line
  
  NEW_ENUM_VALUE: Add support for reading "Unknown" stereo for MDL, and writing it for SMILES.
........
  r4553 | chrismorl | 2011-09-04 05:52:29 -0400 (Sun, 04 Sep 2011) | 1 line
  
  Correct bug #3403862 from Dave Nunn by adding a IMPVAL line.
........
  r4554 | baoilleach | 2011-09-04 08:32:32 -0400 (Sun, 04 Sep 2011) | 1 line
  
  NEW_ENUM_VALUE: Partial revert of smilesformat.cpp (r4552) where I accidentally committed some local changes.
........
  r4555 | baoilleach | 2011-09-04 15:17:33 -0400 (Sun, 04 Sep 2011) | 1 line
  
  depict.cpp: Draw a Wobbly Bond if the bond is UnknownDir (rather than Wedge or Hash). 
........
  r4556 | chrismorl | 2011-09-05 11:53:04 -0400 (Mon, 05 Sep 2011) | 1 line
  
  Try again to correct #3403862 without side-effects.
........
  r4557 | baoilleach | 2011-09-05 14:30:16 -0400 (Mon, 05 Sep 2011) | 1 line
  
  src/parsmart.cpp: Correct code error identified by Chris. Add missing brackets around "for" loop and comment out debugging statements.
........
  r4558 | baoilleach | 2011-09-05 16:35:16 -0400 (Mon, 05 Sep 2011) | 1 line
  
  src/formats/smilesformat.cpp: Add option "I" to smiles output to allow specifying order of atoms in the output. Need to test it.
........
  r4559 | baoilleach | 2011-09-06 04:20:48 -0400 (Tue, 06 Sep 2011) | 1 line
  
  Revert r4558.
........
  r4560 | ghutchis | 2011-09-06 14:47:32 -0400 (Tue, 06 Sep 2011) | 2 lines
  
  Fix for error introduced in r4538. Properly rotate fragments again.
........
  r4561 | ghutchis | 2011-09-06 14:47:58 -0400 (Tue, 06 Sep 2011) | 2 lines
  
  Add initial support for MSI lattice vectors.
........
  r4562 | ghutchis | 2011-09-06 14:48:26 -0400 (Tue, 06 Sep 2011) | 2 lines
  
  Fix formatting.
........
  r4563 | ghutchis | 2011-09-09 11:07:22 -0400 (Fri, 09 Sep 2011) | 2 lines
  
  Fix bugs with connecting dummy-atom fragments like Cp rings.
........
  r4564 | ghutchis | 2011-09-09 11:07:47 -0400 (Fri, 09 Sep 2011) | 2 lines
  
  Improved support for abinit output files.
........
  r4565 | ghutchis | 2011-09-09 12:50:13 -0400 (Fri, 09 Sep 2011) | 3 lines
  
  Add a fake line for dummy atom parameters.
  Also ensure C atoms in Cp rings are typed as aromatic.
........
  r4566 | ghutchis | 2011-09-09 13:25:36 -0400 (Fri, 09 Sep 2011) | 2 lines
  
  Fix bug in unit conversion with abinit coordinates.
........
  r4567 | ghutchis | 2011-09-12 15:51:34 -0400 (Mon, 12 Sep 2011) | 3 lines
  
  Add an exception to deduce coordination numbers for low-valent
  elements (e.g., 4-coordinate (Cp)2TiCl2 = sp3 tetrahedral)
........
  r4568 | ghutchis | 2011-09-12 21:48:05 -0400 (Mon, 12 Sep 2011) | 3 lines
  
  UFF updates, including a change in angle when
  the coordination is updated (e.g., Ferrocene)
........
  r4569 | ghutchis | 2011-09-13 13:35:51 -0400 (Tue, 13 Sep 2011) | 6 lines
  
  Fix regression with UFF test results.
  
  Now provides a more specific test for aromatic Cp rings.
  Also ensures that all bonds in Cp rings are marked BO=1.5.
  Ferrocene now optimizes to Cp-Cp distance of ~3.8 Ang. Not bad!
........
  r4570 | ghutchis | 2011-09-13 13:52:06 -0400 (Tue, 13 Sep 2011) | 2 lines
  
  Revert of r4557.
........
  r4571 | baoilleach | 2011-09-14 05:11:23 -0400 (Wed, 14 Sep 2011) | 1 line
  
  testsym.py, mdlformat.cpp: Updated testsym, and ensure that the "-as" option is working for 3D MOL. This is particularly useful to indicate unspecified stereo in a 3D structure.
........
  r4572 | baoilleach | 2011-09-14 05:11:58 -0400 (Wed, 14 Sep 2011) | 1 line
  
  Fix warning under MSVC, by adding CR at end of file.
........
  r4573 | chrismorl | 2011-09-14 12:25:40 -0400 (Wed, 14 Sep 2011) | 1 line
  
  Fix bug reported by Weerapong Phadungsukanan in which the last element in an XML file was not read properly unless it was followed by whitespace. (Stream tested for !bad rather than good.)
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  r4575 | chrismorl | 2011-09-15 07:16:54 -0400 (Thu, 15 Sep 2011) | 3 lines
  
  Some changes to InChI generation, following a post by Ken Smith.
  Extend the special case for H atoms in OBAtom::GetImplicitValence() so that the InChI of a proton is as recommended.
  Make reuse of an input InChI the default on the commandline or in the GUI, so that conversion of InChI to InChIKey does not go through OBMol. -xr option forces recalculation.
........


