571 lines
23 KiB
Scheme
571 lines
23 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, 2021 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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;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
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;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.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 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 autotools)
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#:use-module (gnu packages backup)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages check)
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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 fontutils)
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#:use-module (gnu packages gl)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages gv)
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#:use-module (gnu packages image)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages perl)
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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 serialization)
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#:use-module (gnu packages sphinx)
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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 avogadrolibs
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(package
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(name "avogadrolibs")
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(version "1.93.0")
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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/OpenChemistry/avogadrolibs")
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(commit version)))
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(sha256
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(base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39"))
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(file-name (git-file-name name version))))
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(build-system cmake-build-system)
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(native-inputs
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(list eigen
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mmtf-cpp
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msgpack
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googletest
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pkg-config
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pybind11))
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(inputs
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(list glew
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libarchive
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libmsym
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molequeue
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python
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spglib
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qtbase-5))
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(arguments
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'(#:configure-flags (list "-DENABLE_TESTING=ON"
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(string-append "-DSPGLIB_INCLUDE_DIR="
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(assoc-ref %build-inputs "spglib")
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"/include"))))
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(home-page "https://www.openchemistry.org/projects/avogadro2/")
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(synopsis "Libraries for chemistry, bioinformatics, and related areas")
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(description
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"Avogadro libraries provide 3D rendering, visualization, analysis and data
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processing useful in computational chemistry, molecular modeling,
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bioinformatics, materials science, and related areas.")
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(license license:bsd-3)))
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(define-public avogadro2
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(package
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(name "avogadro2")
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(version "1.93.0")
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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/OpenChemistry/avogadroapp")
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(commit version)))
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(sha256
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(base32
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"1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
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(file-name (git-file-name name version))))
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(build-system cmake-build-system)
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(native-inputs
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(list eigen pkg-config))
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(inputs
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(list avogadrolibs hdf5 molequeue qtbase-5))
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;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
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(arguments
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'(#:tests? #f))
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(home-page "https://www.openchemistry.org/projects/avogadro2/")
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(synopsis "Advanced molecule editor")
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(description
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"Avogadro 2 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:bsd-3)))
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(define-public inchi
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(package
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(name "inchi")
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;; Update the inchi-doc native input when updating inchi.
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(version "1.06")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://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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"1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28"))
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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 (search-input-file inputs "/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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"1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f"))
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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-public libmsym
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(package
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(name "libmsym")
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(version "0.2.3")
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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/mcodev31/libmsym")
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(commit (string-append "v" version))))
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(sha256
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(base32
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"0a9j28irdsr461qpzlc9z1yjyb9kp64fh5zw7ylspc9zn3189qwk"))
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(file-name (git-file-name name version))))
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(build-system cmake-build-system)
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(arguments
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'(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")
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#:tests? #f)) ; no check target
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(home-page "https://github.com/mcodev31/libmsym")
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(synopsis "C library dealing with point group symmetry in molecules")
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(description "libmsym is a C library dealing with point group symmetry in
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molecules.")
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(license license:expat)))
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(define-public mmtf-cpp
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(package
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(name "mmtf-cpp")
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(version "1.0.0")
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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/rcsb/mmtf-cpp")
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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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"17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l"))))
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(build-system cmake-build-system)
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;; Tests require the soon-to-be-deprecated version 1 of the catch-framework.
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(arguments
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'(#:tests? #f))
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(home-page "https://mmtf.rcsb.org/")
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(synopsis "C++ API for the Macromolecular Transmission Format")
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(description "This package is a library for the
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@acronym{MMTF,macromolecular transmission format}, a binary encoding of
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biological structures.")
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(license license:expat)))
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(define-public molequeue
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(package
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(name "molequeue")
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(version "0.9.0")
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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://github.com/OpenChemistry/molequeue/"
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"releases/download/" version "/molequeue-"
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version ".tar.bz2"))
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(sha256
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(base32
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"1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998"))))
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(build-system cmake-build-system)
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(inputs
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(list qtbase-5))
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(arguments
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'(#:configure-flags '("-DENABLE_TESTING=ON")
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'patch-tests
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(lambda _
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;; TODO: Fix/enable the failing message and clientserver tests.
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;; In the message test, the floating-point value "5.36893473232" on
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;; line 165 of molequeue/app/testing/messagetest.cpp should
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;; (apparently) be truncated, but it is not.
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(substitute* "molequeue/app/testing/messagetest.cpp"
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(("5\\.36893473232") "5.36893"))
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;; It is unclear why the clientserver test fails, so it is
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;; completely disabled.
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(substitute* "molequeue/app/testing/CMakeLists.txt"
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((".*clientserver.*") ""))
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#t))
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(add-before 'check 'set-display
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(lambda _
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;; Make Qt render "offscreen" for the sake of tests.
