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File openbabel.changes of Package openbabel
------------------------------------------------------------------- Thu Apr 5 08:13:07 UTC 2012 - coolo@suse.com - add -32bit libs for avogadro ------------------------------------------------------------------- Fri Mar 23 20:02:36 UTC 2012 - dhall@wustl.edu - Add python bindings ------------------------------------------------------------------- Tue Nov 29 01:55:33 CET 2011 - ro@suse.de - determine arch suffix from _lib macro ------------------------------------------------------------------- Tue Oct 18 00:17:21 UTC 2011 - dhall@wustl.edu - updated to OpenBabel 2.3.1 * Better support for unknown stereochemistry, including a "wobbly" bond in 2D depiction. * Many fixes for rare bugs with stereochemical conversions, including unusual valences. * Significantly improved 2D depiction code, improving performance and cis/trans stereochemical accuracy * Added support for direct 2D depiction to PNG files using the Cairo library, if available. * PNG files from Open Babel contain molecular information and can be read to give the MDL Molfile. * SVG files with 2D depiction can now include a grid of molecules with embedded JavaScript to zoom and scroll. * Molecular formulas now include the total charge (e.g., HCO2-) * Added the EEM partial charge model from Bultinck, et. al. * Fixed problems with FastSearch databases larger than 4GB, now checking for large files. * Improved performance with force field minimization, particularly the UFF and GAFF methods. * Several MMFF94 atom typing bugs fixed. * Updated GAFF parameters from the AmberTools distribution. * Improvements in 3D coordinate generation, particularly more accurate sp3 bond angles * Fixed tests for auto-typing molecules with force fields when running through different isomers. * Improvements in scripting bindings, particularly Python, Ruby, and Java * Pybel now uses the built-in 2D depiction, and no longer needs OASA. * Added initial support for MM3 atom typing with the Tinker package * Significant bug fixes for the PDBQT format. * Reading FASTA files can now generate 3D coordinates for single-stranded DNA in addition to the default double-strand. * Support for reading/writing unit cell information from MOPAC files. * Support for re-numbering SMILES by specifying the first and last atoms with -xf and -xl flags. * Better support for InChI -> InChI key generation by direct conversion, rather than re-perception of the InChI. * Fix for rare stack overflow crash in SMARTS perception. * Improved UNIX man pages. * Many bug fixes and small enhancements * New File Formats * Import and Export: * Gromacs GRO * Import: * ABINIT * XCrySDen XSF * Export: * InChI Key ------------------------------------------------------------------- Sat Jun 18 10:52:25 UTC 2011 - dhall@wustl.edu - use rpm %ifarch ------------------------------------------------------------------- Fri Jun 17 23:55:56 UTC 2011 - dhall@wustl.edu - Updated to OpenBabel 2.3.0 * Completely rewritten stereochemistry perception, including support for tetrahedral, square planar, and higher-order stereochemistry. * Dramatically improved canonicalization algorithm (Note that in general, canonical SMILES have changed since the 2.2.x release.) * 2D depiction, including SVG vector graphics generation using code from MCDL. * New Spectrophore generation, contributed by Silicos NV. * New ChargeMethod API including support for partial charge assignment from Gasteiger, MMFF94, QEq, QTPIE methods and plugin interface for adding more. * Improved 3D coordinate generation. * New conformer generation framework, including support for diverse conformer generation and genetic algorithm lowest-energy searching. * Improved user documentation. * Improved aromaticity / Kekule bond assignment. * Improved unit test suite using the CMake-based CTest program. * Improved support for crystallographic unit cells (e.g., in CIF format). * Improved UFF force field method, including hypervalent 5, 6, 7 and higher coordination numbers. * Support for the GAFF (Generalized Amber Force Field) method. * Support for reading geometry optimizations as multiple conformers from Gaussian, GAMESS-US, and other quantum chemistry packages. * Support for reading molecular orbital energies from quantum chemistry formats. * Several memory leaks fixed. * Fixed many compiler warnings. * Fixed support for MinGW and Cygwin environments. * Fixed bugs with Gaussian 09 output files. * Latest released version of the InChI library (1.0.3) generating standard InChI. * Many more bug fixes and small feature improvements. ------------------------------------------------------------------- Mon Sep 13 00:54:59 UTC 2010 - cristian.rodriguez@opensuse.org - Do not include build dates in binaries. ------------------------------------------------------------------- Sat Sep 11 17:16:44 UTC 2010 - alinm.elena@gmail.com - added pkg-config to remove the error during the build ------------------------------------------------------------------- Sat Sep 11 09:03:40 UTC 2010 - alinm.elena@gmail.com - Updated to OpenBabel 2.2.3 * Improved Java interface * Many fixes to the fingerprint code * Added support of the pH parameter to the GUI * Several bug fixes and small enhancements- ------------------------------------------------------------------- Sat Jul 25 23:48:41 CEST 2009 - beineri@opensuse.org - update to OpenBabel 2.2.2: * Fixed many stereochemistry errors when reading/writing SMILES. * Significantly improved aromaticity and Kekule bond assignment. * Improved 2D -> 3D coordinate generation * Improved coordinate generation using --gen3d command-line operation * Improved performance for coordinate generation. * New --fillUC command-line operation for babel. * Fixes to pH-dependent hydrogen addition. * Added support for reading vibrational data from Molden, Molpro, and NWChem output files. * Updated atomic radii from recent theoretical calculations. * Fixed bug when reading gzip-compressed Mol2 or XML files. * Close files after an error. Fixes a bug with Pybel where files would remain open. * New File Formats Import & Export: - Molpro input and output. -VASP coordinate files (CONTCAR and POSCAR). - update to OpenBabel 2.2.1: * Added support for MACCS fingerprints. * Many fixes and enhancements to the force field code. * Improved 3D coordinate generation, particularly with ring fragments. * Fixed a variety of PDB import errors with atom types. * Added support for reading charges and radii from PQR file formats. * Added support for reading and writing unit cells in PDB formats. * New "output" file format for taking generic ".out", ".log", and ".dat" files and reading with appropriate file type based on contents. * Added improved error handling/reporting when unable to load file formats. * Improved CIF file format support. * Generic "output" format for reading from quantum chemistry files. ------------------------------------------------------------------- Tue Jul 22 14:13:26 CEST 2008 - dmueller@suse.de - cripple tarball to remove binary dll's we don't need (bnc#411171) ------------------------------------------------------------------- Sat Jul 19 12:43:49 CEST 2008 - dmueller@suse.de - various fixes, fix library package name ------------------------------------------------------------------- Wed Jul 9 16:02:10 CEST 2008 - dmueller@suse.de - review last change ------------------------------------------------------------------- Wed Jul 9 15:52:31 CEST 2008 - cniehaus@kde.org - update to OpenBabel 2.2.0: * http://openbabel.org/wiki/Open_Babel_2.2.0 ------------------------------------------------------------------- Sun Oct 21 12:44:24 CEST 2007 - dmueller@suse.de - gcc 4.3 fixes ------------------------------------------------------------------- Tue Oct 9 01:07:21 CEST 2007 - dmueller@suse.de - Initial package (2.1.1)
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