Summary
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.
Versions
v9999 :: 0/7.0.0 :: gentoo
- Modified
- License
- GPL-2
- USE flags
- doc examples inchi json minimal openmp perl png python test wxwidgets
v3.1.1_p20241221-r4 :: 0/7.0.0 :: gentoo
- Modified
- License
- GPL-2
- Keywords
- amd64 ~arm ~x86
- USE flags
- doc examples inchi json minimal openmp perl png python test wxwidgets
v3.1.1_p20241221-r2 :: 0/7.0.0 :: gentoo
- Modified
- License
- GPL-2
- Keywords
- amd64 ~arm ~x86
- USE flags
- doc examples inchi json minimal openmp perl png python test wxwidgets
USE flags
General
- doc
- Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally
- examples
- Install examples, usually source code
- inchi
- Build support for IUPAC International Chemical Identifier format
- json
- Build support for JSON formats (ChemDoodle, PubChem, etc...)
- minimal
- Install a very minimal build (disables, for example, plugins, fonts, most drivers, non-critical features)
- openmp
- Build support for the OpenMP (support parallel computing), requires >=sys-devel/gcc-4.2 built with USE="openmp"
- perl
- Add optional support/bindings for the Perl language
- png
- Add support for libpng (PNG images)
- python
- Add optional support/bindings for the Python language
- test
- Enable dependencies and/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)
- wxwidgets
- Add support for wxWidgets/wxGTK GUI toolkit
cpu_flags_arm
- neon
- Use the NEON instruction set
cpu_flags_x86
- sse2
- Use the SSE2 instruction set
- sse4_2
- Enable SSE4.2 instruction support
perl_features
- debug
- PERL_FEATURES setting enabling internal debug support in Perl
- ithreads
- PERL_FEATURES setting enabling interpreter level threads, has some compatibility problems
- quadmath
- PERL_FEATURES setting enabling 128bit floating point arithmetic via libquadmath
python_targets
- python3_11
- Build with Python 3.11
- python3_12
- Build with Python 3.12
- python3_13
- Build with Python 3.13
- python3_14
- Build with Python 3.14
Dependencies
dev-cpp / eigen : C++ template library for linear algebra
dev-lang / perl : Larry Wall's Practical Extraction and Report Language
dev-lang / python : An interpreted, interactive, object-oriented programming language
dev-libs / libxml2 : XML C parser and toolkit
dev-libs / rapidjson : A fast JSON parser/generator for C++ with both SAX/DOM style API
sci-libs / inchi : Program and library for generating standard and non-standard InChI and InChIKeys
virtual / zlib : Virtual for libz.so providers
x11-libs / cairo : A vector graphics library with cross-device output support
x11-libs / wxGTK : GTK version of wxWidgets, a cross-platform C++ GUI toolkit
Runtime Dependencies
dev-cpp / eigen : C++ template library for linear algebra
dev-lang / perl : Larry Wall's Practical Extraction and Report Language
dev-lang / python : An interpreted, interactive, object-oriented programming language
dev-libs / libxml2 : XML C parser and toolkit
dev-libs / rapidjson : A fast JSON parser/generator for C++ with both SAX/DOM style API
sci-libs / inchi : Program and library for generating standard and non-standard InChI and InChIKeys
virtual / zlib : Virtual for libz.so providers
x11-libs / cairo : A vector graphics library with cross-device output support
x11-libs / wxGTK : GTK version of wxWidgets, a cross-platform C++ GUI toolkit
Depending packages
sci-chemistry / gnome-chemistry-utils : Programs and library containing GTK widgets and C++ classes related to chemistry
sci-chemistry / molsketch : Drawing tool for 2D molecular structures
sci-libs / avogadrolibs : Advanced molecule editor and visualizer 2 - libraries
Bugs
Change logs
- Repository mirror & CI · gentoo
Merge updates from master - Eli Schwartz · gentoo
sci-chemistry/openbabel: Stabilize 3.1.1_p20241221-r4 amd64, #969214
Signed-off-by: Eli Schwartz <eschwartz@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Fabian Groffen · gentoo
*/*: drop *-linux keywords
Bug: https://bugs.gentoo.org/473598 Bug: https://bugs.gentoo.org/720224 Signed-off-by: Fabian Groffen <grobian@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Fabian Groffen · gentoo
*: remove ppc-macos keyword
The arch and OS that matches it are obsolete. Signed-off-by: Fabian Groffen <grobian@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-chemistry/openbabel: drop 3.1.1_p20210225-r3, 3.1.1_p20241221-r3
