diff options
Diffstat (limited to 'gnu/packages/chemistry.scm')
| -rw-r--r-- | gnu/packages/chemistry.scm | 300 |
1 files changed, 222 insertions, 78 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 4aa39a567d..4b0e719959 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> -;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net> +;;; Copyright © 2018, 2021 Kei Kebreau <kkebreau@posteo.net> ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> @@ -29,6 +29,8 @@ #:use-module (guix git-download) #:use-module (gnu packages) #:use-module (gnu packages algebra) + #:use-module (gnu packages autotools) + #:use-module (gnu packages backup) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -43,95 +45,89 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) + #:use-module (gnu packages serialization) #:use-module (gnu packages sphinx) #:use-module (gnu packages xml) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system python)) -(define-public avogadro +(define-public avogadrolibs (package - (name "avogadro") - (version "1.2.0") + (name "avogadrolibs") + (version "1.93.0") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/cryos/avogadro") + (url "https://github.com/OpenChemistry/avogadrolibs") (commit version))) (sha256 - (base32 "0258py3lkba85qhs5ynancinyym61vlp0zaq9yrfs3hhnhpzv9n2")) - (file-name (git-file-name name version)) - (patches - (search-patches "avogadro-eigen3-update.patch" - "avogadro-python-eigen-lib.patch" - "avogadro-boost148.patch")))) + (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39")) + (file-name (git-file-name name version)))) (build-system cmake-build-system) + (native-inputs + `(("eigen" ,eigen) + ("mmtf-cpp" ,mmtf-cpp) + ("msgpack" ,msgpack) + ("googletest" ,googletest) + ("pkg-config" ,pkg-config) + ("pybind11" ,pybind11))) + (inputs + `(("glew" ,glew) + ("libarchive" ,libarchive) + ("libmsym" ,libmsym) + ("molequeue" ,molequeue) + ("python" ,python) + ("spglib" ,spglib) + ("qtbase" ,qtbase))) (arguments - `(#:tests? #f - #:configure-flags - (list "-DENABLE_GLSL=ON" - (string-append "-DPYTHON_LIBRARIES=" - (assoc-ref %build-inputs "python") - "/lib") - (string-append "-DPYTHON_INCLUDE_DIRS=" - (assoc-ref %build-inputs "python") - "/include/python" - ,(version-major+minor - (package-version python)))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-python-lib-path - (lambda* (#:key outputs #:allow-other-keys) - ;; This is necessary to install the Python module in the correct - ;; directory. - (substitute* "libavogadro/src/python/CMakeLists.txt" - (("^EXECUTE_PROCESS.*$") "") - (("^.*from sys import stdout.*$") "") - (("^.*OUTPUT_VARIABLE.*") - (string-append "set(PYTHON_LIB_PATH \"" - (assoc-ref outputs "out") - "/lib/python" - ,(version-major+minor - (package-version python)) - "/site-packages\")"))))) - (add-after 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Make sure 'avogadro' runs with the correct PYTHONPATH. - (let* ((out (assoc-ref outputs "out"))) - (setenv "GUIX_PYTHONPATH" - (string-append - (assoc-ref outputs "out") - "/lib/python" - ,(version-major+minor - (package-version python)) - "/site-packages:" - (getenv "GUIX_PYTHONPATH"))) - (wrap-program (string-append out "/bin/avogadro") - `("GUIX_PYTHONPATH" ":" prefix - (,(getenv "GUIX_PYTHONPATH")))))))))) + '(#:configure-flags (list "-DENABLE_TESTING=ON" + (string-append "-DSPGLIB_INCLUDE_DIR=" + (assoc-ref %build-inputs "spglib") + "/include")))) + (home-page "https://www.openchemistry.org/projects/avogadro2/") + (synopsis "Libraries for chemistry, bioinformatics, and related areas") + (description + "Avogadro libraries provide 3D rendering, visualization, analysis and data +processing useful in computational chemistry, molecular modeling, +bioinformatics, materials science, and related areas.") + (license license:bsd-3))) + +(define-public avogadro2 + (package + (name "avogadro2") + (version "1.93.