;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
+;;; Copyright © 2018 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>
;;;
;;; This file is part of GNU Guix.
;;;
(define-module (gnu packages chemistry)
#:use-module (guix packages)
+ #: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 boost)
+ #:use-module (gnu packages check)
+ #:use-module (gnu packages compression)
+ #:use-module (gnu packages documentation)
+ #:use-module (gnu packages gl)
+ #:use-module (gnu packages graphviz)
+ #:use-module (gnu packages gv)
+ #: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 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
+ (package
+ (name "avogadro")
+ (version "1.2.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cryos/avogadro.git")
+ (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"))))
+ (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)))
+ (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")
+ (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+)))
+
(define-public domainfinder
(package
(name "domainfinder")
`(#:python ,python-2
;; No test suite
#:tests? #f))
- (home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
+ (home-page "http://dirac.cnrs-orleans.fr/DomainFinder.html")
(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
single structure. The software is currently not actively maintained and works
only with Python 2 and NumPy < 1.9.")
(license license:cecill-c)))
+
+(define-public inchi
+ (package
+ (name "inchi")
+ (version "1.05")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://www.inchi-trust.org/download/"
+ (string-join (string-split version #\.) "")
+ "/INCHI-1-SRC.zip"))
+ (sha256
+ (base32
+ "081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
+ (file-name (string-append name "-" version ".zip"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ; no check target
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; no configure script
+ (add-before 'build 'chdir-to-build-directory
+ (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
+ (add-after 'build 'build-library
+ (lambda _
+ (chdir "../../../INCHI_API/libinchi/gcc")
+ (invoke "make")))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (doc (string-append out "/share/doc/inchi"))
+ (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")))
+ (chdir "../../..")
+ ;; Install binary.
+ (with-directory-excursion "INCHI_EXE/bin/Linux"
+ (rename-file "inchi-1" "inchi")
+ (install-file "inchi" bin))
+ ;; Install libraries.
+ (with-directory-excursion "INCHI_API/bin/Linux"
+ (for-each (lambda (file)
+ (install-file file lib))
+ (find-files "." "libinchi\\.so\\.1\\.*")))
+ ;; Install header files.
+ (with-directory-excursion "INCHI_BASE/src"
+ (for-each (lambda (file)
+ (install-file file include-dir))
+ (find-files "." "\\.h$")))
+ ;; Install documentation.
+ (mkdir-p doc)
+ (invoke unzip "-j" "-d" doc inchi-doc)
+ #t))))))
+ (native-inputs
+ `(("unzip" ,unzip)
+ ("inchi-doc"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "http://www.inchi-trust.org/download/"
+ (string-join (string-split version #\.) "")
+ "/INCHI-1-DOC.zip"))
+ (sha256
+ (base32
+ "1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
+ (file-name (string-append name "-" version ".zip"))))))
+ (home-page "https://www.inchi-trust.org")
+ (synopsis "Utility for manipulating machine-readable chemical structures")
+ (description
+ "The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
+chemical structures into machine-readable strings of information. InChIs are
+unique to the compound they describe and can encode absolute stereochemistry
+making chemicals and chemistry machine-readable and discoverable. A simple
+analogy is that InChI is the bar-code for chemistry and chemical structures.")
+ (license (license:non-copyleft
+ "file://LICENCE"
+ "See LICENCE in the distribution."))))
+
+(define with-numpy-1.8
+ (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
+
+(define-public nmoldyn
+ (package
+ (name "nmoldyn")
+ (version "3.0.11")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/khinsen/nMOLDYN3")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r"))))
+ (build-system python-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)))
+ (arguments
+ `(#:python ,python-2
+ #:tests? #f ; No test suite
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'create-linux2-directory
+ (lambda _
+ (mkdir-p "nMOLDYN/linux2")))
+ (add-before 'build 'change-PDF-viewer
+ (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 #f "PREFERENCES['acroread_path'] = '~a'"
+ (which "gv")))
+ (("PREFERENCES\\['ncdump_path'\\] = ''")
+ (format #f "PREFERENCES['ncdump_path'] = '~a'"
+ (which "ncdump")))
+ (("PREFERENCES\\['ncgen_path'\\] = ''")
+ (format #f "PREFERENCES['ncgen_path'] = '~a'"
+ (which "ncgen3")))
+ (("PREFERENCES\\['task_manager_path'\\] = ''")
+ (format #f "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.html")
+ (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)))
+
+(define-public tng
+ (package
+ (name "tng")
+ (version "1.8.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gromacs/tng.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
+ (build-system cmake-build-system)
+ (inputs
+ `(("zlib" ,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)
+ ;; 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
+ `(("fftwf" ,fftwf)
+ ("hwloc" ,hwloc-2 "lib")
+ ("lmfit" ,lmfit)
+ ("openblas" ,openblas)
+ ("perl" ,perl)
+ ("tinyxml2" ,tinyxml2)
+ ("tng" ,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")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/" name "/" name "/"
+ version "/" name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
+ (patches
+ (search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags
+ (list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
+ (string-append "-DINCHI_LIBRARY="
+ (assoc-ref %build-inputs "inchi")
+ "/lib/inchi/libinchi.so.1")
+ (string-append "-DINCHI_INCLUDE_DIR="
+ (assoc-ref %build-inputs "inchi") "/include/inchi"))
+ #:test-target "test"))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("eigen" ,eigen)
+ ("inchi" ,inchi)
+ ("libxml2" ,libxml2)
+ ("zlib" ,zlib)))
+ (home-page "http://openbabel.org/wiki/Main_Page")
+ (synopsis "Chemistry data manipulation toolbox")
+ (description
+ "Open Babel is a chemical toolbox designed to speak the many languages of
+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)))
HCoop / jackhill / guix / guix.git / blobdiff