Revisions of openbabel
Yuchen Lin (maxlin_factory)
accepted
request 647506
from
Guillaume GARDET (Guillaume_G)
(revision 18)
- Backport https://github.com/openbabel/openbabel/commit/e26491 * fix_narrowing.patch - Backport https://github.com/openbabel/openbabel/commit/8d707b * fix_yasara.patch
Yuchen Lin (maxlin_factory)
committed
(revision 17)
branch from 15.0
Ludwig Nussel (lnussel_factory)
accepted
request 607608
from
Wolfgang Bauer (wolfi323)
(revision 16)
- 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)
Ludwig Nussel (lnussel_factory)
accepted
request 579060
from
Leap Reviewbot (leaper)
(revision 15)
Automatic request from openSUSE:Factory by UpdateCrawler
Yuchen Lin (maxlin_factory)
accepted
request 551753
from
Yuchen Lin (maxlin_factory)
(revision 14)
Automated submission of a package from openSUSE:Factory to openSUSE:Leap:15.0 that was included in openSUSE:Leap:42.3
Yuchen Lin (maxlin_factory)
committed
(revision 13)
branch from 15.0
Ludwig Nussel (lnussel_factory)
accepted
request 607608
from
Wolfgang Bauer (wolfi323)
(revision 12)
- 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)
Ludwig Nussel (lnussel_factory)
accepted
request 579060
from
Leap Reviewbot (leaper)
(revision 11)
Automatic request from openSUSE:Factory by UpdateCrawler
Yuchen Lin (maxlin_factory)
accepted
request 551753
from
Yuchen Lin (maxlin_factory)
(revision 10)
Automated submission of a package from openSUSE:Factory to openSUSE:Leap:15.0 that was included in openSUSE:Leap:42.3
Yuchen Lin (maxlin_factory)
committed
(revision 9)
branch from 15.0
Ludwig Nussel (lnussel_factory)
accepted
request 607608
from
Wolfgang Bauer (wolfi323)
(revision 8)
- 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)
Ludwig Nussel (lnussel_factory)
accepted
request 579060
from
Leap Reviewbot (leaper)
(revision 7)
Automatic request from openSUSE:Factory by UpdateCrawler
Yuchen Lin (maxlin_factory)
accepted
request 551753
from
Yuchen Lin (maxlin_factory)
(revision 6)
Automated submission of a package from openSUSE:Factory to openSUSE:Leap:15.0 that was included in openSUSE:Leap:42.3
Yuchen Lin (maxlin_factory)
committed
(revision 5)
branch from 15.0
Yuchen Lin (maxlin_factory)
committed
(revision 4)
branch from 15.0
Ludwig Nussel (lnussel_factory)
accepted
request 607608
from
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)
Ludwig Nussel (lnussel_factory)
accepted
request 579060
from
Leap Reviewbot (leaper)
(revision 2)
Automatic request from openSUSE:Factory by UpdateCrawler
Yuchen Lin (maxlin_factory)
accepted
request 551753
from
Yuchen Lin (maxlin_factory)
(revision 1)
Automated submission of a package from openSUSE:Factory to openSUSE:Leap:15.0 that was included in openSUSE:Leap:42.3
Displaying all 18 revisions