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> - Andreas Sturmlechner · gentoo
sci-chemistry/openbabel: Switch make_desktop_entry to --eapi9
Bug: https://bugs.gentoo.org/967238 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
sci-*/*: update for virtual/zlib
Update done using: ``` git grep -l sys-libs/zlib dev-* | xargs sed -i -e s@sys-libs/zlib@virtual/zlib@g git diff --name-only | xargs copybump git diff --name-only | xargs grep -l PYTHON_COMPAT | xargs gpy-impl -@dead pkgcheck scan --commits -c SourcingCheck,VisibilityCheck --exit error ``` Signed-off-by: Michał Górny <mgorny@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sam James · gentoo
sci-chemistry/openbabel: use PERL_FEATURES
Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Nicolas PARLANT · gentoo
sci-chemistry/openbabel: enable py3.14, drop py3.10
tests passed, included pybel (Python interface) Signed-off-by: Nicolas PARLANT <nicolas.parlant@parhuet.fr> Part-of: https://github.com/gentoo/gentoo/pull/42496 Closes: https://github.com/gentoo/gentoo/pull/42496 Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Repository mirror & CI · gentoo
Merge updates from master - David Seifert · gentoo
sci-chemistry/openbabel: slot op on x11-libs/wxGTK
Signed-off-by: David Seifert <soap@gentoo.org> - Alfred Wingate · gentoo
sci-chemistry/openbabel: add dev-libs/libxml2 subslot op for incoming ABI break
Signed-off-by: Alfred Wingate <parona@protonmail.com> Part-of: https://github.com/gentoo/gentoo/pull/41919 Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sam James · gentoo
sci-chemistry/openbabel: Stabilize 3.1.1_p20241221 amd64, #953710
Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Nicolas PARLANT · gentoo
sci-chemistry/openbabel: cmake4 compat
Closes: https://bugs.gentoo.org/952024 Signed-off-by: Nicolas PARLANT <nicolas.parlant@parhuet.fr> Part-of: https://github.com/gentoo/gentoo/pull/41301 Closes: https://github.com/gentoo/gentoo/pull/41301 Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Nicolas PARLANT · gentoo
sci-chemistry/openbabel: sync live
sync with last version Signed-off-by: Nicolas PARLANT <nicolas.parlant@parhuet.fr> Closes: https://github.com/gentoo/gentoo/pull/41087 Signed-off-by: Sam James <sam@gentoo.org> - Nicolas PARLANT · gentoo
sci-chemistry/openbabel: add 3.1.1_p20241221
New snapshot to include in particular more json features. deps : libxml2/cairo are not required with minimal rm openbabel-perl replace sed : perl LIB_INSTALL_DIR (no-op) -> set PERL_INSTDIR PYTHON_BINDINGS (no-op for test/CMakeLists.txt due to a typo) -> not required examples RUNTIME_DESTINATION -> patch with CMAKE_INSTALL_DOCDIR find_package : use DISABLE_FIND_PACKAGE for Cairo(png), wxWidgets(wxwidgets) and Boost use ADD_INCHI_FORMAT to prevent using bundled inchi openbabel-python-cmake : use target_include_directories instead of include_directories to prevent including all python_targets at the same time for each implementation. tests : skip two more tests with known issues rm -O2 exclusions introduced with 1fce6e91e642ac7fe5c3b9f675c54244be423a53 It seems fixed now (checked with -O2/clang/lto/gcc15/+-openmp/+-cpu_flags). This will require investigation if it reappears. add py3.13 (tests passed) Signed-off-by: Nicolas PARLANT <nicolas.parlant@parhuet.fr> Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Pacho Ramos · gentoo
sci-chemistry/openbabel: sync live ebuild
Signed-off-by: Pacho Ramos <pacho@gentoo.org> - Pacho Ramos · gentoo
sci-chemistry/openbabel: enable py3.12
Closes: https://bugs.gentoo.org/929759 Signed-off-by: Pacho Ramos <pacho@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-chemistry/openbabel: drop 3.1.1_p20210225
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Arthur Zamarin · gentoo
sci-chemistry/openbabel: Stabilize 3.1.1_p20210225-r1 amd64, #929186
Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
Move {app-doc → app-text}/doxygen
Per the category metadata, app-doc/ is reserved for documentation *files* and not software. Move it to app-text/ where it seems a better fit. Signed-off-by: Michał Górny <mgorny@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Pacho Ramos · gentoo
sci-chemistry/openbabel: Works with wxGTK 3.2
Signed-off-by: Pacho Ramos <pacho@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Arthur Zamarin · gentoo
sci-chemistry/openbabel: destabilize for ~x86
Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andrew Ammerlaan · gentoo
sci-chemistry/openbabel: enable py3.11
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - David Seifert · gentoo
*/*: remove py3.8 from PYTHON_COMPAT
Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sam James · gentoo
sci-chemistry/openbabel: fix build with GCC 12
Closes: https://bugs.gentoo.org/851510 Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - David Seifert · gentoo
sci-chemistry/openbabel: [QA] use tc-check-openmp correctly
Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sam James · gentoo
sci-chemistry/openbabel: fix WhitespaceFound
Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-chemistry/openbabel: Drop 2.4.1-r2
Bug: https://bugs.gentoo.org/834115 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Jakov Smolić · gentoo
sci-chemistry/openbabel: Stabilize 3.1.1_p20210225 x86, #834115
Signed-off-by: Jakov Smolić <jsmolic@gentoo.org> - Jakov Smolić · gentoo
sci-chemistry/openbabel: Stabilize 3.1.1_p20210225 amd64, #834115
Signed-off-by: Jakov Smolić <jsmolic@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andrew Ammerlaan · gentoo
sci-chemistry/openbabel: bump EAPI=8, add python310
Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-chemistry/openbabel: Drop 2.4.1-r1
Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sam James · gentoo
sci-chemistry/openbabel: Stabilize 2.4.1-r2 x86, #722860
Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Agostino Sarubbo · gentoo
sci-chemistry/openbabel: amd64 stable wrt bug #722860
Package-Manager: Portage-3.0.13, Repoman-3.0.2 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Pacho Ramos · gentoo
sci-chemistry/openbabel: Fix gcc10 build and use wxGTK:gtk3.0
Thanks-to: Michelangelo Scopelliti Bug: https://bugs.gentoo.org/722860 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Pacho Ramos <pacho@gentoo.org> - Peter Levine · gentoo
sci-chemistry/openbabel: Bump openbabel-3.1.1_p20210225
Closes: https://bugs.gentoo.org/664124 Closes: https://bugs.gentoo.org/716208 Closes: https://bugs.gentoo.org/722860 Closes: https://bugs.gentoo.org/723434 Closes: https://bugs.gentoo.org/766003 Closes: https://bugs.gentoo.org/770493 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Peter Levine <plevine457@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/16182 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> - Peter Levine · gentoo
sci-chemistry/openbabel: Add openbabel-9999
Add an up-to-date live ebuild with a templated versioning scheme, and match the bindings to USE flags. Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Peter Levine <plevine457@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Jakov Smolic · gentoo
sci-chemistry/openbabel: Remove old
Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Agostino Sarubbo · gentoo
sci-chemistry/openbabel: amd64 stable wrt bug #757912
Package-Manager: Portage-3.0.9, Repoman-3.0.2 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Thomas Deutschmann · gentoo
sci-chemistry/openbabel: x86 stable (bug #757912)
Package-Manager: Portage-3.0.10, Repoman-3.0.2 Signed-off-by: Thomas Deutschmann <whissi@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - David Seifert · gentoo
sci-chemistry/openbabel: Inherit optfeature.eclass
Package-Manager: Portage-3.0.5, Repoman-3.0.1 Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - David Seifert · gentoo
sci-chemistry/openbabel: [QA] inherit toolchain-funcs.eclass directly
Package-Manager: Portage-2.3.88, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
*/*: [QA] Fix trivial cases of MissingTestRestrict
The result was achieved via the following pipeline: pkgcheck scan -c RestrictTestCheck -R FormatReporter \ --format '{category}/{package}/{package}-{version}.ebuild' | xargs -n32 grep -L RESTRICT | xargs -n32 sed -i -e '/^IUSE=.*test/aRESTRICT="!test? ( test )"' The resulting metadata was compared before and after the change. Few Go ebuilds had to be fixed manually due to implicit RESTRICT=strip added by the eclass. Two ebuilds have to be fixed because of multiline IUSE. Suggested-by: Robin H. Johnson <robbat2@gentoo.org> Closes: https://github.com/gentoo/gentoo/pull/13942 Signed-off-by: Michał Górny <mgorny@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Pacho Ramos · gentoo
sci-chemistry/openbabel: Fix openmp support, add a desktop file.
