2018-01-05 11:06:22 -05:00
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
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2021-01-22 21:32:41 -05:00
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;;; Copyright © 2018, 2021 Kei Kebreau <kkebreau@posteo.net>
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2018-12-16 15:52:52 -05:00
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;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
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2018-12-23 04:58:55 -05:00
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;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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2020-03-05 03:31:56 -05:00
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;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
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2020-05-03 18:32:38 -04:00
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;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
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2021-09-20 10:00:37 -04:00
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;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
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2024-01-28 18:01:58 -05:00
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;;; Copyright © 2022, 2023, 2024 David Elsing <david.elsing@posteo.net>
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2018-01-05 11:06:22 -05:00
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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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2018-12-16 15:52:52 -05:00
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#:use-module (guix utils)
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2018-01-05 11:06:22 -05:00
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix download)
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2022-10-13 17:04:16 -04:00
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#:use-module (guix gexp)
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2018-12-23 04:58:55 -05:00
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#:use-module (guix git-download)
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2018-07-22 10:19:22 -04:00
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#:use-module (gnu packages)
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2018-07-13 22:44:54 -04:00
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#:use-module (gnu packages algebra)
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2021-01-22 21:32:41 -05:00
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#:use-module (gnu packages autotools)
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2021-01-23 12:23:11 -05:00
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#:use-module (gnu packages backup)
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2022-10-13 17:04:24 -04:00
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#:use-module (gnu packages base)
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2022-10-13 17:04:18 -04:00
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#:use-module (gnu packages bison)
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2018-07-18 14:11:16 -04:00
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#:use-module (gnu packages boost)
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2020-05-03 18:39:36 -04:00
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#:use-module (gnu packages check)
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2018-07-13 09:35:27 -04:00
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#:use-module (gnu packages compression)
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2022-10-13 17:04:17 -04:00
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#:use-module (gnu packages c)
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2022-10-13 17:04:16 -04:00
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#:use-module (gnu packages cpp)
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2018-07-18 14:11:16 -04:00
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#:use-module (gnu packages documentation)
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2022-10-13 17:04:18 -04:00
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#:use-module (gnu packages flex)
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2022-10-13 17:04:24 -04:00
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#:use-module (gnu packages fonts)
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2021-09-20 10:00:37 -04:00
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#:use-module (gnu packages fontutils)
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2022-10-13 17:04:21 -04:00
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#:use-module (gnu packages gcc)
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2018-07-18 14:11:16 -04:00
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#:use-module (gnu packages gl)
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2020-05-03 18:39:36 -04:00
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#:use-module (gnu packages graphviz)
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2022-10-13 17:04:24 -04:00
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#:use-module (gnu packages gtk)
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2018-01-05 11:14:24 -05:00
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#:use-module (gnu packages gv)
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2021-09-20 10:00:37 -04:00
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#:use-module (gnu packages image)
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2018-01-05 11:14:24 -05:00
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#:use-module (gnu packages maths)
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2020-05-03 18:39:36 -04:00
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages perl)
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2018-07-13 22:44:54 -04:00
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#:use-module (gnu packages pkg-config)
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2018-01-05 11:06:22 -05:00
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#:use-module (gnu packages python)
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2022-04-23 05:07:58 -04:00
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#:use-module (gnu packages python-build)
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gnu: Separate Python core packages from the rest.
* gnu/packages/python.scm: Move hundreds of package definitions from here...
* gnu/packages/python-xyz.scm: ...to this new module.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/ada.scm,
gnu/packages/admin.scm,
gnu/packages/android.scm,
gnu/packages/audio.scm,
gnu/packages/backup.scm,
gnu/packages/benchmark.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/bittorrent.scm,
gnu/packages/calendar.scm,
gnu/packages/check.scm,
gnu/packages/chemistry.scm,
gnu/packages/cluster.scm,
gnu/packages/compression.scm,
gnu/packages/connman.scm,
gnu/packages/crypto.scm,
gnu/packages/cups.scm,
gnu/packages/databases.scm,
gnu/packages/dav.scm,
gnu/packages/direct-connect.scm,
gnu/packages/disk.scm,
gnu/packages/django.scm,
gnu/packages/dlang.scm,
gnu/packages/docker.scm,
gnu/packages/ebook.scm,
gnu/packages/elf.scm,
gnu/packages/emacs.scm,
gnu/packages/emulators.scm,
gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm,
gnu/packages/finance.scm,
gnu/packages/fltk.scm,
gnu/packages/fontutils.scm,
gnu/packages/freedesktop.scm,
gnu/packages/game-development.scm,
gnu/packages/games.scm,
gnu/packages/geo.scm,
gnu/packages/gl.scm,
gnu/packages/glib.scm,
gnu/packages/gnome.scm,
gnu/packages/gnupg.scm,
gnu/packages/gnuzilla.scm,
gnu/packages/graph.scm,
gnu/packages/graphics.scm,
gnu/packages/graphviz.scm,
gnu/packages/gtk.scm,
gnu/packages/ham-radio.scm,
gnu/packages/image-processing.scm,
gnu/packages/image-viewers.scm,
gnu/packages/image.scm,
gnu/packages/irc.scm,
gnu/packages/jrnl.scm,
gnu/packages/julia.scm,
gnu/packages/kde-frameworks.scm,
gnu/packages/key-mon.scm,
gnu/packages/libffi.scm,
gnu/packages/libreoffice.scm,
gnu/packages/libusb.scm,
gnu/packages/lirc.scm,
gnu/packages/logging.scm,
gnu/packages/machine-learning.scm,
gnu/packages/mail.scm,
gnu/packages/mate.scm,
gnu/packages/maths.scm,
gnu/packages/medical.scm,
gnu/packages/messaging.scm,
gnu/packages/monitoring.scm,
gnu/packages/mp3.scm,
gnu/packages/mpd.scm,
gnu/packages/music.scm,
gnu/packages/networking.scm,
gnu/packages/nutrition.scm,
gnu/packages/openldap.scm,
gnu/packages/openstack.scm,
gnu/packages/package-management.scm,
gnu/packages/password-utils.scm,
gnu/packages/patchutils.scm,
gnu/packages/pdf.scm,
gnu/packages/photo.scm,
gnu/packages/polkit.scm,
gnu/packages/protobuf.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/qt.scm,
gnu/packages/rdf.scm,
gnu/packages/ruby.scm,
gnu/packages/search.scm,
gnu/packages/selinux.scm,
gnu/packages/serialization.scm,
gnu/packages/shells.scm,
gnu/packages/simulation.scm,
gnu/packages/ssh.scm,
gnu/packages/statistics.scm,
gnu/packages/storage.scm,
gnu/packages/sync.scm,
gnu/packages/terminals.scm,
gnu/packages/textutils.scm,
gnu/packages/time.scm,
gnu/packages/tls.scm,
gnu/packages/tor.scm,
gnu/packages/tryton.scm,
gnu/packages/version-control.scm,
gnu/packages/video.scm,
gnu/packages/virtualization.scm,
gnu/packages/vpn.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm,
gnu/packages/wicd.scm,
gnu/packages/xdisorg.scm,
gnu/packages/xorg.scm: Update module references.
2019-01-15 08:21:30 -05:00
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#:use-module (gnu packages python-xyz)
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2018-07-18 14:11:16 -04:00
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#:use-module (gnu packages qt)
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2021-01-23 12:23:11 -05:00
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#:use-module (gnu packages serialization)
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2020-05-03 18:39:36 -04:00
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#:use-module (gnu packages sphinx)
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2022-10-13 17:04:24 -04:00
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#:use-module (gnu packages sqlite)
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2022-10-13 17:04:16 -04:00
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#:use-module (gnu packages stb)
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2022-10-13 17:04:21 -04:00
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#:use-module (gnu packages tex)
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2022-10-13 17:04:18 -04:00
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#:use-module (gnu packages web)
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2018-07-13 22:44:54 -04:00
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#:use-module (gnu packages xml)
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#:use-module (guix build-system cmake)
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2018-07-13 09:35:27 -04:00
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#:use-module (guix build-system gnu)
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2018-01-05 11:06:22 -05:00
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#:use-module (guix build-system python))
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2021-01-23 12:23:11 -05:00
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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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2021-12-13 11:18:24 -05:00
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(list eigen
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mmtf-cpp
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googletest
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pkg-config
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pybind11))
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2021-01-23 12:23:11 -05:00
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(inputs
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2021-12-13 11:18:24 -05:00
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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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2021-01-23 12:23:11 -05:00
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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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2021-01-23 17:29:50 -05:00
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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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2021-12-13 11:18:24 -05:00
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(list eigen pkg-config))
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2021-01-23 17:29:50 -05:00
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(inputs
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2021-12-13 11:18:24 -05:00
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(list avogadrolibs hdf5 molequeue qtbase-5))
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2021-01-23 17:29:50 -05:00
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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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2018-07-13 09:35:27 -04:00
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(define-public inchi
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(package
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(name "inchi")
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2021-01-26 00:02:01 -05:00
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;; Update the inchi-doc native input when updating inchi.
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(version "1.06")
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2018-07-13 09:35:27 -04:00
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(source (origin
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(method url-fetch)
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2021-01-26 00:02:01 -05:00
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(uri (string-append "https://www.inchi-trust.org/download/"
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2018-07-13 09:35:27 -04:00
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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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2021-01-26 00:02:01 -05:00
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"1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28"))
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2018-07-13 09:35:27 -04:00
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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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2021-07-16 10:50:56 -04:00
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(unzip (search-input-file inputs "/bin/unzip")))
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2018-07-13 09:35:27 -04:00
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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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2021-01-26 00:02:01 -05:00
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"1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f"))
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2018-07-13 09:35:27 -04:00
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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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2021-01-23 14:39:30 -05:00
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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"))
|
|
|
|
(file-name (git-file-name name version))))
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
(arguments
|
|
|
|
'(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")
|
|
|
|
#:tests? #f)) ; no check target
|
|
|
|
(home-page "https://github.com/mcodev31/libmsym")
|
|
|
|
(synopsis "C library dealing with point group symmetry in molecules")
|
|
|
|
(description "libmsym is a C library dealing with point group symmetry in
|
|
|
|
molecules.")
|
|
|
|
(license license:expat)))
|
|
|
|
|
2021-01-22 22:27:21 -05:00
|
|
|
(define-public mmtf-cpp
|
|
|
|
(package
|
|
|
|
(name "mmtf-cpp")
|
2023-08-17 17:31:18 -04:00
|
|
|
(version "1.1.0")
|
2021-01-22 22:27:21 -05:00
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
|
|
|
(url "https://github.com/rcsb/mmtf-cpp")
|
|
|
|
(commit (string-append "v" version))))
|
|
|
|
(file-name (git-file-name name version))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2023-08-17 17:31:18 -04:00
|
|
|
"0rs2f1ppgqz663c3m22p8wsq6z839bj59zy29chci46ypfhwv6ph"))))
|
2021-01-22 22:27:21 -05:00
|
|
|
(build-system cmake-build-system)
|
|
|
|
;; Tests require the soon-to-be-deprecated version 1 of the catch-framework.