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4587 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4577-4580 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

........
  r4577 | ghutchis | 2011-09-15 12:51:55 -0400 (Thu, 15 Sep 2011) | 3 lines
  
  Patch from My Th, fixing issues with internal coordinate assignment.
  Fixes PR#3409984.
........
  r4578 | ghutchis | 2011-09-15 13:00:36 -0400 (Thu, 15 Sep 2011) | 3 lines
  
  Patch from Roger Sayle (via Noel) to fix stack overflow in SMARTS.
  Also adds "radioactive" SMARTS to smartsparse test.
........
  r4579 | ghutchis | 2011-09-15 13:05:34 -0400 (Thu, 15 Sep 2011) | 2 lines
  
  Add support for Gromacs GRO format, PR#3311952.
........
  r4580 | ghutchis | 2011-09-15 13:41:08 -0400 (Thu, 15 Sep 2011) | 2 lines
  
  Add initial support for reading XCrySDen XSF files.
........


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4588 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4589-4598 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

........
  r4589 | baoilleach | 2011-09-15 16:09:59 -0400 (Thu, 15 Sep 2011) | 1 line
  
  Fix bug reported by My Th PR#3399341 (Patches)
........
  r4590 | chrismorl | 2011-09-15 16:25:38 -0400 (Thu, 15 Sep 2011) | 1 line
  
  Add a descriptor "inchikey"
........
  r4591 | baoilleach | 2011-09-16 05:02:34 -0400 (Fri, 16 Sep 2011) | 1 line
  
  groformat: Correct r4579 to use "&&" and "||" instead of "and" and "or" (fails on MSVC).
........
  r4592 | mr_grieves | 2011-09-16 13:02:41 -0400 (Fri, 16 Sep 2011) | 1 line
  
  Clean up vaspformat.cpp and add support for VASP 5.2+ CONTCAR format.
........
  r4593 | baoilleach | 2011-09-17 07:49:47 -0400 (Sat, 17 Sep 2011) | 1 line
  
  scripts/CMakeLists.txt: Another attempt to fix build problems with Eigen2, and make install
........
  r4594 | chrismorl | 2011-09-17 08:51:59 -0400 (Sat, 17 Sep 2011) | 1 line
  
  Fix bug #3349008 by ignoring input molecules only if they have no atoms, no title and no OBPairData properties.
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  r4595 | chrismorl | 2011-09-17 09:02:17 -0400 (Sat, 17 Sep 2011) | 1 line
  
  Allow match with inchikey descriptor with shortened key.
........
  r4596 | baoilleach | 2011-09-17 14:25:37 -0400 (Sat, 17 Sep 2011) | 1 line
  
  formats/fingerprintformat.cpp: Update docstring to explain the FP2 string representation.
........
  r4597 | chrismorl | 2011-09-18 06:01:12 -0400 (Sun, 18 Sep 2011) | 1 line
  
  Add op --addfilename
........
  r4598 | ghutchis | 2011-09-19 16:20:57 -0400 (Mon, 19 Sep 2011) | 4 lines
  
  Patch for copying conformers by Izhar Wallach.
  Make sure when copying conformers to reset to the current
  conformer.
........


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4622 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4601-4602,4604-4621 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

........
  r4601 | ghutchis | 2011-09-22 10:42:33 -0400 (Thu, 22 Sep 2011) | 2 lines
  
  Ensure that spins are written correctly for CNDO-style files.
........
  r4602 | ghutchis | 2011-09-22 10:46:47 -0400 (Thu, 22 Sep 2011) | 2 lines
  
  Read orbital energies from MOPAC output files.
........
  r4604 | ghutchis | 2011-09-22 11:50:43 -0400 (Thu, 22 Sep 2011) | 2 lines
  
  Speed improvements (~20%) to UFF.
........
  r4605 | ghutchis | 2011-09-22 17:07:40 -0400 (Thu, 22 Sep 2011) | 2 lines
  
  Accelerate gen3d by using VDW, electrostatic cutoffs.
........
  r4606 | ghutchis | 2011-09-23 16:46:58 -0400 (Fri, 23 Sep 2011) | 3 lines
  
  Re-use existing energy for line search
  (~10% performance improvement)
........
  r4607 | ghutchis | 2011-09-23 22:42:03 -0400 (Fri, 23 Sep 2011) | 5 lines
  
  Performance improvement for MM+cutoffs
  (All distance cutoffs for VDW and electrostatics
   are now calculated using squares, eliminates
   un-needed sqrt() updates.)
........
  r4608 | ghutchis | 2011-09-24 15:27:29 -0400 (Sat, 24 Sep 2011) | 3 lines
  
