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From: <chr...@us...> - 2013-02-17 11:10:50
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Revision: 5063
http://openbabel.svn.sourceforge.net/openbabel/?rev=5063&view=rev
Author: chrismorl
Date: 2013-02-17 11:10:41 +0000 (Sun, 17 Feb 2013)
Log Message:
-----------
Fix #860 in Moldenformat by removing two unnecessary getlines, which meant only every other atom was read.
Modified Paths:
--------------
openbabel/trunk/src/formats/moldenformat.cpp
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From: <chr...@us...> - 2013-02-10 19:38:08
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Revision: 5062
http://openbabel.svn.sourceforge.net/openbabel/?rev=5062&view=rev
Author: chrismorl
Date: 2013-02-10 19:38:00 +0000 (Sun, 10 Feb 2013)
Log Message:
-----------
Add counting of SMARTS matches to -s option (opisomorph)
Modified Paths:
--------------
openbabel/trunk/src/ops/opisomorph.cpp
openbabel/trunk/src/ops/opisomorph.h
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From: <chr...@us...> - 2013-01-06 16:53:51
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Revision: 5061
http://openbabel.svn.sourceforge.net/openbabel/?rev=5061&view=rev
Author: chrismorl
Date: 2013-01-06 16:53:44 +0000 (Sun, 06 Jan 2013)
Log Message:
-----------
Mod for g94 files, which seem to have one column fewer in the atom table. Fixes bug #841.
Modified Paths:
--------------
openbabel/trunk/src/formats/gaussformat.cpp
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From: <chr...@us...> - 2013-01-05 20:04:35
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Revision: 5060
http://openbabel.svn.sourceforge.net/openbabel/?rev=5060&view=rev
Author: chrismorl
Date: 2013-01-05 20:04:28 +0000 (Sat, 05 Jan 2013)
Log Message:
-----------
Function to assign a specified total charge to atoms, arising from comments from Fulvio Ciriaco on the difficulty of converting gamessformat to InChI. Patch from him for gamessformat, and also for cmlformat to output total charge and spin multiplicity.
Modified Paths:
--------------
openbabel/trunk/include/openbabel/mol.h
openbabel/trunk/include/openbabel/typer.h
openbabel/trunk/src/formats/gamessformat.cpp
openbabel/trunk/src/formats/xml/cmlformat.cpp
openbabel/trunk/src/mol.cpp
openbabel/trunk/src/typer.cpp
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From: <ds...@us...> - 2012-12-26 19:48:38
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Revision: 5059
http://openbabel.svn.sourceforge.net/openbabel/?rev=5059&view=rev
Author: dspoel
Date: 2012-12-26 19:48:29 +0000 (Wed, 26 Dec 2012)
Log Message:
-----------
Added more atom definitions for determining
Enthalpy of vaporization from Gaussian output.
Modified Paths:
--------------
openbabel/trunk/data/atomization-energies.txt
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From: <chr...@us...> - 2012-12-22 11:39:38
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Revision: 5058
http://openbabel.svn.sourceforge.net/openbabel/?rev=5058&view=rev
Author: chrismorl
Date: 2012-12-22 11:39:23 +0000 (Sat, 22 Dec 2012)
Log Message:
-----------
Corrected PNG2Format to allow no molecule title as suggested by Noel in #845, but also moved cairopainter from a class to a local variable in WriteMolecule() so that it it reinitialized between Convert clicks in the GUI.
Modified Paths:
--------------
openbabel/trunk/src/formats/png2format.cpp
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From: <ds...@us...> - 2012-12-14 21:14:00
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Revision: 5057
http://openbabel.svn.sourceforge.net/openbabel/?rev=5057&view=rev
Author: dspoel
Date: 2012-12-14 21:13:53 +0000 (Fri, 14 Dec 2012)
Log Message:
-----------
In the previous patch https://sourceforge.net/p/openbabel/patches/59/
I inadvertedly did not implement a constructor and destructor for a
new class. This is now fixed. Another small fix is that the
end-of-file is now checked for using the normal file stream function,
rather than checking for a string.
Contains a fix in reading CBS-QB3 enthalpies of formation.