Closes: https://bugs.gentoo.org/659148 Package-Manager: Portage-2.3.76, Repoman-2.3.17 Signed-off-by: Pacho Ramos <pacho@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-chemistry/openbabel: Drop 2.3.2-r1
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11 - Sergei Trofimovich · gentoo
sci-chemistry/openbabel: allow gcc-8, bug #654800
openbabel explicitly whitelists list of major GCC versions. The change by Milan allow gcc-8. Newer upstream versions fixed the code to handle in in a more generic way: https://github.com/openbabel/openbabel/commit/00120f89cf62b121c30d0b2a891b159e19b53624 Fixed-by: milan hodoscek Closes: https://bugs.gentoo.org/654800 Package-Manager: Portage-2.3.36, Repoman-2.3.9 - Michael Palimaka · gentoo
sci-chemistry/openbabel: stabilise 2.4.1 for x86
Bug: https://bugs.gentoo.org/625088 Package-Manager: Portage-2.3.8, Repoman-2.3.3 - Matt Turner · gentoo
sci-chemistry/openbabel-2.4.1: dropped ppc keywords, bug 625088 - Tobias Klausmann · gentoo
sci-chemistry/openbabel-2.4.1-r0: amd64 stable
Gentoo-Bug: 625088 - Justin Lecher · gentoo
sci-chemistry/openbabel: Fix API doc installation
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=619140 Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org> - Justin Lecher · gentoo
sci-chemistry/openbabel: Version Bump
which fixes build problems with earlier versions Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=618402 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=618414 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=618542 Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org> - Justin Lecher · gentoo
sci-chemistry/openbabel: Backport Fix for gcc 6/7
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=594154 Package-Manager: Portage-2.3.5, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org> - Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> - Justin Lecher · gentoo
sci-chemistry/openbabel: Only configure WxGtk with USE=wxwidgets
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=565040 Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec@gentoo.org> - Justin Lecher · gentoo
sci-chemistry/openbabel: Drop old
obsoletes Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=449852 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=553104 Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec@gentoo.org> - Agostino Sarubbo · gentoo
sci-chemistry/openbabel: ppc stable wrt bug #564280
Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="ppc" - Mikle Kolyada · gentoo
sci-chemistry/openbabel: x86 stable wrt bug #564280
Package-Manager: portage-2.2.20.1 - Agostino Sarubbo · gentoo
sci-chemistry/openbabel: amd64 stable wrt bug #564280
Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="amd64" - Justin Lecher · gentoo
sci-chemistry/openbabel: Fix for gcc-5
convert mycmakeargs to be an array Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec@gentoo.org> - Pacho Ramos · gentoo
sci-chemistry/openbabel: Support wxGTK:3.0
Package-Manager: portage-2.2.23 - Dion Moult · gentoo
profiles: mask sci-chemistry/babel for removal. Bug #552284 - Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed