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-rw-r--r--gnu/packages/chemistry.scm80
1 files changed, 80 insertions, 0 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 2d7cb7aad1..03120aaeee 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -23,16 +23,96 @@
#:use-module (guix download)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages boost)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages documentation)
+ #:use-module (gnu packages gl)
#:use-module (gnu packages gv)
#:use-module (gnu packages maths)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages qt)
#: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 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"))))
+ (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/python2.7"))
+ #: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/python2.7/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/python2.7/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")