  Change VDW calculation to use distance squared.
  (Saves a sqrt and multiply every evaluation.)
........
  r4609 | baoilleach | 2011-09-25 15:53:32 -0400 (Sun, 25 Sep 2011) | 1 line
  
  include/openbabel/inchiformat.h: Add InChIKey format. Basically a convenience format for "-oinchi -xK".
........
  r4610 | baoilleach | 2011-09-26 14:38:46 -0400 (Mon, 26 Sep 2011) | 1 line
  
  include/openbabel/parsmart.h: Allow OBSmartsPattern::GetSMARTS() to work in the SWIG bindings. Thanks to Mingyue Zheng for reporting.
........
  r4611 | baoilleach | 2011-09-28 16:51:29 -0400 (Wed, 28 Sep 2011) | 1 line
  
  src/formats/inchiformat.cpp: Whoops. The other half of r4609. Thanks to Chris for pointing out that I forgot this.
........
  r4612 | ghutchis | 2011-09-30 13:40:04 -0400 (Fri, 30 Sep 2011) | 4 lines
  
  Fix atom typing with GAFF force field
  PR#3372106 for methacrylic acid.
  Conjugated C=O should be typed as a ketone.
........
  r4613 | ghutchis | 2011-09-30 20:50:34 -0400 (Fri, 30 Sep 2011) | 2 lines
  
  Update with new GAFF parameters from AmberTools 1.5 (GPL'ed).
........
  r4614 | chrismorl | 2011-10-02 11:06:07 -0400 (Sun, 02 Oct 2011) | 2 lines
  
  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.
........
  r4615 | ghutchis | 2011-10-03 12:32:11 -0400 (Mon, 03 Oct 2011) | 3 lines
  
  Add debugging output to indicate the total time and # of iterations per second.
  (Helps with performance optimizations)
........
  r4616 | ghutchis | 2011-10-03 12:33:58 -0400 (Mon, 03 Oct 2011) | 3 lines
  
  Add a default nitrogen parameter (for amines).
  Allows minimization of PDB files without added hydrogens.
........
  r4617 | ghutchis | 2011-10-03 12:35:08 -0400 (Mon, 03 Oct 2011) | 2 lines
  
  Update GAFF capitalization and description.
........
  r4618 | baoilleach | 2011-10-05 14:08:13 -0400 (Wed, 05 Oct 2011) | 1 line
  
  src/mcdlutil.cpp: Fix for segfault reported on openbabel-discuss by hayanface converting from SDF to SVG. Replace hard-coded array limit with dynamically-resized array.
........
  r4619 | baoilleach | 2011-10-08 09:35:12 -0400 (Sat, 08 Oct 2011) | 1 line
  
  src/mcdlutil.cpp: Fix by Sergei Trepalin for layout problems reported on openbabel-discuss by hayanface.
........
  r4620 | baoilleach | 2011-10-08 10:40:52 -0400 (Sat, 08 Oct 2011) | 3 lines
  
  Housekeeping task. Set svn:eol-style to native as follows:
  for f in `find . | egrep "\.cpp$|\.c$|\.h$|\.txt$"`; do svn propset svn:eol-style native $f; done
........
  r4621 | ghutchis | 2011-10-08 15:50:50 -0400 (Sat, 08 Oct 2011) | 2 lines
  
  Fix crash with parsing vibrations from MOPAC, PR#3417992.
........


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4623 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4625 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

........
  r4625 | chrismorl | 2011-10-09 12:22:39 -0400 (Sun, 09 Oct 2011) | 3 lines
  
  Update Windows build files. Data to %ProgramData%, a writeable folder, if present.
  Convert IsMetal, a temporary helper function, to member function in MDLFormat to avoid conflict with similar in InChIFormat.
........


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4633 71e0b675-c112-0410-beda-96664073b5c2
Merged revisions 4634 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk

........
  r4634 | ghutchis | 2011-10-12 16:06:27 -0400 (Wed, 12 Oct 2011) | 3 lines
  
  Fix from RedHat bug: https://bugzilla.redhat.com/show_bug.cgi?id=680292
  Ensure obenergy properly loads forcefields.
........


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4635 71e0b675-c112-0410-beda-96664073b5c2
A possibly improved Windows Installer script

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4637 71e0b675-c112-0410-beda-96664073b5c2
Windows installer: Remove data items. Still doesn't remove links.

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4638 71e0b675-c112-0410-beda-96664073b5c2
Bump README and NEWS for 2.3.1 release.


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4639 71e0b675-c112-0410-beda-96664073b5c2
Bump library version number for 2.3.1 release.


git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4640 71e0b675-c112-0410-beda-96664073b5c2
Windows installer: Now uninstalls everything perfectly. As far as I can see.

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4641 71e0b675-c112-0410-beda-96664073b5c2
In Uninstall remove entry in Add/Remove Programs

git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-3-x@4642 71e0b675-c112-0410-beda-96664073b5c2