120 lines
4.9 KiB
Scheme
120 lines
4.9 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages chemistry)
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#:use-module (guix packages)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix download)
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#:use-module (gnu packages gv)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages python)
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#:use-module (guix build-system python))
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(define-public domainfinder
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(package
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(name "domainfinder")
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(version "2.0.5")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://bitbucket.org/khinsen/"
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"domainfinder/downloads/DomainFinder-"
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version ".tar.gz"))
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(sha256
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(base32
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"1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
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(build-system python-build-system)
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(inputs
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`(("python-mmtk" ,python2-mmtk)))
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(arguments
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`(#:python ,python-2
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;; No test suite
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#:tests? #f))
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(home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
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(synopsis "Analysis of dynamical domains in proteins")
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(description "DomainFinder is an interactive program for the determination
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and characterization of dynamical domains in proteins. It can infer dynamical
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domains by comparing two protein structures, or from normal mode analysis on a
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single structure. The software is currently not actively maintained and works
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only with Python 2 and NumPy < 1.9.")
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(license license:cecill-c)))
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(define with-numpy-1.8
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(package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
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(define-public nmoldyn
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(package
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(name "nmoldyn")
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(version "3.0.11")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://bitbucket.org/khinsen/"
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"nmoldyn3/downloads/nMOLDYN-"
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version ".tar.gz"))
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(sha256
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(base32
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"1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a"))))
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(build-system python-build-system)
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(inputs
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`(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
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("python-scientific", python2-scientific)
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("netcdf", netcdf)
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("gv" ,gv)))
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(propagated-inputs
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`(("python-mmtk" ,python2-mmtk)))
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(arguments
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`(#:python ,python-2
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#:tests? #f ; No test suite
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#:phases
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(modify-phases %standard-phases
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(add-before 'build 'create-linux2-directory
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(lambda _
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(mkdir-p "nMOLDYN/linux2")))
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(add-before 'build 'change-PDF-viewer
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "nMOLDYN/Preferences.py"
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;; Set the paths for external executables, substituting
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;; gv for acroread.
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;; There is also vmd_path, but VMD is not free software
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;; and Guix contains currently no free molecular viewer that
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;; could be substituted.
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(("PREFERENCES\\['acroread_path'\\] = ''")
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(format "PREFERENCES['acroread_path'] = '~a'"
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(which "gv")))
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(("PREFERENCES\\['ncdump_path'\\] = ''")
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(format "PREFERENCES['ncdump_path'] = '~a'"
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(which "ncdump")))
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(("PREFERENCES\\['ncgen_path'\\] = ''")
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(format "PREFERENCES['ncgen_path'] = '~a'"
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(which "ncgen3")))
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(("PREFERENCES\\['task_manager_path'\\] = ''")
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(format "PREFERENCES['task_manager_path'] = '~a'"
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(which "task_manager")))
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;; Show documentation as PDF
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(("PREFERENCES\\['documentation_style'\\] = 'html'")
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"PREFERENCES['documentation_style'] = 'pdf'") ))))))
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(home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/")
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(synopsis "Analysis software for Molecular Dynamics trajectories")
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(description "nMOLDYN is an interactive analysis program for Molecular Dynamics
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simulations. It is especially designed for the computation and decomposition of
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neutron scattering spectra, but also computes other quantities. The software
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is currently not actively maintained and works only with Python 2 and
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NumPy < 1.9.")
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(license license:cecill)))
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