|
2023-08-17 17:31:18 -04:00
|
|
|
(arguments '(#:tests? #f))
|
|
|
|
;; There is no support for modern msgpack versions yet (see:
|
|
|
|
;; https://github.com/rcsb/mmtf-cpp/issues/44).
|
2023-08-17 17:29:08 -04:00
|
|
|
(propagated-inputs (list msgpack-3)) ;included by mmtf/structure_data.hpp
|
2021-01-22 22:27:21 -05:00
|
|
|
(home-page "https://mmtf.rcsb.org/")
|
|
|
|
(synopsis "C++ API for the Macromolecular Transmission Format")
|
|
|
|
(description "This package is a library for the
|
|
|
|
@acronym{MMTF,macromolecular transmission format}, a binary encoding of
|
|
|
|
biological structures.")
|
|
|
|
(license license:expat)))
|
|
|
|
|
2021-01-22 23:44:15 -05:00
|
|
|
(define-public molequeue
|
|
|
|
(package
|
|
|
|
(name "molequeue")
|
|
|
|
(version "0.9.0")
|
|
|
|
(source
|
|
|
|
(origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append "https://github.com/OpenChemistry/molequeue/"
|
|
|
|
"releases/download/" version "/molequeue-"
|
|
|
|
version ".tar.bz2"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998"))))
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
(inputs
|
2021-12-13 11:18:24 -05:00
|
|
|
(list qtbase-5))
|
2021-01-22 23:44:15 -05:00
|
|
|
(arguments
|
|
|
|
'(#:configure-flags '("-DENABLE_TESTING=ON")
|
|
|
|
#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(add-after 'unpack 'patch-tests
|
|
|
|
(lambda _
|
|
|
|
;; TODO: Fix/enable the failing message and clientserver tests.
|
|
|
|
;; In the message test, the floating-point value "5.36893473232" on
|
|
|
|
;; line 165 of molequeue/app/testing/messagetest.cpp should
|
|
|
|
;; (apparently) be truncated, but it is not.
|
|
|
|
(substitute* "molequeue/app/testing/messagetest.cpp"
|
|
|
|
(("5\\.36893473232") "5.36893"))
|
|
|
|
;; It is unclear why the clientserver test fails, so it is
|
|
|
|
;; completely disabled.
|
|
|
|
(substitute* "molequeue/app/testing/CMakeLists.txt"
|
|
|
|
((".*clientserver.*") ""))
|
|
|
|
#t))
|
|
|
|
(add-before 'check 'set-display
|
|
|
|
(lambda _
|
|
|
|
;; Make Qt render "offscreen" for the sake of tests.
|
|
|
|
(setenv "QT_QPA_PLATFORM" "offscreen")
|
|
|
|
#t)))))
|
|
|
|
(home-page "https://www.openchemistry.org/projects/molequeue/")
|
|
|
|
(synopsis "Application for coordinating computational jobs")
|
|
|
|
(description "MoleQueue is a system-tray resident desktop application for
|
|
|
|
abstracting, managing, and coordinating the execution of tasks both locally and
|
|
|
|
on remote computational resources. Users can set up local and remote queues
|
|
|
|
that describe where the task will be executed. Each queue can have programs,
|
|
|
|
with templates to facilitate the execution of the program. Input files can be
|
|
|
|
staged, and output files collected using a standard interface.")
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
2020-05-03 18:32:38 -04:00
|
|
|
(define-public tng
|
|
|
|
(package
|
|
|
|
(name "tng")
|
|
|
|
(version "1.8.2")
|
|
|
|
(source (origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
gnu: Remove ".git" from "https://github/…/….git".
Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix
swh) would sometimes return #f for these because the ".git" URLs are
redirects to the non-".git" URLs. Consequently, 'guix lint -c archival'
would keep saying "scheduled Software Heritage archival"; likewise, the
fallback download code would fail.
* gnu/packages/ada.scm,
gnu/packages/admin.scm,
gnu/packages/aidc.scm,
gnu/packages/algebra.scm,
gnu/packages/android.scm,
gnu/packages/animation.scm,
gnu/packages/arcan.scm,
gnu/packages/assembly.scm,
gnu/packages/audio.scm,
gnu/packages/authentication.scm,
gnu/packages/avr.scm,
gnu/packages/axoloti.scm,
gnu/packages/backup.scm,
gnu/packages/bash.scm,
gnu/packages/benchmark.scm,
gnu/packages/bioconductor.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/bittorrent.scm,
gnu/packages/boost.scm,
gnu/packages/build-tools.scm,
gnu/packages/c.scm,
gnu/packages/calendar.scm,
gnu/packages/cdrom.scm,
gnu/packages/check.scm,
gnu/packages/chemistry.scm,
gnu/packages/chez.scm,
gnu/packages/clojure.scm,
gnu/packages/code.scm,
gnu/packages/compression.scm,
gnu/packages/compton.scm,
gnu/packages/coq.scm,
gnu/packages/cpp.scm,
gnu/packages/cran.scm,
gnu/packages/crypto.scm,
gnu/packages/curl.scm,
gnu/packages/databases.scm,
gnu/packages/datastructures.scm,
gnu/packages/debug.scm,
gnu/packages/disk.scm,
gnu/packages/distributed.scm,
gnu/packages/django.scm,
gnu/packages/dlang.scm,
gnu/packages/dns.scm,
gnu/packages/docker.scm,
gnu/packages/education.scm,
gnu/packages/efi.scm,
gnu/packages/elixir.scm,
gnu/packages/emacs-xyz.scm,
gnu/packages/embedded.scm,
gnu/packages/emulators.scm,
gnu/packages/engineering.scm,
gnu/packages/erlang.scm,
gnu/packages/fabric-management.scm,
gnu/packages/file-systems.scm,
gnu/packages/finance.scm,
gnu/packages/firmware.scm,
gnu/packages/flashing-tools.scm,
gnu/packages/fonts.scm,
gnu/packages/fontutils.scm,
gnu/packages/fpga.scm,
gnu/packages/game-development.scm,
gnu/packages/games.scm,
gnu/packages/genealogy.scm,
gnu/packages/genimage.scm,
gnu/packages/geo.scm,
gnu/packages/gimp.scm,
gnu/packages/gl.scm,
gnu/packages/gnome-xyz.scm,
gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm,
gnu/packages/golang.scm,
gnu/packages/gpodder.scm,
gnu/packages/graph.scm,
gnu/packages/graphics.scm,
gnu/packages/graphviz.scm,
gnu/packages/groff.scm,
gnu/packages/groovy.scm,
gnu/packages/gtk.scm,
gnu/packages/guile-xyz.scm,
gnu/packages/guile.scm,
gnu/packages/hardware.scm,
gnu/packages/haskell-apps.scm,
gnu/packages/haskell-xyz.scm,
gnu/packages/hexedit.scm,
gnu/packages/i2p.scm,
gnu/packages/ibus.scm,
gnu/packages/image-processing.scm,
gnu/packages/image-viewers.scm,
gnu/packages/image.scm,
gnu/packages/ipfs.scm,
gnu/packages/java-graphics.scm,
gnu/packages/java-maths.scm,
gnu/packages/java.scm,
gnu/packages/javascript.scm,
gnu/packages/jrnl.scm,
gnu/packages/julia.scm,
gnu/packages/jupyter.scm,
gnu/packages/kodi.scm,
gnu/packages/language.scm,
gnu/packages/lego.scm,
gnu/packages/less.scm,
gnu/packages/libusb.scm,
gnu/packages/linux.scm,
gnu/packages/lirc.scm,
gnu/packages/lisp-xyz.scm,
gnu/packages/llvm.scm,
gnu/packages/logging.scm,
gnu/packages/lolcode.scm,
gnu/packages/lua.scm,
gnu/packages/lxde.scm,
gnu/packages/lxqt.scm,
gnu/packages/machine-learning.scm,
gnu/packages/mail.scm,
gnu/packages/markup.scm,
gnu/packages/maths.scm,
gnu/packages/maven.scm,
gnu/packages/mes.scm,
gnu/packages/messaging.scm,
gnu/packages/monitoring.scm,
gnu/packages/mpd.scm,
gnu/packages/music.scm,
gnu/packages/networking.scm,
gnu/packages/node-xyz.scm,
gnu/packages/ocaml.scm,
gnu/packages/ocr.scm,
gnu/packages/onc-rpc.scm,
gnu/packages/opencl.scm,
gnu/packages/opencog.scm,
gnu/packages/pantheon.scm,
gnu/packages/password-utils.scm,
gnu/packages/patchutils.scm,
gnu/packages/pdf.scm,
gnu/packages/perl6.scm,
gnu/packages/phabricator.scm,
gnu/packages/popt.scm,
gnu/packages/printers.scm,
gnu/packages/prolog.scm,
gnu/packages/protobuf.scm,
gnu/packages/pulseaudio.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/python-xyz.scm,
gnu/packages/qt.scm,
gnu/packages/radio.scm,
gnu/packages/rails.scm,
gnu/packages/rdf.scm,
gnu/packages/rednotebook.scm,
gnu/packages/rpc.scm,
gnu/packages/rsync.scm,
gnu/packages/ruby.scm,
gnu/packages/rust.scm,
gnu/packages/scheme.scm,
gnu/packages/screen.scm,
gnu/packages/security-token.scm,
gnu/packages/selinux.scm,
gnu/packages/serialization.scm,
gnu/packages/shells.scm,
gnu/packages/shellutils.scm,
gnu/packages/simh.scm,
gnu/packages/sml.scm,
gnu/packages/ssh.scm,
gnu/packages/statistics.scm,
gnu/packages/stenography.scm,
gnu/packages/sync.scm,
gnu/packages/syncthing.scm,
gnu/packages/synergy.scm,
gnu/packages/telephony.scm,
gnu/packages/terminals.scm,
gnu/packages/tex.scm,
gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm,
gnu/packages/textutils.scm,
gnu/packages/time.scm,
gnu/packages/tmux.scm,
gnu/packages/tor.scm,
gnu/packages/toys.scm,
gnu/packages/version-control.scm,
gnu/packages/video.scm,
gnu/packages/vim.scm,
gnu/packages/virtualization.scm,
gnu/packages/vlang.scm,
gnu/packages/vnc.scm,
gnu/packages/vpn.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm,
gnu/packages/wireservice.scm,
gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm,
gnu/packages/xdisorg.scm,
gnu/packages/xml.scm,
gnu/packages/xorg.scm,
tests/lint.scm: Remove trailing ".git" from 'git-reference' URL.