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/OpenChemistry/avogadroapp") + (commit version))) + (sha256 + (base32 + "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7")) + (file-name (git-file-name name version)))) + (build-system cmake-build-system) (native-inputs - `(("doxygen" ,doxygen) + `(("eigen" ,eigen) ("pkg-config" ,pkg-config))) (inputs - `(("boost" ,boost) - ("eigen" ,eigen) - ("glew" ,glew) - ("openbabel" ,openbabel) - ("python" ,python-2) - ("python-numpy" ,python2-numpy) - ("python-pyqt" ,python2-pyqt-4) - ("python-sip" ,python2-sip) - ("qt" ,qt-4) - ("zlib" ,zlib))) - (home-page "https://avogadro.cc") + `(("avogadrolibs" ,avogadrolibs) + ("hdf5" ,hdf5) + ("molequeue" ,molequeue) + ("qtbase" ,qtbase))) + ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. + (arguments + '(#:tests? #f)) + (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Advanced molecule editor") (description - "Avogadro is an advanced molecule editor and visualizer designed for use + "Avogadro 2 is an advanced molecule editor and visualizer designed for use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.") - (license license:gpl2+))) + (license license:bsd-3))) (define-public domainfinder (package @@ -165,15 +161,16 @@ only with Python 2 and NumPy < 1.9.") (define-public inchi (package (name "inchi") - (version "1.05") + ;; Update the inchi-doc native input when updating inchi. + (version "1.06") (source (origin (method url-fetch) - (uri (string-append "http://www.inchi-trust.org/download/" + (uri (string-append "https://www.inchi-trust.org/download/" (string-join (string-split version #\.) "") "/INCHI-1-SRC.zip")) (sha256 (base32 - "081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa")) + "1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28")) (file-name (string-append name "-" version ".zip")))) (build-system gnu-build-system) (arguments @@ -226,7 +223,7 @@ only with Python 2 and NumPy < 1.9.") "/INCHI-1-DOC.zip")) (sha256 (base32 - "1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6")) + "1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f")) (file-name (string-append name "-" version ".zip")))))) (home-page "https://www.inchi-trust.org") (synopsis "Utility for manipulating machine-readable chemical structures") @@ -240,6 +237,103 @@ analogy is that InChI is the bar-code for chemistry and chemical structures.") "file://LICENCE" "See LICENCE in the distribution.")))) +(define-public libmsym + (package + (name "libmsym") + (version "0.2.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mcodev31/libmsym") + (commit (string-append "v" version)))) + (sha256 + (base32 + "0a9j28irdsr461qpzlc9z1yjyb9kp64fh5zw7ylspc9zn3189qwk")) + (file-name (git-file-name name version)))) + (build-system cmake-build-system) + (arguments + '(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") + #:tests? #f)) ; no check target + (home-page "https://github.com/mcodev31/libmsym") + (synopsis "C library dealing with point group symmetry in molecules") + (description "libmsym is a C library dealing with point group symmetry in +molecules.") + (license license:expat))) + +(define-public mmtf-cpp + (package + (name "mmtf-cpp") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rcsb/mmtf-cpp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l")))) + (build-system cmake-build-system) + ;; Tests require the soon-to-be-deprecated version 1 of the catch-framework. + (arguments + '(#:tests? #f)) + (home-page "https://mmtf.rcsb.org/") + (synopsis "C++ API for the Macromolecular Transmission Format") + (description "This package is a library for the +@acronym{MMTF,macromolecular transmission format}, a binary encoding of +biological structures.") + (license license:expat))) + +(define-public molequeue + (package + (name "molequeue") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/OpenChemistry/molequeue/" + "releases/download/" version "/molequeue-" + version ".tar.bz2")) + (sha256 + (base32 + "1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998")))) + (build-system cmake-build-system) + (inputs + `(("qtbase" ,qtbase))) + (arguments + '(#:configure-flags '("-DENABLE_TESTING=ON") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + ;; TODO: Fix/enable the failing message and clientserver tests. + ;; In the message test, the floating-point value "5.36893473232" on + ;; line 165 of molequeue/app/testing/messagetest.cpp should + ;; (apparently) be truncated, but it is not. + (substitute* "molequeue/app/testing/messagetest.cpp" + (("5\\.36893473232") "5.36893")) + ;; It is unclear why the clientserver test fails, so it is + ;; completely disabled. + (substitute* "molequeue/app/testing/CMakeLists.txt" + ((".