;;; 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 (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)
(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)))
+ (list eigen
+ mmtf-cpp
+ msgpack
+ googletest
+ pkg-config
+ pybind11))
(inputs
- `(("glew" ,glew)
- ("libarchive" ,libarchive)
- ("libmsym" ,libmsym)
- ("molequeue" ,molequeue)
- ("python" ,python)
- ("spglib" ,spglib)
- ("qtbase" ,qtbase-5)))
+ (list glew
+ libarchive
+ libmsym
+ molequeue
+ python
+ spglib
+ qtbase-5))
(arguments
'(#:configure-flags (list "-DENABLE_TESTING=ON"
(string-append "-DSPGLIB_INCLUDE_DIR="
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(native-inputs
- `(("eigen" ,eigen)
- ("pkg-config" ,pkg-config)))
+ (list eigen pkg-config))
(inputs
- `(("avogadrolibs" ,avogadrolibs)
- ("hdf5" ,hdf5)
- ("molequeue" ,molequeue)
- ("qtbase" ,qtbase-5)))
+ (list avogadrolibs hdf5 molequeue qtbase-5))
;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
(arguments
'(#:tests? #f))
powerful plugin architecture.")
(license license:bsd-3)))
-(define-public domainfinder
- (package
- (name "domainfinder")
- (version "2.0.5")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "https://bitbucket.org/khinsen/"
- "domainfinder/downloads/DomainFinder-"
- version ".tar.gz"))
- (sha256
- (base32
- "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
- (build-system python-build-system)
- (inputs
- `(("python-mmtk" ,python2-mmtk)))
- (arguments
- `(#:python ,python-2
- ;; No test suite
- #:tests? #f))
- (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
-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)))
-
(define-public inchi
(package
(name "inchi")
"1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998"))))
(build-system cmake-build-system)
(inputs
- `(("qtbase" ,qtbase-5)))
+ (list qtbase-5))
(arguments
'(#:configure-flags '("-DENABLE_TESTING=ON")
#:phases
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))))
-
-(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")
"1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
(build-system cmake-build-system)
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(arguments
`(#:phases
(modify-phases %standard-phases
("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)))
+ (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,
(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
@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