2020-07-12 16:53:28 -04:00
|
|
|
(url "https://github.com/gromacs/tng")
|
2020-05-03 18:32:38 -04:00
|
|
|
(commit (string-append "v" version))))
|
|
|
|
(file-name (git-file-name name version))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
(inputs
|
2021-12-13 11:18:24 -05:00
|
|
|
(list zlib))
|
2020-05-03 18:32:38 -04:00
|
|
|
(arguments
|
|
|
|
`(#:phases
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
(add-after 'unpack 'remove-bundled-zlib
|
|
|
|
(lambda _
|
|
|
|
(delete-file-recursively "external")
|
|
|
|
#t))
|
|
|
|
(replace 'check
|
|
|
|
(lambda _
|
|
|
|
(invoke "../build/bin/tests/tng_testing")
|
|
|
|
#t)))))
|
|
|
|
(home-page "https://github.com/gromacs/tng")
|
|
|
|
(synopsis "Trajectory Next Generation binary format manipulation library")
|
|
|
|
(description "TRAJNG (Trajectory next generation) is a program library for
|
|
|
|
handling molecular dynamics (MD) trajectories. It can store coordinates, and
|
|
|
|
optionally velocities and the H-matrix. Coordinates and velocities are
|
|
|
|
stored with user-specified precision.")
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
2020-05-03 18:39:36 -04:00
|
|
|
(define-public gromacs
|
|
|
|
(package
|
|
|
|
(name "gromacs")
|
2023-01-10 04:34:51 -05:00
|
|
|
(version "2022.4")
|
2020-05-03 18:39:36 -04:00
|
|
|
(source (origin
|
|
|
|
(method url-fetch)
|
|
|
|
(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
|
|
|
|
version ".tar.gz"))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2023-01-10 04:34:51 -05:00
|
|
|
"15vjwasxjq0h18dmzacjkdim51zrvr0ni42hbc30557j5xhbw4f5"))
|
2020-05-03 18:39:36 -04:00
|
|
|
;; Our version of tinyxml2 is far newer than the bundled one and
|
|
|
|
;; require fixing `testutils' code. See patch header for more info
|
|
|
|
(patches (search-patches "gromacs-tinyxml2.patch"))))
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
(arguments
|
2023-01-10 04:53:20 -05:00
|
|
|
(list #:configure-flags
|
|
|
|
#~(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
|
|
|
|
;; Unbundling
|
|
|
|
"-DGMX_USE_LMFIT=EXTERNAL"
|
|
|
|
"-DGMX_BUILD_OWN_FFTW=off"
|
|
|
|
"-DGMX_EXTERNAL_BLAS=on"
|
|
|
|
"-DGMX_EXTERNAL_LAPACK=on"
|
|
|
|
"-DGMX_EXTERNAL_TNG=on"
|
|
|
|
"-DGMX_EXTERNAL_ZLIB=on"
|
|
|
|
"-DGMX_EXTERNAL_TINYXML2=on"
|
|
|
|
(string-append "-DTinyXML2_DIR="
|
|
|
|
#$(this-package-input "tinyxml2"))
|
|
|
|
;; Workaround for cmake/FindSphinx.cmake version parsing that does
|
|
|
|
;; not understand the guix-wrapped `sphinx-build --version' answer
|
|
|
|
(string-append "-DSPHINX_EXECUTABLE_VERSION="
|
|
|
|
#$(package-version python-sphinx)))
|
|
|
|
#:phases
|
|
|
|
#~(modify-phases %standard-phases
|
|
|
|
(add-after 'unpack 'fixes
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
;; Still bundled: part of gromacs, source behind registration
|
|
|
|
;; but free software anyways
|
|
|
|
;;(delete-file-recursively "src/external/vmd_molfile")
|
|
|
|
;; Still bundled: threads-based OpenMPI-compatible fallback
|
|
|
|
;; designed to be bundled like that
|
|
|
|
;;(delete-file-recursively "src/external/thread_mpi")
|
|
|
|
;; Unbundling
|
|
|
|
(delete-file-recursively "src/external/lmfit")
|
|
|
|
(delete-file-recursively "src/external/clFFT")
|
|
|
|
(delete-file-recursively "src/external/fftpack")
|
|
|
|
(delete-file-recursively "src/external/build-fftw")
|
|
|
|
(delete-file-recursively "src/external/tng_io")
|
|
|
|
(delete-file-recursively "src/external/tinyxml2")
|
|
|
|
(delete-file-recursively "src/external/googletest")
|
|
|
|
(copy-recursively #$(package-source googletest)
|
|
|
|
"src/external/googletest")
|
|
|
|
;; This test warns about the build host hardware, disable
|
|
|
|
(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
|
|
|
|
(("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
|
|
|
|
"void __guix_disabled()")))))))
|
2020-05-03 18:39:36 -04:00
|
|
|
(native-inputs
|
2023-01-10 04:53:20 -05:00
|
|
|
(list doxygen
|
|
|
|
graphviz
|
|
|
|
pkg-config
|
|
|
|
python
|
|
|
|
python-pygments
|
|
|
|
python-sphinx))
|
2020-05-03 18:39:36 -04:00
|
|
|
(inputs
|
2021-12-13 11:18:24 -05:00
|
|
|
(list fftwf
|
|
|
|
`(,hwloc-2 "lib")
|
|
|
|
lmfit
|
|
|
|
openblas
|
|
|
|
perl
|
|
|
|
tinyxml2
|
|
|
|
tng))
|
gnu: Use HTTPS package home pages wherever possible.
* gnu/packages/accessibility.scm (florence)[home-page]: Use HTTPS.
* gnu/packages/admin.scm (netcat, nmon)[home-page]: Likewise.
* gnu/packages/algebra.scm (mpfrcx, cm, flint, fftw, r-dtt)[home-page]:
Likewise.
* gnu/packages/apr.scm (apr, apr-util)[home-page]: Likewise.
* gnu/packages/aspell.scm (aspell-dict-it)[home-page]: Likewise.
* gnu/packages/astronomy.scm (casacore, sextractor, libnova)
(xplanet)[home-page]: Likewise.
* gnu/packages/audio.scm (libtimidity, alsa-modular-synth, azr3, tao)
(freepats, rakarrack, liblo, libshout-idjc, timidity++, libsbsms)
(libmodplug, libxmp, xmp, sox, drc, gsm, gnaural)
(streamripper)[home-page]: Likewise.
* gnu/packages/authentication.scm (pamtester)[home-page]: Likewise.
* gnu/packages/backup.scm (grsync)[home-page]: Likewise.
* gnu/packages/bioconductor.scm (r-nmf, r-edger, r-limma)
(r-plgem)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (python-biom-format, bowtie, bowtie1)
(bwa, crossmap, java-htsjdk, java-htsjdk-latest, java-picard)
(java-picard-2.10.3, kaiju, proteinortho, rsem, rseqc, seek, samtools)
(snap-aligner, subread, stringtie, r-centipede, prinseq, emboss, phylip)
(libsbml)[home-page]: Likewise.
* gnu/packages/build-tools.scm (tup)[home-page]: Likewise.
* gnu/packages/cdrom.scm (libcddb, cdrdao, cdrtools)
(cd-discid)[home-page]: Likewise.
* gnu/packages/check.scm (cunit, python-nose)
(python-pyhamcrest)[home-page]: Likewise.
* gnu/packages/chemistry.scm (gromacs)[home-page]: Likewise.
* gnu/packages/chez.scm (chez-fmt)[home-page]: Likewise.
* gnu/packages/code.scm (lcov, uncrustify, cscope)[home-page]: Likewise.
* gnu/packages/compression.scm (p7zip)[home-page]: Likewise.
* gnu/packages/cran.scm (r-emdist, r-proj4, r-zoo, r-ggalluvial)
(r-orgmassspecr, r-polychrome, r-partykit, r-rcpp, r-ff, r-emdbook)
(r-fitdistrplus, r-linprog, r-geometry, r-dtw, r-fst, r-rjags)
(r-intergraph, r-qualv, r-labelled, r-survey, r-coin, r-fmsb, r-tm)
(r-corpcor, r-rmpfr, r-spatialextremes, r-longitudinal, r-genenet)
(r-bayesm, r-seqinr, r-mpm, r-text2vec, r-rgdal, r-seewave, r-hdrcde)
(r-shapes, r-anytime, r-stm, r-d3network, r-tam, r-directlabels)
(r-spatstat-utils, r-spatstat-sparse, r-spatstat-data, r-spatstat-geom)
(r-spatstat-core, r-spatstat-linnet, r-spatstat-random, r-spatstat)
(r-rcpptoml, r-mlecens, r-seurat, r-mlearning, r-zooimage)[home-page]:
Likewise.
* gnu/packages/crates-io.scm (rust-nickel-0.11, rust-thrift-0.13)
(rust-trust-dns-https-0.20, rust-trust-dns-native-tls-0.20)
(rust-trust-dns-openssl-0.20, rust-trust-dns-proto-0.20)
(rust-trust-dns-resolver-0.20, rust-trust-dns-rustls-0.20)
(rust-uint-0.9, rust-yaml-rust-0.4)[home-page]: Likewise.
* gnu/packages/crypto.scm (libdecaf, ccrypt)[home-page]: Likewise.
* gnu/packages/curl.scm (curlpp)[home-page]: Likewise.
* gnu/packages/databases.scm (python-pylibmc, unixodbc, wiredtiger)
(libpqxx, mdbtools, virtuoso-ose, libdbi, libdbi-drivers)
(soci)[home-page]: Likewise.
* gnu/packages/debian.scm (apt-mirror)[home-page]: Likewise.
* gnu/packages/debug.scm (remake)[home-page]: Likewise.
* gnu/packages/disk.scm (sdparm, idle3-tools, duc)[home-page]: Likewise.
* gnu/packages/django.scm (python-django-haystack)[home-page]: Likewise.
* gnu/packages/djvu.scm (djvulibre, djview)[home-page]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[home-page]: Likewise.
* gnu/packages/docbook.scm (dblatex, docbook2x)[home-page]: Likewise.
* gnu/packages/documentation.scm (scrollkeeper)[home-page]: Likewise.
* gnu/packages/ebook.scm (liblinebreak)[home-page]: Likewise.
* gnu/packages/electronics.scm (xoscope)[home-page]: Likewise.
