gnu/packages/chemistry.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
   3 ;;;
   4 ;;; This file is part of GNU Guix.
   5 ;;;
   6 ;;; GNU Guix is free software; you can redistribute it and/or modify it
   7 ;;; under the terms of the GNU General Public License as published by
   8 ;;; the Free Software Foundation; either version 3 of the License, or (at
   9 ;;; your option) any later version.
  10 ;;;
  11 ;;; GNU Guix is distributed in the hope that it will be useful, but
  12 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  13 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  14 ;;; GNU General Public License for more details.
  15 ;;;
  16 ;;; You should have received a copy of the GNU General Public License
  17 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  18
  19 (define-module (gnu packages chemistry)
  20   #:use-module (guix packages)
  21   #:use-module ((guix licenses) #:prefix license:)
  22   #:use-module (guix download)
  23   #:use-module (gnu packages gv)
  24   #:use-module (gnu packages maths)
  25   #:use-module (gnu packages python)
  26   #:use-module (guix build-system python))
  27
  28 (define-public domainfinder
  29   (package
  30     (name "domainfinder")
  31     (version "2.0.5")
  32     (source
  33      (origin
  34        (method url-fetch)
  35        (uri (string-append "https://bitbucket.org/khinsen/"
  36                            "domainfinder/downloads/DomainFinder-"
  37                            version ".tar.gz"))
  38        (sha256
  39         (base32
  40          "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
  41     (build-system python-build-system)
  42     (inputs
  43      `(("python-mmtk" ,python2-mmtk)))
  44     (arguments
  45      `(#:python ,python-2
  46        ;; No test suite
  47        #:tests? #f))
  48     (home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
  49     (synopsis "Analysis of dynamical domains in proteins")
  50     (description "DomainFinder is an interactive program for the determination
  51 and characterization of dynamical domains in proteins.  It can infer dynamical
  52 domains by comparing two protein structures, or from normal mode analysis on a
  53 single structure.  The software is currently not actively maintained and works
  54 only with Python 2 and NumPy < 1.9.")
  55     (license license:cecill-c)))
  56
  57 (define with-numpy-1.8
  58   (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
  59
  60 (define-public nmoldyn
  61   (package
  62     (name "nmoldyn")
  63     (version "3.0.11")
  64     (source
  65      (origin
  66        (method url-fetch)
  67        (uri (string-append "https://bitbucket.org/khinsen/"
  68                            "nmoldyn3/downloads/nMOLDYN-"
  69                            version ".tar.gz"))
  70        (sha256
  71         (base32
  72          "1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a"))))
  73     (build-system python-build-system)
  74     (inputs
  75      `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
  76        ("python-scientific", python2-scientific)
  77        ("netcdf", netcdf)
  78        ("gv" ,gv)))
  79     (propagated-inputs
  80      `(("python-mmtk" ,python2-mmtk)))
  81     (arguments
  82      `(#:python ,python-2
  83        #:tests? #f  ; No test suite
  84        #:phases
  85        (modify-phases %standard-phases
  86          (add-before 'build 'create-linux2-directory
  87            (lambda _
  88              (mkdir-p "nMOLDYN/linux2")))
  89          (add-before 'build 'change-PDF-viewer
  90            (lambda* (#:key inputs #:allow-other-keys)
  91              (substitute* "nMOLDYN/Preferences.py"
  92                ;; Set the paths for external executables, substituting
  93                ;; gv for acroread.
  94                ;; There is also vmd_path, but VMD is not free software
  95                ;; and Guix contains currently no free molecular viewer that
  96                ;; could be substituted.
  97                (("PREFERENCES\\['acroread_path'\\] = ''")
  98                 (format "PREFERENCES['acroread_path'] = '~a'"
  99                         (which "gv")))
 100                (("PREFERENCES\\['ncdump_path'\\] = ''")
 101                 (format "PREFERENCES['ncdump_path'] = '~a'"
 102                         (which "ncdump")))
 103                (("PREFERENCES\\['ncgen_path'\\] = ''")
 104                 (format "PREFERENCES['ncgen_path'] = '~a'"
 105                         (which "ncgen3")))
 106                (("PREFERENCES\\['task_manager_path'\\] = ''")
 107                 (format "PREFERENCES['task_manager_path'] = '~a'"
 108                         (which "task_manager")))
 109                ;; Show documentation as PDF
 110                (("PREFERENCES\\['documentation_style'\\] = 'html'")
 111                 "PREFERENCES['documentation_style'] = 'pdf'") ))))))
 112     (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/")
 113     (synopsis "Analysis software for Molecular Dynamics trajectories")
 114     (description "nMOLDYN is an interactive analysis program for Molecular Dynamics
 115 simulations.  It is especially designed for the computation and decomposition of
 116 neutron scattering spectra, but also computes other quantities.  The software
 117 is currently not actively maintained and works only with Python 2 and
 118 NumPy < 1.9.")
 119     (license license:cecill)))