Changed the re-reading logic of the gaussian file (it is read twice
with a rewind in between) to use the proper C++ function to clear
end-of-file pointers etc. Tested to work on normal and gzipped files.
An additional issue with reading electrostatic potentials as well
which is fixed. The tokenize function was replace in this case by
sscanf that reads in fixed format potential points, because gaussian
uses good old fortran 3(f10.6) with no spaces in between.
Finally a segv was fixed that arose due to orbitals being read in
differently than the symmetries. An additional check is left in the
code where the orbital data is added to the molecule structure, in
case there are broken input files.
A further update of the patch that fixes a bug in computing the
enthalpy of formation. Now reproduces literature data.
Modified Paths:
--------------
openbabel/trunk/include/openbabel/generic.h
openbabel/trunk/src/formats/gaussformat.cpp
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From: <bao...@us...> - 2012-12-11 22:23:29
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Revision: 5056
http://openbabel.svn.sourceforge.net/openbabel/?rev=5056&view=rev
Author: baoilleach
Date: 2012-12-11 22:23:22 +0000 (Tue, 11 Dec 2012)
Log Message:
-----------
mdlvalence.h, mdlformat.cpp: Add Roger's mdlvalence patch that sets the implicit valence at the point of reading a MOL file. This uses the MDL valence model.
Modified Paths:
--------------
openbabel/trunk/src/formats/mdlformat.cpp
Added Paths:
-----------
openbabel/trunk/src/formats/mdlvalence.h
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From: <bao...@us...> - 2012-12-11 22:11:53
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Revision: 5055
http://openbabel.svn.sourceforge.net/openbabel/?rev=5055&view=rev
Author: baoilleach
Date: 2012-12-11 22:11:46 +0000 (Tue, 11 Dec 2012)
Log Message:
-----------
Correct mmff94 test caffeine structure, and update corresponding test results for mmff94. The original structure had two neutral 4-coordinate nitrogens.
Modified Paths:
--------------
openbabel/trunk/test/files/charge-mmff94.txt
openbabel/trunk/test/files/dipole-mmff94.txt
openbabel/trunk/test/files/forcefield.sdf
openbabel/trunk/test/files/mmff94results.txt
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From: <bao...@us...> - 2012-12-10 16:57:46
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Revision: 5054
http://openbabel.svn.sourceforge.net/openbabel/?rev=5054&view=rev
Author: baoilleach
Date: 2012-12-10 16:57:39 +0000 (Mon, 10 Dec 2012)
Log Message:
-----------
mmff94results.txt: Test results updated for buckyball failure due to change of SSSR.
Modified Paths:
--------------
openbabel/trunk/test/files/mmff94results.txt
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From: <ben...@us...> - 2012-12-07 14:19:58
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Revision: 5053
http://openbabel.svn.sourceforge.net/openbabel/?rev=5053&view=rev
Author: benoit-leblanc
Date: 2012-12-07 14:19:51 +0000 (Fri, 07 Dec 2012)
Log Message:
-----------
dded options to the OBStericConformerFilter class, so one can control
the factor applied to VdW radii. Also put a flag to inlcude or not the
hydrogens in the test. Added a new constructor with default values
providing the same behavior as the preceeding one, so it is
transparent to existing code.
Modified Paths:
--------------
openbabel/trunk/include/openbabel/conformersearch.h
openbabel/trunk/src/conformersearch.cpp
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From: <chr...@us...> - 2012-12-05 10:24:44
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Revision: 5052
http://openbabel.svn.sourceforge.net/openbabel/?rev=5052&view=rev
Author: chrismorl
Date: 2012-12-05 10:24:37 +0000 (Wed, 05 Dec 2012)
Log Message:
-----------
Add capability of outputting the duplicate molecules in --unique
Modified Paths:
--------------
openbabel/trunk/src/ops/unique.cpp
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From: <ti...@us...> - 2012-11-30 14:01:19
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Revision: 5051
http://openbabel.svn.sourceforge.net/openbabel/?rev=5051&view=rev
Author: timvdm
Date: 2012-11-30 14:01:08 +0000 (Fri, 30 Nov 2012)
Log Message:
-----------
Update src/formats/smiley.h after testing using MSVC2010.