* gnu/packages/emacs-xyz.scm (emacs-bbdb, emacs-caps-lock, emacs-djvu)
(emacs-pabbrev, emacs-twittering-mode, emacs-filladapt, emacs-rudel)
(emacs-stream, emacspeak, emacs-cc-mode, emacs-eldoc, emacs-jsonrpc)
(emacs-gtk-look, emacs-xclip, emacs-slime-volleyball, emacs-minimap)
(emacs-auto-dictionary-mode, emacs-persist, emacs-shell-command+)
(emacs-map, emacs-xref, emacs-dictionary)[home-page]: Likewise.
* gnu/packages/embedded.scm (sdcc)[home-page]: Likewise.
* gnu/packages/engineering.scm (asco, libngspice, libspnav)
(openctm)[home-page]: Likewise.
* gnu/packages/erlang.scm (erlang-erlware-commons)[home-page]: Likewise.
* gnu/packages/file-systems.scm (jfsutils, curlftpfs)[home-page]:
Likewise.
* gnu/packages/finance.scm (gbonds)[home-page]: Likewise.
* gnu/packages/flashing-tools.scm (dfu-util, srecord)[home-page]:
Likewise.
* gnu/packages/fltk.scm (ntk)[home-page]: Likewise.
* gnu/packages/fonts.scm (font-terminus, font-tex-gyre)
(font-comic-neue)[home-page]: Likewise.
* gnu/packages/fontutils.scm (ttf2pt1, potrace, libspiro)[home-page]:
Likewise.
* gnu/packages/fpga.scm (icestorm, gtkwave, gtkwave)
(python-myhdl)[home-page]: Likewise.
* gnu/packages/freedesktop.scm (libatasmart)[home-page]: Likewise.
* gnu/packages/ftp.scm (weex)[home-page]: Likewise.
* gnu/packages/game-development.scm (dds, python-tmx, sfxr, quesoglc)
(eureka, plib)[home-page]: Likewise.
* gnu/packages/games.scm (abe, alex4, armagetronad, barony)
(foobillard++, golly, ltris, pipewalker, prboom-plus, trigger-rally)
(cmatrix, pinball, pioneers, tennix, chromium-bsu, freeciv, kiki)
(quakespasm, frotz, frotz-dumb-terminal, frotz-sdl, btanks)
(flare-engine, chessx, barrage, cgoban, passage)[home-page]: Likewise.
* gnu/packages/geo.scm (python-geopandas, saga)[home-page]: Likewise.
* gnu/packages/gl.scm (freeglut, gl2ps)[home-page]: Likewise.
* gnu/packages/gnome.scm (cogl, clutter-gtk, clutter-gst, bluefish)
(workrave)[home-page]: Likewise.
* gnu/packages/gnustep.scm (wmnd, wmfire, wmfire)[home-page]: Likewise.
* gnu/packages/graph.scm (mscgen)[home-page]: Likewise.
* gnu/packages/graphics.scm (assimp, alembic, ctl, agg)
(opencsg)[home-page]: Likewise.
* gnu/packages/graphviz.scm (gts)[home-page]: Likewise.
* gnu/packages/gtk.scm (gtkspell3)[home-page]: Likewise.
* gnu/packages/guile-xyz.scm (guile-irregex)[home-page]: Likewise.
* gnu/packages/haskell-apps.scm (cpphs)[home-page]: Likewise.
* gnu/packages/haskell-check.scm (ghc-hunit)[home-page]: Likewise.
* gnu/packages/haskell-web.scm (ghc-http-client-restricted)
(ghc-blaze-html, ghc-happstack-server, ghc-sourcemap)[home-page]:
Likewise.
* gnu/packages/haskell-xyz.scm (ghc-assoc, ghc-cairo, ghc-cborg)
(ghc-csv, ghc-glob, ghc-gtk2hs-buildtools, ghc-hmatrix-gsl-stats)
(ghc-intervalmap, ghc-lens-family-core, ghc-managed, ghc-mountpoints)
(ghc-network-multicast, ghc-optional-args, ghc-regex, ghc-spoon)
(ghc-transformers, ghc-turtle, ghc-utf8-light, ghc-wizards)
(ghc-template-haskell, ghc-boot-th, ghc-binary-orphans)
(ghc-postgresql-simple)[home-page]: Likewise.
* gnu/packages/hexedit.scm (ht, bvi)[home-page]: Likewise.
* gnu/packages/hunspell.scm (hunspell-dict-hu)[home-page]: Likewise.
* gnu/packages/image-processing.scm (mia)[home-page]: Likewise.
* gnu/packages/image-viewers.scm (geeqie, gpicview, luminance-hdr)
(qiv)[home-page]: Likewise.
* gnu/packages/image.scm (libuemf, devil, steghide, optipng, niftilib)
(sng, mtpaint)[home-page]: Likewise.
* gnu/packages/java-xml.scm (java-simple-xml, java-jaxp)
(java-apache-xml-commons-resolver)[home-page]: Likewise.
* gnu/packages/java.scm (java-cisd-base, java-cisd-args4j)
(java-hamcrest-core, java-jsr305, java-eclipse-osgi)
(java-eclipse-equinox-common, java-eclipse-core-jobs)
(java-eclipse-equinox-registry, java-eclipse-equinox-app)
(java-eclipse-equinox-preferences, java-eclipse-core-contenttype)
(java-eclipse-text, java-treelayout, java-aopalliance, java-jeromq)
(java-cdi-api)[home-page]: Likewise.
* gnu/packages/jemalloc.scm (jemalloc-4.5.0)[home-page]: Likewise.
* gnu/packages/julia-xyz.scm (julia-recipespipeline)[home-page]:
Likewise.
* gnu/packages/kde-internet.scm (kget)[home-page]: Likewise.
* gnu/packages/kde-systemtools.scm (dolphin-plugins)
(konsole)[home-page]: Likewise.
* gnu/packages/kodi.scm (fstrcmp)[home-page]: Likewise.
* gnu/packages/language.scm (hime, libchewing)[home-page]: Likewise.
* gnu/packages/lego.scm (nqc)[home-page]: Likewise.
* gnu/packages/lesstif.scm (lesstif)[home-page]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[home-page]: Likewise.
* gnu/packages/libdaemon.scm (libdaemon)[home-page]: Likewise.
* gnu/packages/libffi.scm (libffi)[home-page]: Likewise.
* gnu/packages/libreoffice.scm (libwpd, libwpg, libwps)[home-page]:
Likewise.
* gnu/packages/libusb.scm (libmtp, gmtp)[home-page]: Likewise.
* gnu/packages/linux.scm (e2fsprogs, extundelete, lsscsi, net-tools)
(kbd, sysfsutils, cpuid, libpfm4)[home-page]: Likewise.
* gnu/packages/lisp-check.scm (sbcl-ptester, sbcl-xlunit)[home-page]:
Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-html-encode, sbcl-py-configparser)
(sbcl-cl-utilities, sbcl-series, sbcl-uffi, sbcl-clsql, sbcl-sycamore)
(sbcl-osicat, sbcl-hu.dwim.common, sbcl-caveman, sbcl-trivial-shell)
(sbcl-trivial-benchmark, sbcl-screamer, sbcl-smug)[home-page]: Likewise.
* gnu/packages/lisp.scm (lush2)[home-page]: Likewise.
* gnu/packages/logging.scm (log4cpp)[home-page]: Likewise.
* gnu/packages/lua.scm (lua-ldoc)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (mcl, openfst, rxcpp)[home-page]:
Likewise.
* gnu/packages/mail.scm (muchsync, procmail, sendmail)
(opensmtpd-filter-dkimsign, crm114)[home-page]: Likewise.
* gnu/packages/man.scm (libpipeline, man-db)[home-page]: Likewise.
* gnu/packages/maths.scm (lapack, scalapack, hdf-eos5, itpp, gmsh)
(metamath, p4est, armadillo, suitesparse, atlas, lpsolve, wcalc, why3)
(frama-c)[home-page]: Likewise.
* gnu/packages/mcrypt.scm (mcrypt, libmcrypt, libmhash)[home-page]:
Likewise.
* gnu/packages/minetest.scm (minetest-advtrains)[home-page]: Likewise.
* gnu/packages/monitoring.scm (python-whisper, python-carbon)
(hostscope)[home-page]: Likewise.
* gnu/packages/mp3.scm (id3lib, libmp3splt, mp3splt, mpg321)
(lame)[home-page]: Likewise.
* gnu/packages/multiprecision.scm (mpc)[home-page]: Likewise.
* gnu/packages/music.scm (aria-maestosa, lingot, setbfree, bristol)
(portmidi, python-pyportmidi, zynaddsubfx, yoshimi, aj-snapshot)
(schismtracker, midicsv, midicsv, qmidiarp, qmidiroute, dssi, tap-lv2)
(shiru-lv2)[home-page]: Likewise.
* gnu/packages/ncurses.scm (stfl)[home-page]: Likewise.
* gnu/packages/networking.scm (lksctp-tools, mbuffer, ifstatus, bird)
(tunctl, traceroute)[home-page]: Likewise.
* gnu/packages/node-xyz.scm (node-mersenne)[home-page]: Likewise.
* gnu/packages/ntp.scm (openntpd)[home-page]: Likewise.
* gnu/packages/ocaml.scm (opam, hevea, ocaml-menhir, ocaml-piqilib)
(ocaml-graph, cubicle)[home-page]: Likewise.
* gnu/packages/opencl.scm (python-pyopencl)[home-page]: Likewise.
* gnu/packages/package-management.scm (xstow, modules)[home-page]:
Likewise.
* gnu/packages/parallel.scm (xjobs)[home-page]: Likewise.
* gnu/packages/pdf.scm (podofo, qpdf, xournal, impressive)[home-page]:
Likewise.
* gnu/packages/perl.scm (perl-math-vecstat, perltidy)[home-page]:
Likewise.
* gnu/packages/photo.scm (libpano13, enblend-enfuse, hugin)[home-page]:
Likewise.
* gnu/packages/plan9.scm (drawterm)[home-page]: Likewise.
* gnu/packages/plotutils.scm (guile-charting, ploticus)[home-page]:
Likewise.
* gnu/packages/popt.scm (argtable, popt)[home-page]: Likewise.
* gnu/packages/profiling.scm (otf2)[home-page]: Likewise.
* gnu/packages/pulseaudio.scm (pulseaudio)[home-page]: Likewise.
* gnu/packages/python-check.scm (python-mypy)[home-page]: Likewise.
* gnu/packages/python-web.scm (python-cssutils)
(python-translationstring)[home-page]: Likewise.
* gnu/packages/python-xyz.scm (python-diskcache, python-doxyqml)
(python-docutils, python-pexpect, python-importlib-resources)
(python-simplegeneric, python-urwid, python-xlrd, python-xlwt)
(python-pyasn1, python-pythondialog, python-tftpy, python-random2)
(python-arcp, python-pyopengl, python-sortedcollections)
(python-sortedcontainers, python-yapsy, python-pydispatcher)
(python-posix-ipc)[home-page]: Likewise.