*clientserver.*") "")) + #t)) + (add-before 'check 'set-display + (lambda _ + ;; Make Qt render "offscreen" for the sake of tests. + (setenv "QT_QPA_PLATFORM" "offscreen") + #t))))) + (home-page "https://www.openchemistry.org/projects/molequeue/") + (synopsis "Application for coordinating computational jobs") + (description "MoleQueue is a system-tray resident desktop application for +abstracting, managing, and coordinating the execution of tasks both locally and + on remote computational resources. Users can set up local and remote queues +that describe where the task will be executed. Each queue can have programs, +with templates to facilitate the execution of the program. Input files can be +staged, and output files collected using a standard interface.") + (license license:bsd-3))) + (define with-numpy-1.8 (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8)))) @@ -428,19 +522,23 @@ usual algorithms you expect from a modern molecular dynamics implementation.") (define-public openbabel (package (name "openbabel") - (version "2.4.1") + (version "3.1.1") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/" name "/" name "/" - version "/" name "-" version ".tar.gz")) + (uri (string-append "https://github.com/openbabel/openbabel/" + "releases/download/openbabel-" + (string-replace-substring version "." "-") + "/openbabel-" version "-source.tar.bz2")) (sha256 (base32 - "1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90")) - (patches - (search-patches "openbabel-fix-crash-on-nwchem-output.patch")))) + "0s0f4zib8vshfaywsr5bjjz55jwsg6yiz2qw4i5jm8wysn0q7v56")))) (build-system cmake-build-system) (arguments - `(#:configure-flags + `(;; FIXME: Disable tests on i686 to work around + ;; https://github.com/openbabel/openbabel/issues/2041. + #:tests? ,(or (%current-target-system) + (not (string=? "i686-linux" (%current-system)))) + #:configure-flags (list "-DOPENBABEL_USE_SYSTEM_INCHI=ON" (string-append "-DINCHI_LIBRARY=" (assoc-ref %build-inputs "inchi") @@ -463,3 +561,49 @@ chemical data. It's a collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.") (license license:gpl2))) + +(define-public spglib + (package + (name "spglib") + (version "1.16.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/spglib/spglib") + (commit (string-append "v" version)))) + (sha256 + (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws")) + (file-name (git-file-name name version)))) + (build-system cmake-build-system) + (arguments + '(#:test-target "check" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-header-install-dir + (lambda _ + ;; As of the writing of this package, CMake and GNU build systems + ;; install the header to two different location. This patch makes + ;; the CMake build system's choice of header directory compatible + ;; with the GNU build system's choice and with what avogadrolibs + ;; expects. + ;; See https://github.com/spglib/spglib/issues/75 and the relevant + ;; part of https://github.com/OpenChemistry/avogadroapp/issues/97. + (substitute* "CMakeLists.txt" + (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir) + (string-append include-dir "/spglib"))) + #t))))) + (home-page "https://spglib.github.io/spglib/index.html") + (synopsis "Library for crystal symmetry search") + (description "Spglib is a library for finding and handling crystal +symmetries written in C. Spglib can be used to: + +@enumerate +@item Find symmetry operations +@item Identify space-group type +@item Wyckoff position assignment +@item Refine crystal structure +@item Find a primitive cell +@item Search irreducible k-points +@end enumerate") + (license license:bsd-3))) |