Modified Paths:
--------------
openbabel/trunk/src/formats/smiley.h
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From: <ti...@us...> - 2012-11-25 21:12:54
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Revision: 5050
http://openbabel.svn.sourceforge.net/openbabel/?rev=5050&view=rev
Author: timvdm
Date: 2012-11-25 21:12:48 +0000 (Sun, 25 Nov 2012)
Log Message:
-----------
Add SMILES read-only format using the Smiley parser. File extension is *.smy.
Out of 1M read SMILES, 3604 (0.3%) are not written out exactly the same but
these are problems in the OBFormat, not the Smiley parser.
Modified Paths:
--------------
openbabel/trunk/src/formats/CMakeLists.txt
openbabel/trunk/test/CMakeLists.txt
Added Paths:
-----------
openbabel/trunk/src/formats/smiley.h
openbabel/trunk/src/formats/smileyformat.cpp
openbabel/trunk/test/smileytest.cpp
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From: <bao...@us...> - 2012-11-22 13:54:10
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Revision: 5049
http://openbabel.svn.sourceforge.net/openbabel/?rev=5049&view=rev
Author: baoilleach
Date: 2012-11-22 13:53:58 +0000 (Thu, 22 Nov 2012)
Log Message:
-----------
Contribution from Roger Sayle...
Overhaul ring perception by replacing several algorithms by one efficient O(N) algorithm. Specifically OBBond::IsClosure, OBRing::DetermineFRJ, OBRing::FindRings, OBRing::FindRingAtomsAndBonds now all call the internal function FindRingAtomsAndBonds2 (no API change). Previously this effort was duplicated (i.e. repeated) and was O(N^2).
The particular SSSR returned has changed, and so ringtest and smartstest had to be updated. There is still one failing test for mmff94 that needs to be sorted out.
Modified Paths:
--------------
openbabel/trunk/src/bond.cpp
openbabel/trunk/src/ring.cpp
openbabel/trunk/test/files/ringresults.txt
openbabel/trunk/test/files/smartsresults.txt
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From: <bao...@us...> - 2012-11-22 11:57:07
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Revision: 5048
http://openbabel.svn.sourceforge.net/openbabel/?rev=5048&view=rev
Author: baoilleach
Date: 2012-11-22 11:56:55 +0000 (Thu, 22 Nov 2012)
Log Message:
-----------
mol.cpp: OBMol::Separate(). Update for previous commit. Forgot to handle ImplicitRefs.
Modified Paths:
--------------
openbabel/trunk/src/mol.cpp
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From: <bao...@us...> - 2012-11-21 22:22:35
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Revision: 5047
http://openbabel.svn.sourceforge.net/openbabel/?rev=5047&view=rev
Author: baoilleach
Date: 2012-11-21 22:22:27 +0000 (Wed, 21 Nov 2012)
Log Message:
-----------
smartstest: Bugfix for when a smarts test failure occurs. Previously all tests after a failing test would also fail.
Modified Paths:
--------------
openbabel/trunk/test/smartstest.cpp
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From: <bao...@us...> - 2012-11-21 11:59:31
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Revision: 5046
http://openbabel.svn.sourceforge.net/openbabel/?rev=5046&view=rev
Author: baoilleach
Date: 2012-11-21 11:59:21 +0000 (Wed, 21 Nov 2012)
Log Message:
-----------
mol.cpp: I've updated OBMol::GetNextFragment to the new stereo system. Previously calling OBMol::Separate resulted in a loss of stereo in the separated molecules.