* gnu/packages/qt.scm (qwt, libqglviewer, signond)[home-page]: Likewise.
* gnu/packages/radio.scm (unixcw, gnuais)[home-page]: Likewise.
* gnu/packages/raspberry-pi.scm (bcm2835)[home-page]: Likewise.
* gnu/packages/rdf.scm (clucene, rasqal, redland)[home-page]: Likewise.
* gnu/packages/regex.scm (tre)[home-page]: Likewise.
* gnu/packages/rsync.scm (librsync)[home-page]: Likewise.
* gnu/packages/ruby.scm (ruby-packnga, ruby-nokogiri, ruby-oj, ruby-ox)
(ruby-sinatra, ruby-citrus, ruby-cbor, ruby-roda)[home-page]: Likewise.
* gnu/packages/scheme.scm (scheme48, tinyscheme)[home-page]: Likewise.
* gnu/packages/screen.scm (dtach)[home-page]: Likewise.
* gnu/packages/scsi.scm (sg3-utils)[home-page]: Likewise.
* gnu/packages/sdl.scm (libmikmod, sdl-pango)[home-page]: Likewise.
* gnu/packages/shellutils.scm (hstr, rig)[home-page]: Likewise.
* gnu/packages/simulation.scm (python-dolfin-adjoint)[home-page]:
Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[home-page]: Likewise.
* gnu/packages/speech.scm (espeak)[home-page]: Likewise.
* gnu/packages/stalonetray.scm (stalonetray)[home-page]: Likewise.
* gnu/packages/statistics.scm (jags, r-mass, r-class, r-lattice)
(r-matrix, r-nnet, r-spatial, r-bit, r-bit64, r-digest, r-xtable)
(python-statsmodels, r-ade4, r-latticeextra, r-rcurl, r-xml, r-mvtnorm)
(r-robustbase, r-minqa, r-fdrtool, java-jdistlib, xlispstat)[home-page]:
Likewise.
* gnu/packages/swig.scm (swig)[home-page]: Likewise.
* gnu/packages/task-management.scm (wtime)[home-page]: Likewise.
* gnu/packages/tcl.scm (itcl, tclxml, tclx)[home-page]: Likewise.
* gnu/packages/terminals.scm (libtermkey, mlterm, libvterm)
(libvterm)[home-page]: Likewise.
* gnu/packages/tex.scm (texlive-lm, texlive-lm-math, texlive-cs)
(texlive-csplain, biber, texmaker)[home-page]: Likewise.
* gnu/packages/text-editors.scm (joe)[home-page]: Likewise.
* gnu/packages/textutils.scm (drm-tools, docx2txt)[home-page]: Likewise.
* gnu/packages/tv.scm (tvtime)[home-page]: Likewise.
* gnu/packages/unicode.scm (libunibreak)[home-page]: Likewise.
* gnu/packages/upnp.scm (libupnp)[home-page]: Likewise.
* gnu/packages/version-control.scm (cvs)[home-page]: Likewise.
* gnu/packages/video.scm (transcode, libquicktime, mjpegtools, aalib)
(liba52, libmpeg2, x265, libdv, dvdauthor, aegisub, pitivi, gavl)
(dvdbackup, guvcview, video-contact-sheet)[home-page]: Likewise.
* gnu/packages/virtualization.scm (bochs)[home-page]: Likewise.
* gnu/packages/w3m.scm (w3m)[home-page]: Likewise.
* gnu/packages/web.scm (qjson, libquvi-scripts, libquvi, quvi)
(tidy-html, htmlcxx)[home-page]: Likewise.
* gnu/packages/wm.scm (evilwm, menumaker)[home-page]: Likewise.
* gnu/packages/wv.scm (wv)[home-page]: Likewise.
* gnu/packages/wxwidgets.scm (wxsvg)[home-page]: Likewise.
* gnu/packages/xdisorg.scm (mtdev, xsel)[home-page]: Likewise.
* gnu/packages/xfig.scm (xfig, transfig)[home-page]: Likewise.
* gnu/packages/xml.scm (openjade, python-pyxb, xmlstarlet, xmlrpc-c)
(opensp)[home-page]: Likewise.
* gnu/packages/xorg.scm (xf86-video-qxl)[home-page]: Likewise.
2023-02-11 19:00:00 -05:00
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(home-page "https://www.gromacs.org/")
|
2020-05-03 18:39:36 -04:00
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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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2023-01-10 05:52:19 -05:00
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(license license:lgpl2.1+)
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(properties '((tunable? . #t)))))
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2020-05-03 18:39:36 -04:00
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2018-07-13 22:44:54 -04:00
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(define-public openbabel
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(package
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(name "openbabel")
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2021-01-26 00:38:25 -05:00
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(version "3.1.1")
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2018-07-13 22:44:54 -04:00
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(source (origin
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(method url-fetch)
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2021-01-26 00:38:25 -05:00
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(uri (string-append "https://github.com/openbabel/openbabel/"
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"releases/download/openbabel-"
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(string-replace-substring version "." "-")
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"/openbabel-" version "-source.tar.bz2"))
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2018-07-13 22:44:54 -04:00
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(sha256
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(base32
|
2021-01-26 00:38:25 -05:00
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"0s0f4zib8vshfaywsr5bjjz55jwsg6yiz2qw4i5jm8wysn0q7v56"))))
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2018-07-13 22:44:54 -04:00
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(build-system cmake-build-system)
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(arguments
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2021-01-26 00:38:25 -05:00
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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)
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(not (string=? "i686-linux" (%current-system))))
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#:configure-flags
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2018-07-13 22:44:54 -04:00
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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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2021-12-13 11:18:24 -05:00
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(list pkg-config))
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2018-07-13 22:44:54 -04:00
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(inputs
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2021-12-13 11:18:24 -05:00
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(list eigen inchi libxml2 zlib))
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2018-07-13 22:44:54 -04:00
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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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2021-01-22 21:32:41 -05:00
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(define-public spglib
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(package
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(name "spglib")
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(version "1.16.0")
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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/spglib/spglib")
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(commit (string-append "v" version))))
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(sha256
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(base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
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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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'(#:test-target "check"
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'patch-header-install-dir
|
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(lambda _
|
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;; As of the writing of this package, CMake and GNU build systems
|
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;; install the header to two different location. This patch makes
|
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;; the CMake build system's choice of header directory compatible
|
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;; with the GNU build system's choice and with what avogadrolibs
|
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;; expects.
|
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;; See https://github.com/spglib/spglib/issues/75 and the relevant
|
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;; part of https://github.com/OpenChemistry/avogadroapp/issues/97.
|
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|
(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)))
|
2021-09-20 10:00:37 -04:00
|
|
|
|
|
|
|
(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")))))
|
2023-07-03 17:31:10 -04:00
|
|
|
;; Prevent deleting the leading / in the __init__.py path in the
|
|
|
|
;; launch script.
|
|
|
|
(add-after 'unpack 'disable-unchroot
|
|
|
|
(lambda _
|
|
|
|
(substitute* "setup.py"
|
|
|
|
(("self\\.unchroot") ""))))
|
2021-09-20 10:00:37 -04:00
|
|
|
;; 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
|
2021-12-13 11:18:24 -05:00
|
|
|
(list freetype
|
|
|
|
libpng
|
|
|
|
freeglut
|
|
|
|
glew
|
|
|
|
libxml2
|
|
|
|
mmtf-cpp
|
|
|
|
python-pyqt
|
|
|
|
glm
|
|
|
|
netcdf))
|
2023-07-03 17:31:10 -04:00
|
|
|
(native-inputs (list catch2))
|
2021-09-20 10:00:37 -04:00
|
|
|
(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)))
|
2022-10-13 17:04:17 -04:00
|
|
|
|
|
|
|
(define-public gemmi
|
|
|
|
(package
|
|
|
|
(name "gemmi")
|
2024-01-28 18:01:56 -05:00
|
|
|
(version "0.6.4")
|
2022-10-13 17:04:17 -04:00
|
|
|
(source (origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
|
|
|
(url "https://github.com/project-gemmi/gemmi")
|
|
|
|
(commit (string-append "v" version))))
|
|
|
|
(file-name (git-file-name name version))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2024-01-28 18:01:56 -05:00
|
|
|
"0wciqqswc4p4v4kglfv36gnvyyimqn4lnywdzd0pgrjn443i860y"))
|
2022-10-13 17:04:17 -04:00
|
|
|
(patches
|
|
|
|
(search-patches "gemmi-fix-sajson-types.patch"
|
|
|
|
"gemmi-fix-pegtl-usage.patch"))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
'(begin
|
|
|
|
(delete-file-recursively "include/gemmi/third_party")
|
|
|
|
(delete-file-recursively "third_party")))))
|
|
|
|
(outputs '("out" "bin" "python"))
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
(arguments
|
|
|
|
(list
|
|
|
|
#:modules '((guix build cmake-build-system)
|
|
|
|
(guix build utils)
|
|
|
|
((guix build python-build-system)
|
|
|
|
#:select (site-packages)))
|
|
|
|
#:imported-modules (append %cmake-build-system-modules
|
|
|
|
'((guix build python-build-system)))
|
|
|
|
#:configure-flags
|
|
|
|
#~(list "-DUSE_PYTHON=ON"
|
|
|
|
(string-append "-DPYTHON_INSTALL_DIR="
|
|
|
|
(site-packages %build-inputs %outputs)))
|
|
|
|
#:phases
|
|
|
|
#~(modify-phases %standard-phases
|
|
|
|
(add-after 'unpack 'patch-includes
|
|
|
|
(lambda _
|
2024-01-28 18:01:56 -05:00
|
|
|
(substitute* (list "src/sprintf.cpp"
|
2022-10-13 17:04:17 -04:00
|
|
|
"include/gemmi/dirwalk.hpp"
|
|
|
|
"include/gemmi/cif.hpp"
|
|
|
|
"include/gemmi/json.hpp"
|
|
|
|
"python/gemmi.cpp"
|
|
|
|
"include/gemmi/atof.hpp"
|
|
|
|
"include/gemmi/numb.hpp"
|
|
|
|
"include/gemmi/fourier.hpp")
|
|
|
|
(("<stb/stb_sprintf.h>") "<stb_sprintf.h>")
|
|
|
|
(("\"third_party/tinydir.h\"") "<tinydir.h>")
|
|
|
|
(("\"third_party/tao/pegtl.hpp\"") "<tao/pegtl.hpp>")
|
|
|
|
(("\"third_party/sajson.h\"") "<sajson.h>")
|
|
|
|
(("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
|
|
|
|
"<tao/pegtl/parse_error.hpp>")
|
|
|
|
(("\"third_party/fast_float.h\"")
|
|
|
|
"<fast_float/fast_float.h>")
|
|
|
|
(("\"third_party/pocketfft_hdronly.h\"")
|
|
|
|
"<pocketfft_hdronly.h>"))))
|
|
|
|
(add-after 'unpack 'change-bin-prefix
|
|
|
|
(lambda _
|
|
|
|
(substitute* "CMakeLists.txt"
|
|
|
|
(("install\\(TARGETS program DESTINATION bin\\)")
|
|
|
|
(string-append
|
|
|
|
"install(TARGETS program DESTINATION "
|
|
|
|
#$output:bin "/bin)")))))
|
|
|
|
(replace 'check
|
|
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
|
|
(when tests?
|
|
|
|
(with-directory-excursion "../source"
|
|
|
|
(setenv "PYTHONPATH" "../build")
|
|
|
|
(invoke "python3" "-m" "unittest" "discover" "-v"
|
|
|
|
"-s" "tests"))))))))
|
|
|
|
(inputs (list python zlib))
|
|
|
|
(native-inputs
|
|
|
|
(list fast-float
|
|
|
|
optionparser
|
|
|
|
pegtl
|
|
|
|
pocketfft-cpp
|
|
|
|
pybind11
|
|
|
|
sajson-for-gemmi
|
|
|
|
stb-sprintf
|
|
|
|
tinydir))
|
|
|
|
(home-page "https://gemmi.readthedocs.io/en/latest/")
|
|
|
|
(synopsis "Macromolecular crystallography library and utilities")
|
|
|
|
(description "GEMMI is a C++ library for macromolecular crystallography.
|
|
|
|
It can be used for working with
|
|
|
|
@enumerate
|
|
|
|
@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
|
|
|
|
@item refinement restraints (CIF files),
|
|
|
|
@item reflection data (MTZ and mmCIF formats),
|
|
|
|
@item data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
|
|
|
|
@item crystallographic symmetry.
|
|
|
|
@end enumerate")
|
|
|
|
(license license:mpl2.0)))
|
2022-10-13 17:04:18 -04:00
|
|
|
|
|
|
|
(define-public freesasa
|
|
|
|
(package
|
|
|
|
(name "freesasa")
|
|
|
|
(version "2.1.2")
|
|
|
|
(source (origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
|
|
|
(url "https://github.com/mittinatten/freesasa")
|
|
|
|
(commit version)))
|
|
|
|
(file-name (git-file-name name version))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f"))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
'(begin
|
|
|
|
;; Remove C files generated by Flex and Bison
|
|
|
|
(for-each delete-file
|
|
|
|
'("src/parser.c" "src/parser.h"
|
|
|
|
"src/lexer.c" "src/lexer.h"))))))
|
|
|
|
(outputs '("out" "doc"))
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
(list
|
|
|
|
#:configure-flags
|
|
|
|
#~(list "--enable-check"
|
|
|
|
"--enable-parser-generator"
|
|
|
|
"CXXFLAGS=-std=c++17"
|
2024-01-28 18:02:01 -05:00
|
|
|
"--enable-doxygen"
|
|
|
|
;; Some tests rely on replacing malloc with a wrapper which
|
|
|
|
;; fails in a controlled way, but this does not work if the call
|
|
|
|
;; is replaced. This was fixed upstream, remove once there is a
|
|
|
|
;; new release.
|
|
|
|
"CFLAGS=-fno-builtin-malloc")
|
2022-10-13 17:04:18 -04:00
|
|
|
#:phases
|
|
|
|
#~(modify-phases %standard-phases
|
|
|
|
(add-after 'unpack 'remove-libc++-linking
|
|
|
|
(lambda _
|
|
|
|
(substitute* "src/Makefile.am"
|
|
|
|
(("-lc\\+\\+") ""))))
|
|
|
|
(add-after 'unpack 'build-shared-library
|
|
|
|
(lambda _
|
|
|
|
(substitute* "src/Makefile.am"
|
|
|
|
(("lib_LIBRARIES") "lib_LTLIBRARIES")
|
|
|
|
(("libfreesasa\\.a") "libfreesasa.la")
|
|
|
|
(("freesasa_LDADD \\+= libfreesasa\\.la" prev)
|
|
|
|
(string-append prev "\nlibfreesasa_la_LIBADD"
|
2024-01-28 18:01:56 -05:00
|
|
|
" = -ljson-c -lgemmi_cpp ${libxml2_LIBS}\n"))
|
2022-10-13 17:04:18 -04:00
|
|
|
(("_a_SOURCES") "_la_SOURCES"))
|
|
|
|
(substitute* "configure.ac"
|
|
|
|
(("AC_PROG_INSTALL" inst)
|
|
|
|
(string-append "AM_PROG_LIBTOOL\n" inst)))
|
|
|
|
(substitute* "tests/Makefile.am"
|
|
|
|
(("libfreesasa\\.a") "libfreesasa.la"))))
|
|
|
|
(add-before 'build 'build-lexer-and-parser
|
|
|
|
(lambda _
|
|
|
|
(with-directory-excursion "src"
|
|
|
|
(invoke "make" "lexer.h" "parser.h"))))
|
|
|
|
(add-after 'install 'install-doc
|
|
|
|
(lambda _
|
|
|
|
(copy-recursively
|
|
|
|
"doc/html"
|
|
|
|
(string-append #$output:doc "/share/doc/"
|
|
|
|
#$name "-" #$version)))))))
|
|
|
|
(inputs (list gemmi json-c libxml2))
|
|
|
|
(native-inputs
|
|
|
|
(list autoconf
|
|
|
|
automake
|
|
|
|
bison
|
|
|
|
check
|
|
|
|
doxygen
|
|
|
|
fast-float
|
|
|
|
flex
|
|
|
|
libtool
|
|
|
|
pegtl
|
|
|
|
perl
|
|
|
|
pkg-config))
|
|
|
|
(home-page "https://freesasa.github.io/")
|
|
|
|
(synopsis "Calculate the solvent accessible surface area (SASA) of
|
|
|
|
molecules")
|
|
|
|
(description "FreeSASA is a command line tool and C-library for
|
|
|
|
calculating @acronym{SASAs, solvent accessible surface areas}. By default Lee
|
|
|
|
& Richards' algorithm is used, but Shrake & Rupley's is also available. Both
|
|
|
|
can be parameterized to arbitrary precision, and for high resolution versions
|
|
|
|
of the algorithms, the calculations give identical results.")
|
|
|
|
(license license:expat)))
|
2022-10-13 17:04:19 -04:00
|
|
|
|
|
|
|
(define-public maeparser
|
|
|
|
(package
|
|
|
|
(name "maeparser")
|
2024-01-28 18:01:57 -05:00
|
|
|
(version "1.3.1")
|
2022-10-13 17:04:19 -04:00
|
|
|
(source (origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
|
|
|
(url "https://github.com/schrodinger/maeparser")
|
|
|
|
(commit (string-append "v" version))))
|
|
|
|
(file-name (git-file-name name version))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2024-01-28 18:01:57 -05:00
|
|
|
"0mr5glg4br04ql5grby8yqni9fqq1l1cc75wyc159a1b9lwr7q7r"))))
|
2022-10-13 17:04:19 -04:00
|
|
|
(build-system cmake-build-system)
|
|
|
|
(inputs (list boost zlib))
|
|
|
|
(home-page "https://github.com/schrodinger/maeparser")
|
|
|
|
(synopsis "Maestro file parser")
|
|
|
|
(description "maeparser is a parser for Schrodinger Maestro files.")
|
|
|
|
(license license:expat)))
|
2022-10-13 17:04:20 -04:00
|
|
|
|
|
|
|
(define-public coordgenlibs
|
|
|
|
(package
|
|
|
|
(name "coordgenlibs")
|
2024-01-28 18:01:58 -05:00
|
|
|
(version "3.0.2")
|
2022-10-13 17:04:20 -04:00
|
|
|
(source (origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
|
|
|
(url "https://github.com/schrodinger/coordgenlibs/")
|
|
|
|
(commit (string-append "v" version))))
|
|
|
|
(file-name (git-file-name name version))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2024-01-28 18:01:58 -05:00
|
|
|
"1wjaxwaihjy9xm5ys23f5abl50zcar1h9pww5ajdkgygsqy0bavi"))))
|
2022-10-13 17:04:20 -04:00
|
|
|
(build-system cmake-build-system)
|
|
|
|
(arguments
|
|
|
|
(list
|
|
|
|
#:configure-flags
|
|
|
|
#~(list "-DCOORDGEN_RIGOROUS_BUILD=OFF"
|
|
|
|
"-DCOORDGEN_USE_MAEPARSER=ON")))
|
|
|
|
(inputs (list boost maeparser))
|
|
|
|
(home-page "https://github.com/schrodinger/coordgenlibs/")
|
|
|
|
(synopsis "2D molecule coordinate generation")
|
|
|
|
(description "@code{coordgenlibs} contains algorithms to generate 2D
|
|
|
|
coordinates of molecules including macrocycles and metal complexes. It has an
|
|
|
|
emphasis on quality rather than speed.")
