;;; 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>
+;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
+;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix utils)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix download)
+ #: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)
#:use-module (gnu packages documentation)
+ #:use-module (gnu packages fontutils)
#:use-module (gnu packages gl)
+ #:use-module (gnu packages graphviz)
#:use-module (gnu packages gv)
+ #:use-module (gnu packages image)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages mpi)
+ #:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#: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")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/cryos/avogadro/archive/"
- version ".tar.gz"))
- (sha256
- (base32
- "02v4h6hi1m7ilv0apdf74a8l1cm6dxnxyqp0rdaidrp3i9pf6lv4"))
- (file-name (string-append name "-" version ".tar.gz"))
- (patches
- (search-patches "avogadro-eigen3-update.patch"
- "avogadro-python-eigen-lib.patch"
- "avogadro-boost148.patch"))))
+ (name "avogadrolibs")
+ (version "1.93.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/OpenChemistry/avogadrolibs")
+ (commit version)))
+ (sha256
+ (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39"))
+ (file-name (git-file-name name version))))
(build-system cmake-build-system)
- (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\")")))
- #t))
- (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 "PYTHONPATH"
- (string-append
- (assoc-ref outputs "out")
- "/lib/python"
- ,(version-major+minor
- (package-version python))
- "/site-packages:"
- (getenv "PYTHONPATH")))
- (wrap-program (string-append out "/bin/avogadro")
- `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
- #t)))))
(native-inputs
- `(("doxygen" ,doxygen)
- ("pkg-config" ,pkg-config)))
+ (list eigen
+ mmtf-cpp
+ msgpack
+ googletest
+ pkg-config
+ pybind11))
(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")
- (synopsis "Advanced molecule editor")
+ (list glew
+ libarchive
+ libmsym
+ molequeue
+ python
+ spglib
+ qtbase-5))
+ (arguments
+ '(#: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 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+)))
+ "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 domainfinder
+(define-public avogadro2
(package
- (name "domainfinder")
- (version "2.0.5")
+ (name "avogadro2")
+ (version "1.93.0")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://bitbucket.org/khinsen/"
- "domainfinder/downloads/DomainFinder-"
- version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/OpenChemistry/avogadroapp")
+ (commit version)))
(sha256
(base32
- "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
- (build-system python-build-system)
+ "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
+ (file-name (git-file-name name version))))
+ (build-system cmake-build-system)
+ (native-inputs
+ (list eigen pkg-config))
(inputs
- `(("python-mmtk" ,python2-mmtk)))
+ (list avogadrolibs hdf5 molequeue qtbase-5))
+ ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
(arguments
- `(#:python ,python-2
- ;; No test suite
- #:tests? #f))
- (home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
- (synopsis "Analysis of dynamical domains in proteins")
- (description "DomainFinder is an interactive program for the determination
-and characterization of dynamical domains in proteins. It can infer dynamical
-domains by comparing two protein structures, or from normal mode analysis on a
-single structure. The software is currently not actively maintained and works
-only with Python 2 and NumPy < 1.9.")
- (license license:cecill-c)))
+ '(#:tests? #f))
+ (home-page "https://www.openchemistry.org/projects/avogadro2/")
+ (synopsis "Advanced molecule editor")
+ (description
+ "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:bsd-3)))
(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
(include-dir (string-append out "/include/inchi"))
(lib (string-append out "/lib/inchi"))
(inchi-doc (assoc-ref inputs "inchi-doc"))
- (unzip (string-append (assoc-ref inputs "unzip")
- "/bin/unzip")))
+ (unzip (search-input-file inputs "/bin/unzip")))
(chdir "../../..")
;; Install binary.
(with-directory-excursion "INCHI_EXE/bin/Linux"
"/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")
"file://LICENCE"
"See LICENCE in the distribution."))))
-(define with-numpy-1.8
- (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
+(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 nmoldyn
+(define-public mmtf-cpp
(package
- (name "nmoldyn")
- (version "3.0.11")
+ (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://bitbucket.org/khinsen/"
- "nmoldyn3/downloads/nMOLDYN-"
- version ".tar.gz"))
+ (uri (string-append "https://github.com/OpenChemistry/molequeue/"
+ "releases/download/" version "/molequeue-"
+ version ".tar.bz2"))
(sha256
(base32
- "1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a"))))
- (build-system python-build-system)
+ "1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998"))))
+ (build-system cmake-build-system)
(inputs
- `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
- ("python-scientific" ,python2-scientific)
- ("netcdf" ,netcdf)
- ("gv" ,gv)))
- (propagated-inputs
- `(("python-mmtk" ,python2-mmtk)))
+ (list qtbase-5))
(arguments
- `(#:python ,python-2
- #:tests? #f ; No test suite
+ '(#:configure-flags '("-DENABLE_TESTING=ON")
#:phases
(modify-phases %standard-phases
- (add-before 'build 'create-linux2-directory
+ (add-after 'unpack 'patch-tests
(lambda _
- (mkdir-p "nMOLDYN/linux2")))
- (add-before 'build 'change-PDF-viewer
+ ;; 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-public tng
+ (package
+ (name "tng")
+ (version "1.8.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gromacs/tng")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list zlib))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'remove-bundled-zlib
+ (lambda _
+ (delete-file-recursively "external")
+ #t))
+ (replace 'check
+ (lambda _
+ (invoke "../build/bin/tests/tng_testing")
+ #t)))))
+ (home-page "https://github.com/gromacs/tng")
+ (synopsis "Trajectory Next Generation binary format manipulation library")
+ (description "TRAJNG (Trajectory next generation) is a program library for
+handling molecular dynamics (MD) trajectories. It can store coordinates, and
+optionally velocities and the H-matrix. Coordinates and velocities are
+stored with user-specified precision.")
+ (license license:bsd-3)))
+
+(define-public gromacs
+ (package
+ (name "gromacs")
+ (version "2020.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
+ ;; Our version of tinyxml2 is far newer than the bundled one and
+ ;; require fixing `testutils' code. See patch header for more info
+ (patches (search-patches "gromacs-tinyxml2.patch"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags
+ (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
+ ;; Unbundling
+ "-DGMX_USE_LMFIT=EXTERNAL"
+ "-DGMX_BUILD_OWN_FFTW=off"
+ "-DGMX_EXTERNAL_BLAS=on"
+ "-DGMX_EXTERNAL_LAPACK=on"
+ "-DGMX_EXTERNAL_TNG=on"
+ "-DGMX_EXTERNAL_ZLIB=on"
+ "-DGMX_EXTERNAL_TINYXML2=on"
+ (string-append "-DTinyXML2_DIR="
+ (assoc-ref %build-inputs "tinyxml2"))
+ ;; Workaround for cmake/FindSphinx.cmake version parsing that does
+ ;; not understand the guix-wrapped `sphinx-build --version' answer
+ (string-append "-DSPHINX_EXECUTABLE_VERSION="
+ ,(package-version python-sphinx)))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fixes
(lambda* (#:key inputs #:allow-other-keys)
- (substitute* "nMOLDYN/Preferences.py"
- ;; Set the paths for external executables, substituting
- ;; gv for acroread.
- ;; There is also vmd_path, but VMD is not free software
- ;; and Guix contains currently no free molecular viewer that
- ;; could be substituted.
- (("PREFERENCES\\['acroread_path'\\] = ''")
- (format "PREFERENCES['acroread_path'] = '~a'"
- (which "gv")))
- (("PREFERENCES\\['ncdump_path'\\] = ''")
- (format "PREFERENCES['ncdump_path'] = '~a'"
- (which "ncdump")))
- (("PREFERENCES\\['ncgen_path'\\] = ''")
- (format "PREFERENCES['ncgen_path'] = '~a'"
- (which "ncgen3")))
- (("PREFERENCES\\['task_manager_path'\\] = ''")
- (format "PREFERENCES['task_manager_path'] = '~a'"
- (which "task_manager")))
- ;; Show documentation as PDF
- (("PREFERENCES\\['documentation_style'\\] = 'html'")
- "PREFERENCES['documentation_style'] = 'pdf'") ))))))
- (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/")
- (synopsis "Analysis software for Molecular Dynamics trajectories")
- (description "nMOLDYN is an interactive analysis program for Molecular Dynamics
-simulations. It is especially designed for the computation and decomposition of
-neutron scattering spectra, but also computes other quantities. The software
-is currently not actively maintained and works only with Python 2 and
-NumPy < 1.9.")
