diff options
| -rw-r--r-- | gnu/packages/chemistry.scm | 66 |
1 files changed, 66 insertions, 0 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 0cd1585e92..ed883072b4 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -20,6 +20,8 @@ #:use-module (guix packages) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) + #:use-module (gnu packages gv) + #:use-module (gnu packages maths) #:use-module (gnu packages python) #:use-module (guix build-system python)) @@ -51,3 +53,67 @@ 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 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 url-fetch) + (uri (string-append "https://bitbucket.org/khinsen/" + "nmoldyn3/downloads/nMOLDYN-" + version ".tar.gz")) + (sha256 + (base32 + "1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a")))) + (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 "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))) |