|
|
|
|
(license license:bsd-3)))
|
2022-10-13 17:04:21 -04:00
|
|
|
|
|
|
|
(define-public yaehmop
|
|
|
|
(package
|
|
|
|
(name "yaehmop")
|
2024-01-28 18:01:59 -05:00
|
|
|
(version "2023.03.1")
|
2022-10-13 17:04:21 -04:00
|
|
|
(source (origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
|
|
|
(url "https://github.com/greglandrum/yaehmop")
|
|
|
|
(commit (string-append "v" version))))
|
|
|
|
(file-name (git-file-name name version))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2024-01-28 18:01:59 -05:00
|
|
|
"18xnxqn8i7vswy3iffapfh9q2iimpnd23ps45hn4xxbs6dqgzprb"))
|
2022-10-13 17:04:21 -04:00
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
'(begin
|
|
|
|
;; Separate program
|
|
|
|
(delete-file-recursively "viewkel")
|
|
|
|
;; Remove example output (some are corrupted)
|
|
|
|
(for-each delete-file (find-files "examples" "\\.Z$"))
|
|
|
|
;; Documentation outputs
|
|
|
|
(for-each delete-file (find-files "docs" "\\.(ps|pdf)$"))
|
|
|
|
;; These are transpiled from Fortran to C, but we build the
|
|
|
|
;; Fortran code instead
|
|
|
|
(delete-file-recursively "tightbind/f2c_files")
|
|
|
|
(with-directory-excursion "tightbind"
|
|
|
|
(for-each delete-file '("abfns.c"
|
|
|
|
"cboris.c"
|
|
|
|
"diag.c"
|
|
|
|
"lovlap.c")))))))
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
(arguments
|
|
|
|
(list
|
|
|
|
#:configure-flags
|
|
|
|
#~(list
|
|
|
|
"-DUSE_BLAS_LAPACK=ON"
|
|
|
|
(string-append "-DPARM_FILE_LOC=" #$output
|
|
|
|
"/share/" #$name "-" #$version "/eht_parms.dat")
|
|
|
|
"-DBIND_EXE_NAME=yaehmop-bind")
|
|
|
|
#:phases
|
|
|
|
#~(modify-phases %standard-phases
|
|
|
|
(add-after 'unpack 'chdir
|
|
|
|
(lambda _
|
|
|
|
(chdir "tightbind")))
|
|
|
|
(add-after 'chdir 'patch-fortran-functions
|
|
|
|
(lambda _
|
|
|
|
(substitute* '("mov.c" "prototypes.h")
|
|
|
|
(("lovlap\\(") "lovlap_(")
|
|
|
|
(("abfns\\(") "abfns_("))))
|
|
|
|
(add-after 'chdir 'patch-cmake
|
|
|
|
(lambda _
|
|
|
|
(substitute* "CMakeLists.txt"
|
|
|
|
(("project\\(yaehmop C\\)") "project(yaehmop C Fortran)")
|
|
|
|
(("abfns.c") "fortran77/abfns.f")
|
|
|
|
(("lovlap.c") "fortran77/lovlap.f")
|
|
|
|
(("(set\\(PARM_FILE_LOC.*)\\)" all init)
|
|
|
|
(string-append init " CACHE STRING \"\")"))
|
|
|
|
(("add_library\\(yaehmop_eht" lib)
|
|
|
|
(string-append lib " SHARED "))
|
|
|
|
(("target_link_libraries\\(test_eht \\$\\{LAPACK_LIBRARIES\\}.*"
|
|
|
|
all)
|
|
|
|
(string-append all "\ntarget_link_libraries(yaehmop_eht "
|
|
|
|
"${LAPACK_LIBRARIES})\n")))))
|
|
|
|
(add-after 'build 'build-doc
|
|
|
|
(lambda _
|
|
|
|
(with-directory-excursion "../docs"
|
|
|
|
(substitute* "bind_manual.tex"
|
|
|
|
(("\\\\usepackage\\{bindpage\\}")
|
|
|
|
(string-append
|
|
|
|
"\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
|
|
|
|
"{geometry}\n"
|
|
|
|
"\\pdfsuppressptexinfo=-1\n")))
|
|
|
|
(substitute* "Zmat_appendix.tex"
|
|
|
|
(("file=dihedral\\.eps")
|
|
|
|
"file=figs/dihedral.eps"))
|
|
|
|
(setenv "FORCE_SOURCE_DATE" "1")
|
|
|
|
(invoke "latexmk" "-pdf" "bind_manual.tex"))))
|
|
|
|
(add-after 'install 'install-eht-parms
|
|
|
|
(lambda _
|
|
|
|
(install-file "../tightbind/eht_parms.dat"
|
|
|
|
(string-append #$output "/share/"
|
|
|
|
#$name "-" #$version))))
|
|
|
|
(add-after 'install-eht-parms 'install-doc
|
|
|
|
(lambda _
|
|
|
|
(install-file "../docs/bind_manual.pdf"
|
|
|
|
(string-append #$output "/share/doc/"
|
|
|
|
#$name "-" #$version))))
|
|
|
|
(delete 'check)
|
|
|
|
(add-after 'install-doc 'check
|
|
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
|
|
(when tests?
|
|
|
|
(invoke "./test_eht")))))))
|
|
|
|
(inputs (list openblas))
|
|
|
|
(native-inputs
|
|
|
|
(list gfortran
|
2023-05-13 05:54:41 -04:00
|
|
|
(texlive-updmap.cfg
|
2023-07-03 06:51:49 -04:00
|
|
|
(list texlive-epstopdf
|
2023-06-28 17:57:20 -04:00
|
|
|
texlive-latexmk))))
|
2022-10-13 17:04:21 -04:00
|
|
|
(home-page "https://github.com/greglandrum/yaehmop")
|
|
|
|
(synopsis "Perform extended Hückel calculations")
|
|
|
|
(description "@acronym{YAeHMOP, Yet Another extended Hueckel Molecular
|
|
|
|
Orbital Package} contains a program and library for performing extended Hückel
|
|
|
|
calculations and analyzing the results.")
|
|
|
|
(license license:bsd-2)))
|
2022-10-13 17:04:22 -04:00
|
|
|
|
|
|
|
(define-public avalon-toolkit
|
|
|
|
(package
|
|
|
|
(name "avalon-toolkit")
|
2024-01-28 18:02:00 -05:00
|
|
|
(version "2.0.5a")
|
|
|
|
(source (origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
|
|
|
(url "https://github.com/rohdebe1/ava-formake")
|
|
|
|
(commit (string-append "AvalonToolkit_" version))))
|
|
|
|
(file-name (git-file-name name version))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1mfg40y5xc17sm59zdfc5sk22n9zm5zk0z1aw47chvl6hp465szk"))
|
|
|
|
(patches
|
|
|
|
(search-patches "avalon-toolkit-rdkit-fixes.patch"))
|
|
|
|
(modules '((guix build utils) (ice-9 ftw)))
|
|
|
|
(snippet
|
|
|
|
#~(begin
|
|
|
|
(delete-file-recursively "src/main/java")
|
|
|
|
(delete-file-recursively "src/test/target")))))
|
2022-10-13 17:04:22 -04:00
|
|
|
(build-system gnu-build-system)
|
|
|
|
(arguments
|
|
|
|
(list
|
2024-01-28 18:02:00 -05:00
|
|
|
;; There is only one test, which is missing a file
|
2022-10-13 17:04:22 -04:00
|
|
|
#:tests? #f
|
|
|
|
#:phases
|
2024-01-28 18:02:00 -05:00
|
|
|
#~(modify-phases %standard-phases
|
|
|
|
(delete 'configure)
|
|
|
|
(replace 'build
|
|
|
|
(lambda* (#:key parallel-build? #:allow-other-keys)
|
|
|
|
(mkdir "build")
|
|
|
|
(mkdir-p "target/executables")
|
|
|
|
(mkdir-p "target/libraries")
|
|
|
|
(invoke "make" "programs" "-j"
|
|
|
|
(if parallel-build?
|
|
|
|
(number->string (parallel-job-count))
|
|
|
|
"1"))))
|
|
|
|
(replace 'install
|
|
|
|
(lambda _
|
|
|
|
;; Executables
|
|
|
|
(let ((programs '("canonizer" "matchtest" "smi2mol" "struchk")))
|
2022-10-13 17:04:22 -04:00
|
|
|
(for-each
|
|
|
|
(lambda (program)
|
2024-01-28 18:02:00 -05:00
|
|
|
(install-file (string-append "target/executables/" program)
|
|
|
|
(string-append #$output "/bin")))
|
|
|
|
programs))
|
|
|
|
(for-each
|
|
|
|
(lambda (name)
|
|
|
|
(symlink (string-append #$output "/bin/smi2mol")
|
|
|
|
(string-append #$output "/bin/" name)))
|
|
|
|
'("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
|
|
|
|
;; Library
|
|
|
|
(install-file "target/libraries/libavalon_tools.a"
|
|
|
|
(string-append #$output "/lib"))
|
|
|
|
(install-file "target/libraries/libavalon4rdkit.a"
|
|
|
|
(string-append #$output "/lib"))
|
|
|
|
(for-each
|
|
|
|
(lambda (file)
|
|
|
|
(install-file file (string-append #$output
|
|
|
|
"/include/avalontoolkit")))
|
|
|
|
(find-files "src/main/C/include" "\\.h$"))
|
|
|
|
(install-file "license.txt"
|
|
|
|
(string-append #$output "/share/doc/"
|
|
|
|
#$name "-" #$version "/")))))))
|
2022-10-13 17:04:22 -04:00
|
|
|
(home-page "https://sourceforge.net/projects/avalontoolkit/")
|
|
|
|
(synopsis "Tools for SMILES and MOL files and for structure fingerprinting")
|
|
|
|
(description "This package contains a library and programs for
|
|
|
|
canonicalization of SMILES and MOL files, molecular structure fingerprinting
|
|
|
|
and rendering molecules.")
|
|
|
|
(license license:bsd-3)))
|
2022-10-13 17:04:23 -04:00
|
|
|
|
|
|
|
(define-public ringdecomposerlib
|
|
|
|
(package
|
|
|
|
(name "ringdecomposerlib")
|
|
|
|
(version "1.1.3")
|
|
|
|
(source (origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
|
|
|
(url "https://github.com/rareylab/RingDecomposerLib")
|
|
|
|
(commit (string-append "v" version "_rdkit"))))
|
|
|
|
(file-name (git-file-name name version))
|
|
|
|
(sha256
|
|
|
|
(base32
|
|
|
|
"1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi"))))
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
(arguments
|
|
|
|
(list
|
|
|
|
#:configure-flags
|
|
|
|
#~(list "-DBUILD_PYTHON_WRAPPER=ON"
|
|
|
|
"-DPYTHON_EXECUTABLE=python3"
|
|
|
|
(string-append "-DPYTHON_FLAGS=;--prefix=" #$output ";--root=/"))
|
|
|
|
#:imported-modules (append %cmake-build-system-modules
|
|
|
|
'((guix build python-build-system)))
|
|
|
|
#:modules '((guix build cmake-build-system)
|
|
|
|
(guix build utils)
|
|
|
|
((guix build python-build-system)
|
|
|
|
#:select (add-installed-pythonpath)))
|
|
|
|
#:phases
|
|
|
|
#~(modify-phases %standard-phases
|
|
|
|
(add-before 'configure 'patch-cmake
|
|
|
|
(lambda _
|
|
|
|
(substitute* (list "src/Test/CMakeLists.txt"
|
|
|
|
"src/RingDecomposerLib/CMakeLists.txt")
|
|
|
|
(("build_.*STATIC") "#"))
|
|
|
|
(substitute* "test/CMakeLists.txt"
|
|
|
|
(("STATIC_TEST") "SHARED_TEST"))
|
|
|
|
;; Link Python library against shared library
|
|
|
|
(substitute* "src/python/CMakeLists.txt"
|
|
|
|
(("RingDecomposerLibStatic") "RingDecomposerLib"))
|
|
|
|
(substitute* "src/python/setup.py.in"
|
|
|
|
(("static_libs =.*") "static_libs = []\n")
|
|
|
|
(("shared_libs\\s*=.*")
|
|
|
|
(string-append
|
|
|
|
"shared_libs = ['RingDecomposerLib']"))
|
|
|
|
(("library_dirs\\s*=\\s*\\[\\]")
|
|
|
|
"library_dirs = ['${CMAKE_BINARY_DIR}/src/RingDecomposerLib']")
|
|
|
|
(("extra_objects=.*")
|
|
|
|
(string-append
|
|
|
|
"extra_link_args=['-Wl,-rpath=" #$output "/lib'],\n")))))
|
|
|
|
(add-after 'build 'build-doc
|
|
|
|
(lambda _
|
|
|
|
;; Disable redundant LaTeX documentation
|
|
|
|
(substitute* "../source/documentation/sphinx/conf.py"
|
|
|
|
(("^(subprocess.*latex|shutil).*") ""))
|
|
|
|
(substitute* "../source/documentation/doxygen.cfg"
|
|
|
|
(("GENERATE_LATEX.*YES") "GENERATE_LATEX = NO"))
|
|
|
|
;; Build HTML documentation
|
|
|
|
(invoke "sphinx-build" "-b" "html"
|
|
|
|
"../source/documentation/sphinx" "html")))
|
|
|
|
(add-after 'install 'install-doc
|
|
|
|
(lambda _
|
|
|
|
;; Not reproducible
|
|
|
|
(delete-file-recursively "html/.doctrees")
|
|
|
|
(copy-recursively "html"
|
|
|
|
(string-append #$output "/share/doc/"
|
|
|
|
#$name "-" #$version "/html"))))
|
|
|
|
(delete 'check)
|
|
|
|
(add-after 'install 'check
|
|
|
|
(assoc-ref %standard-phases 'check))
|
|
|
|
(add-before 'check 'set-pythonpath
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
(add-installed-pythonpath inputs outputs))))))
|
|
|
|
(inputs (list python))
|
|
|
|
(native-inputs (list doxygen python python-cython python-sphinx))
|
|
|
|
(home-page "https://github.com/rareylab/RingDecomposerLib")
|
|
|
|
(synopsis "Calculate ring topology descriptions")
|
|
|
|
(description "RingDecomposerLib is a library for the calculation of
|
|
|
|
unique ring families, relevant cycles, the smallest set of smallest rings and
|
|
|
|
other ring topology descriptions.")