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(setenv "QT_QPA_PLATFORM" "offscreen")
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#t)))))
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(home-page "https://www.openchemistry.org/projects/molequeue/")
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(synopsis "Application for coordinating computational jobs")
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(description "MoleQueue is a system-tray resident desktop application for
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abstracting, managing, and coordinating the execution of tasks both locally and
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on remote computational resources. Users can set up local and remote queues
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that describe where the task will be executed. Each queue can have programs,
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with templates to facilitate the execution of the program. Input files can be
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staged, and output files collected using a standard interface.")
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(license license:bsd-3)))
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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 tng
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(package
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(name "tng")
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(version "1.8.2")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/gromacs/tng")
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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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"1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
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(build-system cmake-build-system)
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(inputs
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(list zlib))
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'remove-bundled-zlib
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(lambda _
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(delete-file-recursively "external")
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#t))
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(replace 'check
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(lambda _
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(invoke "../build/bin/tests/tng_testing")
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#t)))))
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(home-page "https://github.com/gromacs/tng")
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(synopsis "Trajectory Next Generation binary format manipulation library")
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(description "TRAJNG (Trajectory next generation) is a program library for
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handling molecular dynamics (MD) trajectories. It can store coordinates, and
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optionally velocities and the H-matrix. Coordinates and velocities are
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stored with user-specified precision.")
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(license license:bsd-3)))
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(define-public gromacs
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(package
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(name "gromacs")
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(version "2020.2")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
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version ".tar.gz"))
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(sha256
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(base32
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"1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
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;; Our version of tinyxml2 is far newer than the bundled one and
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;; require fixing `testutils' code. See patch header for more info
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(patches (search-patches "gromacs-tinyxml2.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 "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
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;; Unbundling
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"-DGMX_USE_LMFIT=EXTERNAL"
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"-DGMX_BUILD_OWN_FFTW=off"
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"-DGMX_EXTERNAL_BLAS=on"
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"-DGMX_EXTERNAL_LAPACK=on"
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"-DGMX_EXTERNAL_TNG=on"
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"-DGMX_EXTERNAL_ZLIB=on"
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"-DGMX_EXTERNAL_TINYXML2=on"
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(string-append "-DTinyXML2_DIR="
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(assoc-ref %build-inputs "tinyxml2"))
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;; Workaround for cmake/FindSphinx.cmake version parsing that does
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;; not understand the guix-wrapped `sphinx-build --version' answer
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(string-append "-DSPHINX_EXECUTABLE_VERSION="
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,(package-version python-sphinx)))
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#:phases
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|
(modify-phases %standard-phases
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|
(add-after 'unpack 'fixes
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(lambda* (#:key inputs #:allow-other-keys)
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;; Still bundled: part of gromacs, source behind registration
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;; but free software anyways
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;;(delete-file-recursively "src/external/vmd_molfile")
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;; Still bundled: threads-based OpenMPI-compatible fallback
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;; designed to be bundled like that
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;;(delete-file-recursively "src/external/thread_mpi")
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;; Unbundling
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|
(delete-file-recursively "src/external/lmfit")
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|
(delete-file-recursively "src/external/clFFT")
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|
(delete-file-recursively "src/external/fftpack")
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(delete-file-recursively "src/external/build-fftw")
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(delete-file-recursively "src/external/tng_io")
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(delete-file-recursively "src/external/tinyxml2")
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(delete-file-recursively "src/external/googletest")
|
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(copy-recursively (assoc-ref inputs "googletest-source")
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|
"src/external/googletest")
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|
;; This test warns about the build host hardware, disable
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|
(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
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(("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
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"void __guix_disabled()"))
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#t)))))
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(native-inputs
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`(("doxygen" ,doxygen)
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("googletest-source" ,(package-source googletest))
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("graphviz" ,graphviz)
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("pkg-config" ,pkg-config)
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("python" ,python)
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("python-pygments" ,python-pygments)
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("python-sphinx" ,python-sphinx)))
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(inputs
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(list fftwf
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`(,hwloc-2 "lib")
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lmfit
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openblas
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perl
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tinyxml2
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tng))
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(home-page "http://www.gromacs.org/")
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(synopsis "Molecular dynamics software package")
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(description "GROMACS is a versatile package to perform molecular dynamics,
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i.e. simulate the Newtonian equations of motion for systems with hundreds to
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millions of particles. It is primarily designed for biochemical molecules like
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proteins, lipids and nucleic acids that have a lot of complicated bonded
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interactions, but since GROMACS is extremely fast at calculating the nonbonded
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interactions (that usually dominate simulations) many groups are also using it
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for research on non-biological systems, e.g. polymers. GROMACS supports all the
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usual algorithms you expect from a modern molecular dynamics implementation.")