- (license license:cecill)))
+ ;; Still bundled: part of gromacs, source behind registration
+ ;; but free software anyways
+ ;;(delete-file-recursively "src/external/vmd_molfile")
+ ;; Still bundled: threads-based OpenMPI-compatible fallback
+ ;; designed to be bundled like that
+ ;;(delete-file-recursively "src/external/thread_mpi")
+ ;; Unbundling
+ (delete-file-recursively "src/external/lmfit")
+ (delete-file-recursively "src/external/clFFT")
+ (delete-file-recursively "src/external/fftpack")
+ (delete-file-recursively "src/external/build-fftw")
+ (delete-file-recursively "src/external/tng_io")
+ (delete-file-recursively "src/external/tinyxml2")
+ (delete-file-recursively "src/external/googletest")
+ (copy-recursively (assoc-ref inputs "googletest-source")
+ "src/external/googletest")
+ ;; This test warns about the build host hardware, disable
+ (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
+ (("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
+ "void __guix_disabled()"))
+ #t)))))
+ (native-inputs
+ `(("doxygen" ,doxygen)
+ ("googletest-source" ,(package-source googletest))
+ ("graphviz" ,graphviz)
+ ("pkg-config" ,pkg-config)
+ ("python" ,python)
+ ("python-pygments" ,python-pygments)
+ ("python-sphinx" ,python-sphinx)))
+ (inputs
+ (list fftwf
+ `(,hwloc-2 "lib")
+ lmfit
+ openblas
+ perl
+ tinyxml2
+ tng))
+ (home-page "http://www.gromacs.org/")
+ (synopsis "Molecular dynamics software package")
+ (description "GROMACS is a versatile package to perform molecular dynamics,
+i.e. simulate the Newtonian equations of motion for systems with hundreds to
+millions of particles. It is primarily designed for biochemical molecules like
+proteins, lipids and nucleic acids that have a lot of complicated bonded
+interactions, but since GROMACS is extremely fast at calculating the nonbonded
+interactions (that usually dominate simulations) many groups are also using it
+for research on non-biological systems, e.g. polymers. GROMACS supports all the
+usual algorithms you expect from a modern molecular dynamics implementation.")
+ (license license:lgpl2.1+)))
(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")
(assoc-ref %build-inputs "inchi") "/include/inchi"))
#:test-target "test"))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(inputs
- `(("eigen" ,eigen)
- ("inchi" ,inchi)
- ("libxml2" ,libxml2)
- ("zlib" ,zlib)))
+ (list eigen inchi libxml2 zlib))
(home-page "http://openbabel.org/wiki/Main_Page")
(synopsis "Chemistry data manipulation toolbox")
(description
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)))
+
+(define-public python-pymol
+ (package
+ (name "python-pymol")
+ (version "2.5.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/schrodinger/pymol-open-source")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "08zmfgclkbjkqjpq8xs1mphs1i8rpqj76mcw7m2mrhvma5qj1nr5"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:configure-flags
+ (list "--glut" "--testing")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'make-reproducible
+ (lambda _
+ (substitute* "create_shadertext.py"
+ (("time\\.time\\(\\)") "0"))))
+ (add-after 'unpack 'add-include-directories
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-append (assoc-ref inputs "freetype")
+ "/include/freetype2:"
+ (assoc-ref inputs "libxml2")
+ "/include/libxml2:"
+ (getenv "CPLUS_INCLUDE_PATH")))))
+ ;; The setup.py script does not support one of the Python build
+ ;; system's default flags, "--single-version-externally-managed".
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (invoke "python" "setup.py" "install"
+ (string-append "--prefix=" (assoc-ref outputs "out"))
+ "--root=/"))))))
+ (inputs
+ (list freetype
+ libpng
+ freeglut
+ glew
+ libxml2
+ mmtf-cpp
+ msgpack
+ python-pyqt
+ glm
+ netcdf))
+ (native-inputs
+ (list catch2 python-setuptools))
+ (home-page "https://pymol.org")
+ (synopsis "Molecular visualization system")
+ (description "PyMOL is a capable molecular viewer and renderer. It can be
+used to prepare publication-quality figures, to share interactive results with
+your colleagues, or to generate pre-rendered animations.")
+ (license license:bsd-3)))
HCoop / jackhill / guix / guix.git / blobdiff