|
|
|
|
(license license:bsd-3)))
|
2022-10-13 17:04:24 -04:00
|
|
|
|
|
|
|
(define-public rdkit
|
|
|
|
(package
|
|
|
|
(name "rdkit")
|
2024-01-28 18:02:02 -05:00
|
|
|
(version "2023.09.4")
|
2022-10-13 17:04:24 -04:00
|
|
|
(source (origin
|
|
|
|
(method git-fetch)
|
|
|
|
(uri (git-reference
|
|
|
|
(url "https://github.com/rdkit/rdkit")
|
|
|
|
(commit
|
|
|
|
(string-append
|
|
|
|
"Release_" (string-replace-substring version "." "_")))))
|
|
|
|
(file-name (git-file-name name version))
|
|
|
|
(sha256
|
|
|
|
(base32
|
2024-01-28 18:02:02 -05:00
|
|
|
"1lgcgijlzzwpfxndsdlx13npdfk7hcii11zg25cvpmzhbpn6vyn8"))
|
2022-10-13 17:04:24 -04:00
|
|
|
(patches
|
|
|
|
(search-patches "rdkit-unbundle-external-dependencies.patch"))
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
(snippet
|
|
|
|
#~(begin
|
|
|
|
;; Remove pickle files (only used in tests),
|
|
|
|
;; as they are compiled programs
|
|
|
|
(for-each
|
|
|
|
(lambda (name)
|
|
|
|
(display (string-append name "\n"))
|
|
|
|
(delete-file name))
|
|
|
|
(find-files "." "\\.pkl(\\.gz)?$"))
|
|
|
|
;; Remove SQLite data files (can be generated)
|
|
|
|
(delete-file "Data/RDData.sqlt")
|
|
|
|
(delete-file "Data/RDTests.sqlt")))))
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
(arguments
|
|
|
|
(list
|
|
|
|
#:imported-modules (append %cmake-build-system-modules
|
|
|
|
'((guix build python-build-system)))
|
|
|
|
#:modules '((guix build cmake-build-system)
|
|
|
|
(guix build utils)
|
|
|
|
((guix build python-build-system)
|
|
|
|
#:select (add-installed-pythonpath)))
|
|
|
|
#:configure-flags
|
|
|
|
#~(list "-DRDK_BUILD_AVALON_SUPPORT=ON"
|
|
|
|
"-DRDK_BUILD_CAIRO_SUPPORT=ON"
|
|
|
|
"-DRDK_BUILD_FREESASA_SUPPORT=ON"
|
|
|
|
"-DRDK_BUILD_INCHI_SUPPORT=ON"
|
|
|
|
"-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
|
|
|
|
(string-append "-DCATCH_DIR="
|
|
|
|
(search-input-directory %build-inputs
|
|
|
|
"/include/catch2"))
|
|
|
|
"-DRDK_INSTALL_INTREE=OFF"
|
|
|
|
"-DRDK_INSTALL_STATIC_LIBS=OFF"
|
|
|
|
(string-append
|
|
|
|
"-DRDK_OPTIMIZE_POPCNT="
|
|
|
|
#$(let ((system (or (%current-target-system)
|
|
|
|
(%current-system))))
|
|
|
|
(cond
|
|
|
|
((string-prefix? "x86_64" system) "ON")
|
|
|
|
((string-prefix? "i686" system) "ON")
|
|
|
|
(else "OFF"))))
|
|
|
|
"-DRDK_USE_FLEXBISON=ON"
|
|
|
|
(string-append
|
|
|
|
"-DCMAKE_INCLUDE_PATH="
|
|
|
|
(search-input-directory %build-inputs "/include/avalontoolkit")))
|
|
|
|
#:phases
|
|
|
|
#~(modify-phases %standard-phases
|
|
|
|
(add-after 'unpack 'copy-external-dependencies
|
|
|
|
(lambda _
|
|
|
|
(symlink
|
|
|
|
(string-append
|
|
|
|
(search-input-file
|
|
|
|
%build-inputs "/share/fonts/truetype/ComicNeue-Regular.ttf"))
|
|
|
|
"Data/Fonts/ComicNeue-Regular.ttf")))
|
|
|
|
(add-after 'unpack 'fix-inchi-include
|
|
|
|
(lambda _
|
|
|
|
(substitute* "Code/cmake/Modules/FindInchi.cmake"
|
|
|
|
(("inchi_api.h.*\\)") "inchi/inchi_api.h)")
|
|
|
|
(("INCHI_LIBRARY NAMES.*\\)")
|
|
|
|
"INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
|
|
|
|
(("find_library" prev)
|
|
|
|
(string-append
|
|
|
|
"list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
|
|
|
|
prev)))
|
|
|
|
(substitute* "External/INCHI-API/inchi.cpp"
|
|
|
|
(("<inchi_api.h>") "<inchi/inchi_api.h>"))))
|
|
|
|
(add-before 'build 'enable-bytecode-determinism
|
|
|
|
(lambda _
|
|
|
|
(setenv "PYTHONHASHSEED" "0")
|
|
|
|
(setenv "PYTHONDONTWRITEBYTECODE" "1")))
|
|
|
|
(add-after 'install 'pre-check
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
(with-directory-excursion "../source"
|
|
|
|
(invoke "sqlite3" "Data/RDData.sqlt"
|
|
|
|
".read rdkit/Dbase/test_data/RDData.sqlite")
|
|
|
|
(invoke "sqlite3" "Data/RDTests.sqlt"
|
|
|
|
".read rdkit/Dbase/test_data/RDTests.sqlite")
|
|
|
|
(setenv "RDBASE" (canonicalize-path ".")))
|
|
|
|
(add-installed-pythonpath inputs outputs)))
|
|
|
|
(delete 'check)
|
|
|
|
(add-after 'pre-check 'check
|
|
|
|
(lambda* (#:key tests? parallel-tests? #:allow-other-keys)
|
|
|
|
(when tests?
|
|
|
|
(let ((job-count (number->string
|
|
|
|
(if parallel-tests? (parallel-job-count) 1))))
|
|
|
|
(invoke
|
|
|
|
"ctest" "-j" job-count
|
|
|
|
"-E" (string-append
|
|
|
|
"("
|
|
|
|
(string-join
|
|
|
|
'(;; need pickled data
|
|
|
|
"pyDiscreteValueVect" "pySparseIntVect"
|
|
|
|
"graphmoltestPickler" "pyPartialCharges"
|
|
|
|
"substructLibraryTest" "pyFeatures"
|
|
|
|
"pythonTestDirML" "pythonTestDirChem"
|
|
|
|
;; Catching Python exception fails
|
2024-01-28 18:02:02 -05:00
|
|
|
"pyRanker"
|
|
|
|
;; Flaky test depending on floating point rounding
|
|
|
|
"testConrec"
|
|
|
|
) "|")
|
2022-10-13 17:04:24 -04:00
|
|
|
")")))))))))
|
|
|
|
(inputs
|
|
|
|
(list avalon-toolkit
|
|
|
|
cairo
|
|
|
|
coordgenlibs
|
|
|
|
font-comic-neue
|
|
|
|
freetype
|
|
|
|
inchi
|
|
|
|
maeparser
|
|
|
|
python
|
|
|
|
ringdecomposerlib
|
|
|
|
sqlite
|
|
|
|
yaehmop))
|
|
|
|
(native-inputs
|
|
|
|
(list bison
|
|
|
|
boost
|
2024-01-28 18:02:02 -05:00
|
|
|
catch2-3
|
2022-10-13 17:04:24 -04:00
|
|
|
eigen
|
|
|
|
flex
|
|
|
|
freesasa
|
|
|
|
pkg-config
|
|
|
|
rapidjson
|
|
|
|
tar))
|
|
|
|
(propagated-inputs
|
|
|
|
(list python-numpy python-cairocffi python-pillow))
|
|
|
|
(home-page "https://rdkit.org/")
|
|
|
|
(synopsis "Collection of cheminformatics software")
|
|
|
|
(description "RDKit is a C++ and Python library for cheminformatics, which
|
|
|
|
includes (among other things) the analysis and modification of molecules in 2D
|
|
|
|
and 3D and descriptor generation for machine learning.")
|
2024-01-28 18:02:02 -05:00
|
|
|
;; For 32 bit systems, there is a bug in Boost.Python:
|
|
|
|
;; https://github.com/boostorg/python/issues/312. Additionally, several
|
|
|
|
;; other test fail.
|
|
|
|
(supported-systems %64bit-supported-systems)
|
2022-10-13 17:04:24 -04:00
|
|
|
(license license:bsd-3)))
|