Open Babel - The Open Source Chemistry Toolbox

Edit Package openbabel

Open Babel is a chemical toolbox designed to speak the many languages
of chemical data. It's an open, collaborative project allowing anyone
to search, convert, analyze, or store data from molecular modeling,
chemistry, solid-state materials, biochemistry, or related areas.

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Source Files
Filename Size Changed
baselibs.conf 0000000024 24 Bytes
openbabel-2.4.1.tar.gz 0011618304 11.1 MB
openbabel.changes 0000011303 11 KB
openbabel.spec 0000005234 5.11 KB
Latest Revision
Ludwig Nussel's avatar Ludwig Nussel (lnussel_factory) accepted request 607608 from Wolfgang Bauer's avatar Wolfgang Bauer (wolfi323) (revision 3)
- Don't delete command line tools, include them in the main package
  as with openbabel < 2.4
- Pass -ULIB_INSTALL_DIR to unset this var, the %cmake macro sets
  it to %{_libdir} resulting in a duplicate /usr in the module
  search path which causes the plugins not to be found (boo#997190)
- Provide/Obsolete libopenbabel-devel for compatibility
- Fix RPM groups. Update descriptions.
- Force python2 by passing -DPYTHON_EXECUTABLE=%{_bindir}/python2
  to cmake to fix build on Tumbleweed
- build with wxWidgets support
- add baselibs.conf
- enable python support (for real now)
- add libinchi0 and openbabel sub packages
- correct the .so version suffix for libopenbabel
- Drop openbabel-2.3.1-no-build-date.patch
- Update to version 2.4.1, see
  https://sourceforge.net/projects/openbabel/files/openbabel/2.4.0
  for changelog
- Dropped cripple_source.sh
- Replaced openbabel-2.2.3-no-build-date.patch with
  sed regex
- Dropped build-checks.diff due to significant source
  changes
- Dropped python-installdir.patch (included upstream)
- Dropped openbabel-gcc5.patch (included upstream)
- openbabel-gcc6.patch: remove obsolete hunk
- Fix errors seen by 02-check-gcc-output script.
- Version update to 2.3.2 and cripple the tarball
  * various small bugfixes, the git is far away from this but
    upstream seems not to do releases
  * Add patch to properly install bindings to right location:
    + python-installdir.patch
- Add patch to build with gcc6 openbabel-gcc6.patch
- Add openbabel-gcc5.patch: Fix build with gcc5.
- enable CMAKE_SKIP_INSTALL_RPATH option so RPATH is ommited from 
  install tree
- Fix the SLES build (%make_install is not expanded on SLES)
- add -32bit libs for avogadro
- Add python bindings
- determine arch suffix from _lib macro 
- 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
- use rpm %ifarch
- 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.
- Do not include build dates in binaries. 
- added pkg-config to remove the error during the build 
- 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- 
- 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.
- cripple tarball to remove binary dll's we don't need (bnc#411171)
- various fixes, fix library package name
- review last change
- update to OpenBabel 2.2.0:
  * http://openbabel.org/wiki/Open_Babel_2.2.0
- gcc 4.3 fixes 
- Initial package (2.1.1) 
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