341 lines
14 KiB
Scheme
341 lines
14 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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;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
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;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
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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 utils)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (gnu packages)
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#:use-module (gnu packages algebra)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages gl)
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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 pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages qt)
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#:use-module (gnu packages xml)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system python))
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(define-public avogadro
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(package
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(name "avogadro")
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(version "1.2.0")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/cryos/avogadro.git")
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(commit version)))
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(sha256
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(base32 "0258py3lkba85qhs5ynancinyym61vlp0zaq9yrfs3hhnhpzv9n2"))
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(file-name (git-file-name name version))
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(patches
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(search-patches "avogadro-eigen3-update.patch"
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"avogadro-python-eigen-lib.patch"
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"avogadro-boost148.patch"))))
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(build-system cmake-build-system)
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(arguments
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`(#:tests? #f
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#:configure-flags
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(list "-DENABLE_GLSL=ON"
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(string-append "-DPYTHON_LIBRARIES="
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(assoc-ref %build-inputs "python")
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"/lib")
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(string-append "-DPYTHON_INCLUDE_DIRS="
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(assoc-ref %build-inputs "python")
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"/include/python"
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,(version-major+minor
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(package-version python))))
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'patch-python-lib-path
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(lambda* (#:key outputs #:allow-other-keys)
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;; This is necessary to install the Python module in the correct
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;; directory.
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(substitute* "libavogadro/src/python/CMakeLists.txt"
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(("^EXECUTE_PROCESS.*$") "")
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(("^.*from sys import stdout.*$") "")
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(("^.*OUTPUT_VARIABLE.*")
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(string-append "set(PYTHON_LIB_PATH \""
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(assoc-ref outputs "out")
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"/lib/python"
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,(version-major+minor
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(package-version python))
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"/site-packages\")")))
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#t))
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(add-after 'install 'wrap-program
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(lambda* (#:key inputs outputs #:allow-other-keys)
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;; Make sure 'avogadro' runs with the correct PYTHONPATH.
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(let* ((out (assoc-ref outputs "out")))
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(setenv "PYTHONPATH"
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(string-append
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(assoc-ref outputs "out")
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"/lib/python"
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,(version-major+minor
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(package-version python))
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"/site-packages:"
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(getenv "PYTHONPATH")))
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(wrap-program (string-append out "/bin/avogadro")
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`("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
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#t)))))
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(native-inputs
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`(("doxygen" ,doxygen)
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("pkg-config" ,pkg-config)))
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(inputs
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`(("boost" ,boost)
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("eigen" ,eigen)
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("glew" ,glew)
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("openbabel" ,openbabel)
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("python" ,python-2)
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("python-numpy" ,python2-numpy)
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("python-pyqt" ,python2-pyqt-4)
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("python-sip" ,python2-sip)
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("qt" ,qt-4)
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("zlib" ,zlib)))
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(home-page "https://avogadro.cc")
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(synopsis "Advanced molecule editor")
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(description
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"Avogadro is an advanced molecule editor and visualizer designed for use
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in computational chemistry, molecular modeling, bioinformatics, materials
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science, and related areas. It offers flexible high quality rendering and a
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powerful plugin architecture.")
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(license license:gpl2+)))
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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.html")
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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-public inchi
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(package
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(name "inchi")
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(version "1.05")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://www.inchi-trust.org/download/"
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(string-join (string-split version #\.) "")
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"/INCHI-1-SRC.zip"))
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(sha256
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(base32
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"081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
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(file-name (string-append name "-" version ".zip"))))
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(build-system gnu-build-system)
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(arguments
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'(#:tests? #f ; no check target
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#:phases
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(modify-phases %standard-phases
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(delete 'configure) ; no configure script
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(add-before 'build 'chdir-to-build-directory
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(lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
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(add-after 'build 'build-library
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(lambda _
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(chdir "../../../INCHI_API/libinchi/gcc")
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(invoke "make")))
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(replace 'install
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin"))
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(doc (string-append out "/share/doc/inchi"))
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(include-dir (string-append out "/include/inchi"))
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(lib (string-append out "/lib/inchi"))
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(inchi-doc (assoc-ref inputs "inchi-doc"))
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(unzip (string-append (assoc-ref inputs "unzip")
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"/bin/unzip")))
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(chdir "../../..")
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;; Install binary.
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(with-directory-excursion "INCHI_EXE/bin/Linux"
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(rename-file "inchi-1" "inchi")
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(install-file "inchi" bin))
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;; Install libraries.
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(with-directory-excursion "INCHI_API/bin/Linux"
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(for-each (lambda (file)
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(install-file file lib))
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(find-files "." "libinchi\\.so\\.1\\.*")))
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;; Install header files.
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(with-directory-excursion "INCHI_BASE/src"
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(for-each (lambda (file)
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(install-file file include-dir))
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(find-files "." "\\.h$")))
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;; Install documentation.
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(mkdir-p doc)
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(invoke unzip "-j" "-d" doc inchi-doc)
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#t))))))
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(native-inputs
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`(("unzip" ,unzip)
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("inchi-doc"
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,(origin
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(method url-fetch)
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(uri (string-append "http://www.inchi-trust.org/download/"
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(string-join (string-split version #\.) "")
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"/INCHI-1-DOC.zip"))
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(sha256
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(base32
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"1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
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(file-name (string-append name "-" version ".zip"))))))
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(home-page "https://www.inchi-trust.org")
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(synopsis "Utility for manipulating machine-readable chemical structures")
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(description
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"The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
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chemical structures into machine-readable strings of information. InChIs are
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unique to the compound they describe and can encode absolute stereochemistry
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making chemicals and chemistry machine-readable and discoverable. A simple
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analogy is that InChI is the bar-code for chemistry and chemical structures.")
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(license (license:non-copyleft
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"file://LICENCE"
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"See LICENCE in the distribution."))))
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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 git-fetch)
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(uri (git-reference
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(url "https://github.com/khinsen/nMOLDYN3")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r"))))
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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.html")
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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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(define-public openbabel
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(package
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(name "openbabel")
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(version "2.4.1")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://sourceforge/" name "/" name "/"
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version "/" name "-" version ".tar.gz"))
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(sha256
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(base32
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"1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
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(patches
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(search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
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(build-system cmake-build-system)
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(arguments
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`(#:configure-flags
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(list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
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(string-append "-DINCHI_LIBRARY="
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(assoc-ref %build-inputs "inchi")
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"/lib/inchi/libinchi.so.1")
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(string-append "-DINCHI_INCLUDE_DIR="
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(assoc-ref %build-inputs "inchi") "/include/inchi"))
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#:test-target "test"))
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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(inputs
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`(("eigen" ,eigen)
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("inchi" ,inchi)
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("libxml2" ,libxml2)
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("zlib" ,zlib)))
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(home-page "http://openbabel.org/wiki/Main_Page")
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(synopsis "Chemistry data manipulation toolbox")
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(description
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"Open Babel is a chemical toolbox designed to speak the many languages of
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chemical data. It's a collaborative project allowing anyone to search, convert,
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analyze, or store data from molecular modeling, chemistry, solid-state
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materials, biochemistry, or related areas.")
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(license license:gpl2)))
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