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(license license:lgpl2.1+)))
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(define-public openbabel
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(package
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(name "openbabel")
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(version "3.1.1")
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(source (origin
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(method url-fetch)
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|
(uri (string-append "https://github.com/openbabel/openbabel/"
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"releases/download/openbabel-"
|
|
(string-replace-substring version "." "-")
|
|
"/openbabel-" version "-source.tar.bz2"))
|
|
(sha256
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|
(base32
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"0s0f4zib8vshfaywsr5bjjz55jwsg6yiz2qw4i5jm8wysn0q7v56"))))
|
|
(build-system cmake-build-system)
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|
(arguments
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`(;; FIXME: Disable tests on i686 to work around
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|
;; https://github.com/openbabel/openbabel/issues/2041.
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|
#:tests? ,(or (%current-target-system)
|
|
(not (string=? "i686-linux" (%current-system))))
|
|
#:configure-flags
|
|
(list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
|
|
(string-append "-DINCHI_LIBRARY="
|
|
(assoc-ref %build-inputs "inchi")
|
|
"/lib/inchi/libinchi.so.1")
|
|
(string-append "-DINCHI_INCLUDE_DIR="
|
|
(assoc-ref %build-inputs "inchi") "/include/inchi"))
|
|
#:test-target "test"))
|
|
(native-inputs
|
|
(list pkg-config))
|
|
(inputs
|
|
(list eigen inchi libxml2 zlib))
|
|
(home-page "http://openbabel.org/wiki/Main_Page")
|
|
(synopsis "Chemistry data manipulation toolbox")
|
|
(description
|
|
"Open Babel is a chemical toolbox designed to speak the many languages of
|
|
chemical data. It's a collaborative project allowing anyone to search, convert,
|
|
analyze, or store data from molecular modeling, chemistry, solid-state
|
|
materials, biochemistry, or related areas.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public spglib
|
|
(package
|
|
(name "spglib")
|
|
(version "1.16.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/spglib/spglib")
|
|
(commit (string-append "v" version))))
|
|
(sha256
|
|
(base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
|
|
(file-name (git-file-name name version))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
'(#:test-target "check"
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'patch-header-install-dir
|
|
(lambda _
|
|
;; As of the writing of this package, CMake and GNU build systems
|
|
;; install the header to two different location. This patch makes
|
|
;; the CMake build system's choice of header directory compatible
|
|
;; with the GNU build system's choice and with what avogadrolibs
|
|
;; expects.
|
|
;; See https://github.com/spglib/spglib/issues/75 and the relevant
|
|
;; part of https://github.com/OpenChemistry/avogadroapp/issues/97.
|
|
(substitute* "CMakeLists.txt"
|
|
(("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir)
|
|
(string-append include-dir "/spglib")))
|
|
#t)))))
|
|
(home-page "https://spglib.github.io/spglib/index.html")
|
|
(synopsis "Library for crystal symmetry search")
|
|
(description "Spglib is a library for finding and handling crystal
|
|
symmetries written in C. Spglib can be used to:
|
|
|
|
@enumerate
|
|
@item Find symmetry operations
|
|
@item Identify space-group type
|
|
@item Wyckoff position assignment
|
|
@item Refine crystal structure
|
|
@item Find a primitive cell
|
|
@item Search irreducible k-points
|
|
@end enumerate")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-pymol
|
|
(package
|
|
(name "python-pymol")
|
|
(version "2.5.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/schrodinger/pymol-open-source")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "08zmfgclkbjkqjpq8xs1mphs1i8rpqj76mcw7m2mrhvma5qj1nr5"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:configure-flags
|
|
(list "--glut" "--testing")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'make-reproducible
|
|
(lambda _
|
|
(substitute* "create_shadertext.py"
|
|
(("time\\.time\\(\\)") "0"))))
|
|
(add-after 'unpack 'add-include-directories
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(setenv "CPLUS_INCLUDE_PATH"
|
|
(string-append (assoc-ref inputs "freetype")
|
|
"/include/freetype2:"
|
|
(assoc-ref inputs "libxml2")
|
|
"/include/libxml2:"
|
|
(getenv "CPLUS_INCLUDE_PATH")))))
|
|
;; The setup.py script does not support one of the Python build
|
|
;; system's default flags, "--single-version-externally-managed".
|
|
(replace 'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(invoke "python" "setup.py" "install"
|
|
(string-append "--prefix=" (assoc-ref outputs "out"))
|
|
"--root=/"))))))
|
|
(inputs
|
|
(list freetype
|
|
libpng
|
|
freeglut
|
|
glew
|
|
libxml2
|
|
mmtf-cpp
|
|
msgpack
|
|
python-pyqt
|
|
glm
|
|
netcdf))
|
|
(native-inputs
|
|
(list catch-framework2 python-setuptools))
|
|
(home-page "https://pymol.org")
|
|
(synopsis "Molecular visualization system")
|
|
(description "PyMOL is a capable molecular viewer and renderer. It can be
|
|
used to prepare publication-quality figures, to share interactive results with
|
|
your colleagues, or to generate pre-rendered animations.")
|
|
(license license:bsd-3)))
|