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author | Leo Famulari <leo@famulari.name> | 2018-01-11 14:22:50 -0800 |
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committer | Leo Famulari <leo@famulari.name> | 2018-01-11 14:22:50 -0800 |
commit | 4adb40bffc0dda8871878283887a0e0cd88d9578 (patch) | |
tree | 74d5fb686116002da72de4a1075d0ed8f307cec1 /gnu/packages/chemistry.scm | |
parent | 4610ab7c9a5327df0d475262817bc081a5891aa8 (diff) | |
parent | 138c08899ba73049de8afd2b74a8cf6845a1d9e1 (diff) | |
download | guix-patches-4adb40bffc0dda8871878283887a0e0cd88d9578.tar guix-patches-4adb40bffc0dda8871878283887a0e0cd88d9578.tar.gz |
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages/chemistry.scm')
-rw-r--r-- | gnu/packages/chemistry.scm | 119 |
1 files changed, 119 insertions, 0 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm new file mode 100644 index 0000000000..ed883072b4 --- /dev/null +++ b/gnu/packages/chemistry.scm @@ -0,0 +1,119 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. + +(define-module (gnu packages chemistry) + #: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)) + +(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") + (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 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))) |