Modified Paths:
--------------
openbabel/trunk/src/mol.cpp
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From: <chr...@us...> - 2012-11-17 17:58:01
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Revision: 5045
http://openbabel.svn.sourceforge.net/openbabel/?rev=5045&view=rev
Author: chrismorl
Date: 2012-11-17 17:57:54 +0000 (Sat, 17 Nov 2012)
Log Message:
-----------
Patch from David van der Spoel to extract from Gaussian: true enthalpy of formation, quadrupole, polarizability tensor, electrostatic potential fitting points and potential values, and info on program name and version, method of the calculation (e.g. B3LYP) and basis set. #59
Modified Paths:
--------------
openbabel/trunk/data/CMakeLists.txt
openbabel/trunk/include/openbabel/data.h
openbabel/trunk/include/openbabel/generic.h
openbabel/trunk/src/data.cpp
openbabel/trunk/src/formats/gaussformat.cpp
Added Paths:
-----------
openbabel/trunk/data/atomization-energies.txt
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From: <bao...@us...> - 2012-10-30 16:18:11
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Revision: 5044
http://openbabel.svn.sourceforge.net/openbabel/?rev=5044&view=rev
Author: baoilleach
Date: 2012-10-30 16:18:00 +0000 (Tue, 30 Oct 2012)
Log Message:
-----------
Update the Windows Python installer.
Modified Paths:
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openbabel/trunk/windows-vc2008/Distribution/Python/b_obpython.bat
openbabel/trunk/windows-vc2008/Distribution/Python/setup.py
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From: <bao...@us...> - 2012-10-29 15:26:59
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Revision: 5043
http://openbabel.svn.sourceforge.net/openbabel/?rev=5043&view=rev
Author: baoilleach
Date: 2012-10-29 15:26:47 +0000 (Mon, 29 Oct 2012)
Log Message:
-----------
Drat! Trival fix to re-enable Molecule.draw() after recent changes to PNG2.
Modified Paths:
--------------
openbabel/trunk/scripts/python/pybel.py
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From: <chr...@us...> - 2012-10-28 20:04:06
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Revision: 5042
http://openbabel.svn.sourceforge.net/openbabel/?rev=5042&view=rev
Author: chrismorl
Date: 2012-10-28 20:03:59 +0000 (Sun, 28 Oct 2012)
Log Message:
-----------
FastSearchFormat can have the molecules with dative bonds in both the datafile and the target in either form, e.g. -N(=O)=O and -[N+](=O)[O-]. Can use multiple target mols in a file (like -s option).
New function OBMol::MakeDativeBonds() (mols with 5-valent N only). Accessible as -B option.
OBAtom::BOSum() handles quadruple bonds.
Opisomorph (-s option) more efficient and can accept secondary input mols, e.g. isomers sent from FastSearchFormat.
smilesformat -xh option slightly extended to avoid implicit H being added to a SMARTS
Modified Paths:
--------------
openbabel/trunk/include/openbabel/mol.h
openbabel/trunk/src/atom.cpp
openbabel/trunk/src/formats/fastsearchformat.cpp
openbabel/trunk/src/formats/smilesformat.cpp
openbabel/trunk/src/mol.cpp
openbabel/trunk/src/ops/opisomorph.cpp
openbabel/trunk/src/ops/opisomorph.h
openbabel/trunk/src/transform.cpp
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From: <chr...@us...> - 2012-10-17 19:28:44
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Revision: 5041
http://openbabel.svn.sourceforge.net/openbabel/?rev=5041&view=rev
Author: chrismorl
Date: 2012-10-17 19:28:33 +0000 (Wed, 17 Oct 2012)
Log Message:
-----------
Make the extraction of metadata in gaussformat more robust
Modified Paths:
--------------
openbabel/trunk/src/formats/gaussformat.cpp
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From: <th...@us...> - 2012-10-15 12:18:14
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Revision: 5040
http://openbabel.svn.sourceforge.net/openbabel/?rev=5040&view=rev
Author: th9
Date: 2012-10-15 12:18:03 +0000 (Mon, 15 Oct 2012)
Log Message:
-----------
setup.py: There are no separate pybel_pyX.py files anymore
Modified Paths:
--------------
openbabel/trunk/scripts/python/setup.py
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From: <th...@us...> - 2012-10-14 21:49:02
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Revision: 5039
http://openbabel.svn.sourceforge.net/openbabel/?rev=5039&view=rev
Author: th9
Date: 2012-10-14 21:48:55 +0000 (Sun, 14 Oct 2012)
Log Message:
-----------
cmake: Use LIB_SUFFIX also for tests and tools
Modified Paths:
--------------
openbabel/trunk/test/CMakeLists.txt
openbabel/trunk/tools/CMakeLists.txt
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