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From: <chr...@us...> - 2013-02-17 11:10:50
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <chr...@us...> - 2013-02-10 19:38:08
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <chr...@us...> - 2013-01-06 16:53:51
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <chr...@us...> - 2013-01-05 20:04:35
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ds...@us...> - 2012-12-26 19:48:38
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <chr...@us...> - 2012-12-22 11:39:38
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ds...@us...> - 2012-12-14 21:14:00
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <bao...@us...> - 2012-12-11 22:23:29
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <bao...@us...> - 2012-12-11 22:11:53
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <bao...@us...> - 2012-12-10 16:57:46
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ben...@us...> - 2012-12-07 14:19:58
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <chr...@us...> - 2012-12-05 10:24:44
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ti...@us...> - 2012-11-30 14:01:19
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ti...@us...> - 2012-11-25 21:12:54
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <bao...@us...> - 2012-11-22 13:54:10
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <bao...@us...> - 2012-11-22 11:57:07
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <chr...@us...> - 2012-11-17 17:58:01
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <bao...@us...> - 2012-10-30 16:18:11
|
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: -------------- openbabel/trunk/windows-vc2008/Distribution/Python/b_obpython.bat openbabel/trunk/windows-vc2008/Distribution/Python/setup.py This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <bao...@us...> - 2012-10-29 15:26:59
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <chr...@us...> - 2012-10-28 20:04:06
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <chr...@us...> - 2012-10-17 19:28:44
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |