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0c3cac7e0e
* gnu/packages/chemistry.scm (python-geometric): Fix build. [native-inputs]: Remove python-wheel. [arguments] <#:phases>: Remove six dependency. Change-Id: I2dd5191bf2b41719dc3b56c8b914eb090161b090 Reviewed-by: Nicolas Graves <ngraves@ngraves.fr> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
1786 lines
72 KiB
Scheme
1786 lines
72 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
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;;; Copyright © 2018, 2021 Kei Kebreau <kkebreau@posteo.net>
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;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
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;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
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;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2022, 2023, 2024, 2025 David Elsing <david.elsing@posteo.net>
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;;;
|
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;;; This file is part of GNU Guix.
|
||
;;;
|
||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||
;;; under the terms of the GNU General Public License as published by
|
||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||
;;; your option) any later version.
|
||
;;;
|
||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||
;;; GNU General Public License for more details.
|
||
;;;
|
||
;;; You should have received a copy of the GNU General Public License
|
||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||
|
||
(define-module (gnu packages chemistry)
|
||
#:use-module ((guix licenses) #:prefix license:)
|
||
#:use-module (guix build-system cmake)
|
||
#:use-module (guix build-system gnu)
|
||
#:use-module (guix build-system pyproject)
|
||
#:use-module (guix build-system python)
|
||
#:use-module (guix download)
|
||
#:use-module (guix gexp)
|
||
#:use-module (guix git-download)
|
||
#:use-module (guix packages)
|
||
#:use-module (guix utils)
|
||
#:use-module (gnu packages)
|
||
#:use-module (gnu packages algebra)
|
||
#:use-module (gnu packages autotools)
|
||
#:use-module (gnu packages backup)
|
||
#:use-module (gnu packages base)
|
||
#:use-module (gnu packages bison)
|
||
#:use-module (gnu packages boost)
|
||
#:use-module (gnu packages c)
|
||
#:use-module (gnu packages check)
|
||
#:use-module (gnu packages cmake)
|
||
#:use-module (gnu packages compression)
|
||
#:use-module (gnu packages cpp)
|
||
#:use-module (gnu packages documentation)
|
||
#:use-module (gnu packages flex)
|
||
#:use-module (gnu packages fonts)
|
||
#:use-module (gnu packages fontutils)
|
||
#:use-module (gnu packages fortran-xyz)
|
||
#:use-module (gnu packages gcc)
|
||
#:use-module (gnu packages gl)
|
||
#:use-module (gnu packages graphviz)
|
||
#:use-module (gnu packages gtk)
|
||
#:use-module (gnu packages gv)
|
||
#:use-module (gnu packages image)
|
||
#:use-module (gnu packages lisp)
|
||
#:use-module (gnu packages maths)
|
||
#:use-module (gnu packages mpi)
|
||
#:use-module (gnu packages perl)
|
||
#:use-module (gnu packages pkg-config)
|
||
#:use-module (gnu packages python)
|
||
#:use-module (gnu packages python-build)
|
||
#:use-module (gnu packages python-science)
|
||
#:use-module (gnu packages python-xyz)
|
||
#:use-module (gnu packages qt)
|
||
#:use-module (gnu packages serialization)
|
||
#:use-module (gnu packages sphinx)
|
||
#:use-module (gnu packages sqlite)
|
||
#:use-module (gnu packages stb)
|
||
#:use-module (gnu packages tex)
|
||
#:use-module (gnu packages web)
|
||
#:use-module (gnu packages xml)
|
||
#:use-module (srfi srfi-1))
|
||
|
||
;;; Please: Try to add new module packages in alphabetic order.
|
||
;;;
|
||
;;; Code:
|
||
|
||
(define-public avogadrolibs
|
||
(package
|
||
(name "avogadrolibs")
|
||
(version "1.100.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/OpenChemistry/avogadrolibs")
|
||
(commit version)))
|
||
(sha256
|
||
(base32 "1l9bp3ba8yx9mk2in5v375jzi1w4y7l1xl37xqv869810drgjffc"))
|
||
(file-name (git-file-name name version))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
(list eigen
|
||
mmtf-cpp
|
||
googletest
|
||
pkg-config
|
||
pybind11))
|
||
(inputs
|
||
`(("glew" ,glew)
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||
("libarchive" ,libarchive)
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||
("libmsym" ,libmsym)
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||
("molequeue" ,molequeue)
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||
("python" ,python)
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||
("spglib" ,spglib)
|
||
("qtbase-5" ,qtbase-5)
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||
("qtsvg-5" ,qtsvg-5)
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||
("avogadro-molecules"
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||
,(origin
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||
(method git-fetch)
|
||
(uri
|
||
(git-reference
|
||
(url "https://github.com/openchemistry/molecules")
|
||
(commit "8a37883")))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"00mfx0bwmqazbiklrvaijjd5n4wa5lp3z73291ihm78q0v9dzhl4"))))
|
||
("avogadro-crystals"
|
||
,(origin
|
||
(method git-fetch)
|
||
(uri
|
||
(git-reference
|
||
(url "https://github.com/openchemistry/crystals")
|
||
(commit "28404bd")))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0kcz99q5nfl2v2qmm9cqnbb2c2qqzw79vsnv557i7x64bxsxrw1m"))))
|
||
("avogadro-fragments"
|
||
,(origin
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||
(method git-fetch)
|
||
(uri
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||
(git-reference
|
||
(url "https://github.com/openchemistry/fragments")
|
||
(commit "c4943b5")))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
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||
"17l6qmkc25wb0nvic708l25fxiy89b3vfs0x5d40qcnn27bid32n"))))))
|
||
(arguments
|
||
(list
|
||
#:configure-flags #~(list "-DENABLE_TESTING=ON")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'symlink
|
||
(lambda _
|
||
(begin
|
||
(symlink (assoc-ref %build-inputs "avogadro-molecules")
|
||
"../molecules")
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||
(symlink (assoc-ref %build-inputs "avogadro-crystals")
|
||
"../crystals")
|
||
(symlink (assoc-ref %build-inputs "avogadro-fragments")
|
||
"../fragments")))))))
|
||
(home-page "https://www.openchemistry.org/projects/avogadro2/")
|
||
(synopsis "Libraries for chemistry, bioinformatics, and related areas")
|
||
(description
|
||
"Avogadro libraries provide 3D rendering, visualization, analysis and data
|
||
processing useful in computational chemistry, molecular modeling,
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||
bioinformatics, materials science, and related areas.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public avogadro2
|
||
(package
|
||
(name "avogadro2")
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||
(version "1.100.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/OpenChemistry/avogadroapp")
|
||
(commit version)))
|
||
(sha256
|
||
(base32 "19cd5aqvcw6xj0x1kmzmxl0vrnbhk5ymnl9p2p4d9504ma5k6aim"))
|
||
(file-name (git-file-name name version))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
`(("eigen" ,eigen)
|
||
("pkg-config" ,pkg-config)
|
||
("avogadro-i18n"
|
||
,(origin
|
||
(method git-fetch)
|
||
(uri
|
||
(git-reference
|
||
(url "https://github.com/openchemistry/avogadro-i18n")
|
||
(commit "07bee85")))
|
||
(file-name (git-file-name name
|
||
version))
|
||
(sha256
|
||
(base32
|
||
"1vhjh0gilmm90269isrkvyzwwh1cj3bwcxls394psadw1a89mk14"))))))
|
||
(inputs (list avogadrolibs hdf5 molequeue openbabel qtbase-5 qtsvg-5))
|
||
;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
|
||
(arguments
|
||
(list
|
||
#:tests? #f
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'symlink
|
||
(lambda _
|
||
(begin
|
||
(symlink (assoc-ref %build-inputs "avogadro-i18n")
|
||
"../avogadro-i18n"))))
|
||
(add-after 'install 'wrap-program
|
||
(lambda _
|
||
(wrap-program (string-append #$output "/bin/avogadro2")
|
||
(list
|
||
"PATH"
|
||
'suffix
|
||
(list (string-append #$openbabel "/bin")))
|
||
(list
|
||
"QT_PLUGIN_PATH"
|
||
'suffix
|
||
(list (string-append #$qtsvg-5 "/lib/qt5/plugins")))))))))
|
||
(home-page "https://www.openchemistry.org/projects/avogadro2/")
|
||
(synopsis "Advanced molecule editor")
|
||
(description
|
||
"Avogadro 2 is an advanced molecule editor and visualizer designed for use
|
||
in computational chemistry, molecular modeling, bioinformatics, materials
|
||
science, and related areas. It offers flexible high quality rendering and a
|
||
powerful plugin architecture.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public inchi
|
||
(package
|
||
(name "inchi")
|
||
;; Update the inchi-doc native input when updating inchi.
|
||
(version "1.07.3")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/IUPAC-InChI/InChI")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0r32f6i5d8ir96ic3nvqb5lywxrznwrkk6hnz1q0a4bgsw5pmk0n"))
|
||
(modules '((guix build utils)))
|
||
(snippet '(delete-file-recursively "INCHI-1-BIN"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(list
|
||
#:tests? #f ; no check target
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(delete 'configure) ; no configure script
|
||
(add-after 'unpack 'chdir-to-build-directory
|
||
(lambda _ (chdir "INCHI-1-SRC/INCHI_EXE/inchi-1/gcc")))
|
||
(add-after 'build 'build-library
|
||
(lambda* (#:key parallel-build? #:allow-other-keys)
|
||
(chdir "../../../INCHI_API/libinchi/gcc")
|
||
(invoke "make" "-j" (if parallel-build?
|
||
(number->string (parallel-job-count))
|
||
"1"))))
|
||
(replace 'install
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let* ((bin (string-append #$output "/bin"))
|
||
(doc (string-append #$output "/share/doc/inchi"))
|
||
(include-dir (string-append #$output "/include/inchi"))
|
||
(lib (string-append #$output "/lib/inchi")))
|
||
(chdir "../../..")
|
||
;; Install binary.
|
||
(with-directory-excursion "INCHI_EXE/bin/Linux"
|
||
(rename-file "inchi-1" "inchi")
|
||
(install-file "inchi" bin))
|
||
;; Install library.
|
||
(with-directory-excursion "INCHI_API/bin/Linux"
|
||
(let ((libname (basename
|
||
(car
|
||
(find-files "." "libinchi\\.so\\.1\\.*")))))
|
||
(install-file libname lib)
|
||
(with-directory-excursion lib
|
||
(symlink libname "libinchi.so.1")
|
||
(symlink "libinchi.so.1" "libinchi.so"))))
|
||
;; Install header files.
|
||
(with-directory-excursion "INCHI_BASE/src"
|
||
(for-each (lambda (file)
|
||
(install-file file include-dir))
|
||
(find-files "." "\\.h$")))
|
||
;; Install documentation.
|
||
(with-directory-excursion "../INCHI-1-DOC"
|
||
(for-each
|
||
(lambda (file)
|
||
(install-file file doc))
|
||
(find-files "." "\\.pdf$")))))))))
|
||
(native-inputs (list unzip))
|
||
(home-page "https://www.inchi-trust.org")
|
||
(synopsis "Utility for manipulating machine-readable chemical structures")
|
||
(description
|
||
"The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
|
||
chemical structures into machine-readable strings of information. InChIs are
|
||
unique to the compound they describe and can encode absolute stereochemistry
|
||
making chemicals and chemistry machine-readable and discoverable. A simple
|
||
analogy is that InChI is the bar-code for chemistry and chemical structures.")
|
||
(license license:expat)))
|
||
|
||
(define-public libcint
|
||
(package
|
||
(name "libcint")
|
||
(version "6.1.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/sunqm/libcint")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1vlzgkgdhf94w3l1nk9rswf50sqbw4l9981hmnivgwwv905mq4ji"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; Autogenerated code
|
||
(delete-file-recursively "src/autocode")
|
||
(delete-file "doc/program_ref.pdf")))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
#:configure-flags
|
||
#~(list "-DWITH_RANGE_COULOMB=1"
|
||
"-DWITH_CINT2_INTERFACE=1"
|
||
"-DMIN_EXPCUTOFF=20"
|
||
"-DQUICK_TEST=ON"
|
||
"-DENABLE_TEST=ON")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'autogenerate-integrals
|
||
(lambda _
|
||
(mkdir "src/autocode")
|
||
(with-directory-excursion "scripts"
|
||
(invoke "clisp" "auto_intor.cl")
|
||
(for-each
|
||
(lambda (file)
|
||
(rename-file file (string-append
|
||
"../src/autocode/" (basename file))))
|
||
(find-files "." "\\.c$")))))
|
||
(add-after 'unpack 'adjust-build-path
|
||
(lambda _
|
||
(substitute* (find-files "testsuite" "\\.py$")
|
||
(("\\.\\./\\.\\./build") "../../../build")))))))
|
||
(native-inputs
|
||
(list clisp
|
||
python
|
||
python-numpy))
|
||
(inputs
|
||
(list openblas))
|
||
(home-page "https://github.com/sunqm/libcint")
|
||
(synopsis "General GTO integrals for quantum chemistry")
|
||
(description
|
||
"@code{libcint} is a C library (also with a Fortran API) to evaluate one-
|
||
and two-electron integrals for @acronym{GTO, Gaussian Type Function}s.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public libmsym
|
||
(package
|
||
(name "libmsym")
|
||
(version "0.2.3")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/mcodev31/libmsym")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32
|
||
"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)))
|
||
|
||
(define-public mmtf-cpp
|
||
(package
|
||
(name "mmtf-cpp")
|
||
(version "1.1.0")
|
||
(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
|
||
"0rs2f1ppgqz663c3m22p8wsq6z839bj59zy29chci46ypfhwv6ph"))))
|
||
(build-system cmake-build-system)
|
||
;; Tests require the soon-to-be-deprecated version 1 of the catch-framework.
|
||
(arguments '(#:tests? #f))
|
||
;; There is no support for modern msgpack versions yet (see:
|
||
;; https://github.com/rcsb/mmtf-cpp/issues/44).
|
||
(propagated-inputs (list msgpack-3)) ;included by mmtf/structure_data.hpp
|
||
(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)))
|
||
|
||
(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
|
||
(list qtbase-5))
|
||
(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)))
|
||
|
||
(define-public tng
|
||
(package
|
||
(name "tng")
|
||
(version "1.8.2")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/gromacs/tng")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
|
||
(build-system cmake-build-system)
|
||
(inputs
|
||
(list zlib))
|
||
(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)))
|
||
|
||
(define-public gromacs
|
||
(package
|
||
(name "gromacs")
|
||
(version "2022.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"15vjwasxjq0h18dmzacjkdim51zrvr0ni42hbc30557j5xhbw4f5"))
|
||
;; 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
|
||
(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()")))))))
|
||
(native-inputs
|
||
(list doxygen
|
||
graphviz
|
||
pkg-config
|
||
python
|
||
python-pygments
|
||
python-sphinx))
|
||
(inputs
|
||
(list fftwf
|
||
`(,hwloc-2 "lib")
|
||
lmfit
|
||
openblas
|
||
perl
|
||
tinyxml2
|
||
tng))
|
||
(home-page "https://www.gromacs.org/")
|
||
(synopsis "Molecular dynamics software package")
|
||
(description "GROMACS is a versatile package to perform molecular dynamics,
|
||
i.e. simulate the Newtonian equations of motion for systems with hundreds to
|
||
millions of particles. It is primarily designed for biochemical molecules like
|
||
proteins, lipids and nucleic acids that have a lot of complicated bonded
|
||
interactions, but since GROMACS is extremely fast at calculating the nonbonded
|
||
interactions (that usually dominate simulations) many groups are also using it
|
||
for research on non-biological systems, e.g. polymers. GROMACS supports all the
|
||
usual algorithms you expect from a modern molecular dynamics implementation.")
|
||
(license license:lgpl2.1+)
|
||
(properties '((tunable? . #t)))))
|
||
|
||
(define-public openbabel
|
||
(package
|
||
(name "openbabel")
|
||
(version "3.1.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/openbabel/openbabel")
|
||
(commit (string-append
|
||
"openbabel-"
|
||
(string-replace-substring version "." "-")))))
|
||
(sha256
|
||
(base32 "1ijl4px8nw9824znrsw9nsv4qf9xy0zgd8wrw8hhl15jy1sn02n1"))
|
||
(file-name (git-file-name name version))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
;; FIXME: Disable tests on i686 to work around
|
||
;; https://github.com/openbabel/openbabel/issues/2041.
|
||
#:tests? (or (%current-target-system)
|
||
(not (string=? "i686-linux" (%current-system))))
|
||
#:configure-flags
|
||
'(list
|
||
"-DOPENBABEL_USE_SYSTEM_INCHI=ON"
|
||
(string-append
|
||
"-DINCHI_LIBRARY="
|
||
(search-input-file %build-inputs "/lib/inchi/libinchi.so.1"))
|
||
(string-append "-DINCHI_INCLUDE_DIR="
|
||
(search-input-directory %build-inputs "/include/inchi")))
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
;; Fixed upstream:
|
||
;; https://github.com/openbabel/openbabel/commit/c0570bfeb2d7e0a6a6de1f257cf28e7f3cac8739
|
||
(add-after 'unpack 'fix-time-check
|
||
(lambda _
|
||
(substitute* "src/config.h.cmake"
|
||
(("(#ifdef HAVE_(SYS_)?TIME)(.*)$" _ old _ suffix)
|
||
(string-append old "_H" suffix))))))))
|
||
(native-inputs
|
||
(list pkg-config))
|
||
(inputs
|
||
(list eigen inchi libxml2 rapidjson zlib))
|
||
(home-page "https://openbabel.org/")
|
||
(synopsis "Chemistry data manipulation toolbox")
|
||
(description
|
||
"Open Babel is a chemical toolbox designed to speak the many languages of
|
||
chemical data. It's a collaborative project allowing anyone to search, convert,
|
||
analyze, or store data from molecular modeling, chemistry, solid-state
|
||
materials, biochemistry, or related areas.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public spglib
|
||
(package
|
||
(name "spglib")
|
||
(version "2.5.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/spglib/spglib")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32 "0x5igrqwx7r2shysmi9sqcjg4hpb7hba3ddlwg05z6c57a3ifbqc"))
|
||
(file-name (git-file-name name version))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
'(#:tests? #f ; tests want to clone a git repository, which won't work
|
||
#:configure-flags '("-DSPGLIB_WITH_TESTS=OFF")
|
||
#:phases (modify-phases %standard-phases
|
||
(add-before 'configure 'patch-files (lambda _ (substitute* "CMakeLists.txt"
|
||
(("include\\(cmake/DynamicVersion.cmake\\)")
|
||
"")
|
||
(("dynamic_version.*")
|
||
"")
|
||
(("PROJECT_PREFIX.*")
|
||
"")
|
||
(("FALLBACK_VERSION.*")
|
||
"set (PROJECT_VERSION 2.5.0")
|
||
(("\\$\\{PROJECT_VERSION_FULL\\}")
|
||
"2.5.0")
|
||
(("\\$\\{GIT_COMMIT\\}")
|
||
"\"\""))
|
||
(substitute* "src/CMakeLists.txt"
|
||
((".*Spglib_GitHash.*")
|
||
""))))
|
||
(add-after 'unpack 'patch-header-install-dir
|
||
(lambda _
|
||
;; As of the writing of this package, CMake and GNU build systems
|
||
;; install the header to two different location. This patch makes
|
||
;; the CMake build system's choice of header directory compatible
|
||
;; with the GNU build system's choice and with what avogadrolibs
|
||
;; expects.
|
||
;; See https://github.com/spglib/spglib/issues/75 and the relevant
|
||
;; part of https://github.com/OpenChemistry/avogadroapp/issues/97.
|
||
(substitute* "CMakeLists.txt"
|
||
(("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir)
|
||
(string-append include-dir "/spglib"))))))))
|
||
(home-page "https://spglib.github.io/spglib/index.html")
|
||
(synopsis "Library for crystal symmetry search")
|
||
(description "Spglib is a library for finding and handling crystal
|
||
symmetries written in C. Spglib can be used to:
|
||
|
||
@enumerate
|
||
@item Find symmetry operations
|
||
@item Identify space-group type
|
||
@item Wyckoff position assignment
|
||
@item Refine crystal structure
|
||
@item Find a primitive cell
|
||
@item Search irreducible k-points
|
||
@end enumerate")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-geometric
|
||
(package
|
||
(name "python-geometric")
|
||
(version "1.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/leeping/geomeTRIC")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0w3c71wvhnc44pfafcjfgqkjimkcdkpjk3bahg9v6l1z8c0cyhfy"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'remove-six
|
||
(lambda _
|
||
(substitute* "geometric/nifty.py"
|
||
(("import six") "")
|
||
(("six\\.string_types") "str"))
|
||
(substitute* "setup.py"
|
||
(("'six',") "")))))))
|
||
(native-inputs
|
||
(list python-pytest
|
||
python-setuptools))
|
||
(propagated-inputs
|
||
(list python-numpy
|
||
python-scipy
|
||
python-networkx))
|
||
(home-page "https://github.com/leeping/geomeTRIC")
|
||
(synopsis "Geometry optimization of molecular structures")
|
||
(description
|
||
"@code{geomeTRIC} is a Python library and program for geometry
|
||
optimization of molecular structures, which works with different external
|
||
quantum chemistry (and molecular mechanics) softwares.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-pymol
|
||
(package
|
||
(name "python-pymol")
|
||
(version "3.1.0")
|
||
(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 "199zhpdljsvfjnvs7h7q17ib7ajnjiwg790rg8xxhaszjd968byq"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
;; XXX: Most tests fail with import errors.
|
||
#:tests? #f
|
||
#: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-join
|
||
(list
|
||
(search-input-directory inputs "/include/freetype2")
|
||
(search-input-directory inputs "/include/libxml2")
|
||
(getenv "CPLUS_INCLUDE_PATH"))
|
||
":"))))
|
||
;; Prevent deleting the leading / in the __init__.py path in the
|
||
;; launch script.
|
||
(add-after 'unpack 'disable-unchroot
|
||
(lambda _
|
||
(substitute* "setup.py"
|
||
(("self\\.unchroot")
|
||
""))))
|
||
;; The setup.py script does not support one of the Python build
|
||
;; system's default flags, "--single-version-externally-managed".
|
||
(delete 'build)
|
||
(replace 'install
|
||
(lambda _
|
||
(invoke "python" "setup.py" "install"
|
||
(string-append "--prefix=" #$output) "--root=/"))))))
|
||
(inputs (list freetype
|
||
libpng
|
||
freeglut
|
||
glew
|
||
libxml2
|
||
mmtf-cpp
|
||
python-pyqt
|
||
glm
|
||
netcdf))
|
||
(native-inputs (list cmake-minimal catch2 python-pytest python-setuptools))
|
||
(propagated-inputs (list python-numpy))
|
||
(home-page "https://pymol.org")
|
||
(synopsis "Molecular visualization system")
|
||
(description
|
||
"PyMOL is a capable molecular viewer and renderer. It can be used to
|
||
prepare publication-quality figures, to share interactive results with your
|
||
colleagues, or to generate pre-rendered animations.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-pyscf
|
||
(package
|
||
(name "python-pyscf")
|
||
(version "2.9.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pyscf/pyscf")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1lj48c749aqf9zd5xbshjsfr0y972r2nsm8lf3760jbfadg9jdsi"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:modules
|
||
'((guix build pyproject-build-system)
|
||
(guix build utils)
|
||
(ice-9 textual-ports))
|
||
;; Some tests take a very long time and libxc support is not enabled.
|
||
#:tests? #f
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-before 'build 'set-cmake-arguments
|
||
(lambda _
|
||
;; Copied from cmake-build-system. This is passed to 'cmake' in
|
||
;; setup.py.
|
||
(setenv "CMAKE_CONFIGURE_ARGS"
|
||
(string-join
|
||
`("-DCMAKE_BUILD_TYPE=RelWithDebInfo"
|
||
,(string-append "-DCMAKE_INSTALL_PREFIX=" #$output)
|
||
;; ensure that the libraries are installed into /lib
|
||
"-DCMAKE_INSTALL_LIBDIR=lib"
|
||
;; add input libraries to rpath
|
||
"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE"
|
||
;; add (other) libraries of the project itself to rpath
|
||
,(string-append "-DCMAKE_INSTALL_RPATH=" #$output "/lib")
|
||
;; enable verbose output from builds
|
||
"-DCMAKE_VERBOSE_MAKEFILE=ON"
|
||
"-DENABLE_LIBXC=OFF"
|
||
"-DBUILD_LIBXC=OFF"
|
||
"-DBUILD_XCFUN=OFF"
|
||
"-DBUILD_LIBCINT=OFF"))))))))
|
||
(native-inputs
|
||
(list
|
||
cmake-minimal
|
||
;; HACK: Add gcc, make tune work.
|
||
;; build-system-with-tuning-compiler on guix/transformations.scm
|
||
;; want to find compiler on the build-inputs, but gcc is on the
|
||
;; python-build-system's host-inputs, so when tune it , will report:
|
||
;; "failed to determine which compiler is used"
|
||
(canonical-package gcc)
|
||
python-setuptools
|
||
python-wheel))
|
||
(inputs
|
||
(list
|
||
;; Use qcint when tuning for x86_64.
|
||
(if (and (assq 'cpu-tuning (package-properties this-package))
|
||
(target-x86-64?))
|
||
qcint
|
||
libcint)
|
||
xcfun
|
||
openblas))
|
||
(propagated-inputs
|
||
(list python-numpy
|
||
python-scipy
|
||
python-h5py))
|
||
(home-page "https://github.com/pyscf/pyscf")
|
||
(synopsis "Python library for quantum chemistry calculations")
|
||
(description
|
||
"@code{PySCF} (Python-based Simulations of Chemistry Framework) is a
|
||
Python library for quantum chemistry calculations and method development.
|
||
Most of the functionality is implemented in Python, while computationally
|
||
critical parts are implemented in C.")
|
||
(properties '((tunable? . #t)))
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-pyscf-dispersion
|
||
(package
|
||
(name "python-pyscf-dispersion")
|
||
(version "1.2.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pyscf/dispersion")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0za1qmn0v948zalw1j6j0qdbj7cnfz398aq1lf145frxddmprz8n"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
;; This tries to download and build Simple DFT-D3 and DFT-D4.
|
||
(add-after 'unpack 'disable-build
|
||
(lambda _
|
||
(substitute* "setup.py"
|
||
(("packages=modules.*")
|
||
"packages=modules,")
|
||
(("cmdclass=.*") ""))))
|
||
(add-after 'install 'symlink
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((outdir (string-append (site-packages inputs outputs)
|
||
"/pyscf/lib")))
|
||
(mkdir-p outdir)
|
||
(symlink (string-append #$(this-package-input "fortran-simple-dftd3")
|
||
"/lib/libs-dftd3.so")
|
||
(string-append outdir "/libs-dftd3.so"))
|
||
(symlink (string-append #$(this-package-input "fortran-dftd4")
|
||
"/lib/libdftd4.so")
|
||
(string-append outdir "/libdftd4.so"))))))))
|
||
(native-inputs
|
||
(list python-pytest
|
||
python-setuptools
|
||
python-wheel))
|
||
(inputs
|
||
(list fortran-simple-dftd3
|
||
fortran-dftd4))
|
||
(propagated-inputs
|
||
(list python-pyscf))
|
||
(home-page "https://github.com/pyscf/dispersion")
|
||
(synopsis "PySCF extensions for dispersion calculations")
|
||
(description
|
||
"This package is a wrapper around simple-dftd3 and dftd4 for use with pyscf.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-pyscf-properties
|
||
(let ((commit "4eee5a430fb47eca5962f36fdcaf75c2b87e7ede")
|
||
(revision "1"))
|
||
(package
|
||
(name "python-pyscf-properties")
|
||
(version (git-version "0.1" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pyscf/properties")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0jzyfqhk6hcn1dpc311iiamc5dnwp71q5087432f5gqqvpg1zz94"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments (list #:tests? #f)) ; no tests
|
||
(native-inputs
|
||
(list python-setuptools
|
||
python-wheel))
|
||
(propagated-inputs
|
||
(list python-pyscf))
|
||
(home-page "https://github.com/pyscf/properties")
|
||
(synopsis "PySCF electronic properties extension")
|
||
(description
|
||
"This extension to python-pyscf provides calculations of different
|
||
electromagnetic properties for molecules and crystals.")
|
||
(license license:asl2.0))))
|
||
|
||
;; Depends on at least SSE3 and should only be used for a tuned build of
|
||
;; python-pyscf.
|
||
(define-public qcint
|
||
(hidden-package
|
||
(let ((base libcint))
|
||
(package
|
||
(inherit base)
|
||
(name "qcint")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/sunqm/qcint")
|
||
(commit (string-append "v" (package-version base)))))
|
||
(file-name (git-file-name name (package-version base)))
|
||
(sha256
|
||
(base32
|
||
"17cgb2m93n48fagl5m2kr8n6kk8m9j6bxkhmh492ms3dbm0xpxml"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; Autogenerated code
|
||
(delete-file-recursively "src/autocode")))))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments base)
|
||
((#:configure-flags flags '())
|
||
#~(cons "-DBUILD_MARCH_NATIVE=OFF"
|
||
#$flags))
|
||
((#:phases phases)
|
||
#~(modify-phases #$phases
|
||
(delete 'adjust-build-path)))
|
||
;; Tests require python-pyscf.
|
||
((#:tests? _ #f) #f)))
|
||
(native-inputs
|
||
(modify-inputs (package-native-inputs base)
|
||
(prepend (package-source base))))
|
||
(supported-systems '("x86_64-linux"))
|
||
(home-page "https://github.com/sunqm/qcint")
|
||
(synopsis "General GTO integrals for quantum chemistry (SIMD version
|
||
for x86_64)")
|
||
(description "@code{qcint} is an optimized version of @code{libcint}, a
|
||
C library (also with a Fortran API) to evaluate one- and two-electron
|
||
integrals for Gaussian type functions.")
|
||
(properties `((tunable? . #t)))
|
||
(license license:gpl3+)))))
|
||
|
||
(define-public gemmi
|
||
(package
|
||
(name "gemmi")
|
||
(version "0.7.3")
|
||
(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
|
||
"01fdpb695gqsl5xznrlqjydnrckqbfndzr8fj66pryzv8d0fdfsg"))
|
||
(patches
|
||
(search-patches "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 _
|
||
(substitute* (list "src/json.cpp"
|
||
"src/sprintf.cpp"
|
||
"include/gemmi/dirwalk.hpp"
|
||
"include/gemmi/cif.hpp"
|
||
"include/gemmi/json.hpp"
|
||
"python/gemmi.cpp"
|
||
"python/serial.h"
|
||
"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>")
|
||
(("\"\\.\\./third_party/serializer.h\"")
|
||
"<zpp/serializer.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/py")
|
||
(invoke "python3" "-m" "unittest" "discover" "-v"
|
||
"-s" "tests"))))))))
|
||
(inputs (list python zlib))
|
||
(native-inputs
|
||
(list fast-float
|
||
optionparser
|
||
pegtl
|
||
pocketfft-cpp
|
||
python-nanobind
|
||
sajson-for-gemmi
|
||
stb-sprintf
|
||
tinydir
|
||
zpp-serializer))
|
||
(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)))
|
||
|
||
(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"
|
||
"--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")
|
||
#: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"
|
||
" = -ljson-c -lgemmi_cpp ${libxml2_LIBS}\n"))
|
||
(("_a_SOURCES") "_la_SOURCES"))
|
||
(substitute* "configure.ac"
|
||
(("AC_PROG_INSTALL" inst)
|
||
(string-append "AM_PROG_LIBTOOL\n" inst)))
|
||
(substitute* "tests/Makefile.am"
|
||
(("libfreesasa\\.a") "libfreesasa.la"))))
|
||
(add-after 'unpack 'fix-new-gemmi
|
||
(lambda _
|
||
(substitute* "src/cif.cc"
|
||
(("models\\[i\\]\\.name")
|
||
"std::to_string(models[i].num)")
|
||
(("convert_pair_to_loop") "ensure_loop"))))
|
||
(add-before 'build 'build-lexer-and-parser
|
||
(lambda _
|
||
(with-directory-excursion "src"
|
||
(invoke "make" "lexer.h" "parser.h"))))
|
||
(add-after 'install 'install-doc
|
||
(lambda _
|
||
(copy-recursively
|
||
"doc/html"
|
||
(string-append #$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)))
|
||
|
||
(define-public maeparser
|
||
(package
|
||
(name "maeparser")
|
||
(version "1.3.1")
|
||
(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
|
||
"0mr5glg4br04ql5grby8yqni9fqq1l1cc75wyc159a1b9lwr7q7r"))))
|
||
(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)))
|
||
|
||
(define-public coordgenlibs
|
||
(package
|
||
(name "coordgenlibs")
|
||
(version "3.0.2")
|
||
(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
|
||
"1wjaxwaihjy9xm5ys23f5abl50zcar1h9pww5ajdkgygsqy0bavi"))))
|
||
(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)))
|
||
|
||
(define-public yaehmop
|
||
(package
|
||
(name "yaehmop")
|
||
(version "2024.03.1")
|
||
(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
|
||
"1wy38cfqfs203p1k3qqsizzlpvasldjcfxmlng54y5mxzw97n55f"))
|
||
(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"
|
||
;; Some functions are written in Fortran.
|
||
"-DCMAKE_C_FLAGS=-Wno-implicit-function-declaration"
|
||
(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 "
|
||
"${LAPACK_LIBRARIES})\n")))))
|
||
(add-after 'build 'build-doc
|
||
(lambda _
|
||
(with-directory-excursion "../docs"
|
||
(substitute* "bind_manual.tex"
|
||
(("\\\\usepackage\\{bindpage\\}")
|
||
(string-append
|
||
"\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
|
||
"{geometry}\n"
|
||
"\\pdfsuppressptexinfo=-1\n")))
|
||
(substitute* "Zmat_appendix.tex"
|
||
(("file=dihedral\\.eps")
|
||
"file=figs/dihedral.eps"))
|
||
(setenv "FORCE_SOURCE_DATE" "1")
|
||
(setenv "TEXMFVAR" "/tmp")
|
||
(invoke "latexmk" "-pdf" "bind_manual.tex"))))
|
||
(add-after 'install 'install-eht-parms
|
||
(lambda _
|
||
(install-file "../tightbind/eht_parms.dat"
|
||
(string-append #$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
|
||
(texlive-local-tree
|
||
(list texlive-epstopdf
|
||
texlive-latexmk))))
|
||
(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)))
|
||
|
||
(define-public avalon-toolkit
|
||
(package
|
||
(name "avalon-toolkit")
|
||
(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")))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(list
|
||
;; There is only one test, which is missing a file
|
||
#:tests? #f
|
||
#:phases
|
||
#~(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")))
|
||
(for-each
|
||
(lambda (program)
|
||
(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 "-" #$version "/")))))))
|
||
(home-page "https://sourceforge.net/projects/avalontoolkit/")
|
||
(synopsis "Tools for SMILES and MOL files and for structure fingerprinting")
|
||
(description "This package contains a library and programs for
|
||
canonicalization of SMILES and MOL files, molecular structure fingerprinting
|
||
and rendering molecules.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public ringdecomposerlib
|
||
(package
|
||
(name "ringdecomposerlib")
|
||
(version "1.1.3")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/rareylab/RingDecomposerLib")
|
||
(commit (string-append "v" version "_rdkit"))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
#:configure-flags
|
||
#~(list "-DBUILD_PYTHON_WRAPPER=ON"
|
||
"-DPYTHON_EXECUTABLE=python3"
|
||
(string-append "-DPYTHON_FLAGS=;--prefix=" #$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 "-" #$version "/html"))))
|
||
(delete 'check)
|
||
(add-after 'install 'check
|
||
(assoc-ref %standard-phases 'check))
|
||
(add-before 'check 'set-pythonpath
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(add-installed-pythonpath inputs outputs))))))
|
||
(inputs (list python))
|
||
(native-inputs (list doxygen python python-cython-0 python-sphinx))
|
||
(home-page "https://github.com/rareylab/RingDecomposerLib")
|
||
(synopsis "Calculate ring topology descriptions")
|
||
(description "RingDecomposerLib is a library for the calculation of
|
||
unique ring families, relevant cycles, the smallest set of smallest rings and
|
||
other ring topology descriptions.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public pubchem-align3d
|
||
(let ((commit "daefab3dd0c90ca56da9d3d5e375fe4d651e6be3")
|
||
(revision "0"))
|
||
(package
|
||
(name "pubchem-align3d")
|
||
(version (git-version "0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/ncbi/pubchem-align3d")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1nj1zz5nvn5h3dyj66zi11mmvmzpq3b8y51fld9bkxnsmk17h05m"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(list
|
||
#:tests? #f ; circular dependency with rdkit
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(delete 'configure)
|
||
(replace 'build
|
||
(lambda _
|
||
(invoke "g++"
|
||
"-o" "libpubchem-align3d.so"
|
||
"-O2" "-g" "-fPIC" "-shared"
|
||
"shape_functions1.cpp" "shape_functions2.cpp"
|
||
"shape_neighbor.cpp")))
|
||
(replace 'install
|
||
(lambda _
|
||
(for-each
|
||
(lambda (file)
|
||
(install-file
|
||
file
|
||
(string-append #$output "/include/pubchem-align3d")))
|
||
(find-files "." "\\.hpp"))
|
||
(install-file "libpubchem-align3d.so"
|
||
(string-append #$output "/lib")))))))
|
||
(home-page "https://github.com/ncbi/pubchem-align3d")
|
||
(synopsis "C++ library for aligning small molecules")
|
||
(description "This is a generic C++ library that can be used to rapidly
|
||
align two small molecules in 3D space, with shape - and optionally color -
|
||
Tanimoto scoring.")
|
||
(license license:public-domain))))
|
||
|
||
(define-public rdkit
|
||
(package
|
||
(name "rdkit")
|
||
(version "2024.09.6")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/rdkit/rdkit")
|
||
(commit
|
||
(string-append
|
||
"Release_" (string-replace-substring version "." "_")))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0nagqy5c9b86ip8qr1rnvby235am1zyc4sqm0z7wphbb70cqazxg"))
|
||
(patches
|
||
(search-patches "rdkit-unbundle-external-dependencies.patch"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
#~(begin
|
||
;; Remove pickle files (only used in tests),
|
||
;; as they are compiled programs
|
||
(for-each
|
||
(lambda (name)
|
||
(display (string-append name "\n"))
|
||
(delete-file name))
|
||
(find-files "." "\\.pkl(\\.gz)?$"))
|
||
;; 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"
|
||
"pyRealValueVect" "pyDiscreteValueVect"
|
||
"pickleTestsCatch"
|
||
;; Catching Python exception fails
|
||
"pyRanker"
|
||
;; Flaky test depending on floating point rounding
|
||
"testConrec"
|
||
;; Expensive test which may time out
|
||
"pySynthonSpaceSearch"
|
||
;; Circular import
|
||
"pythonSourceTests"
|
||
) "|")
|
||
")")))))))))
|
||
(inputs
|
||
(list avalon-toolkit
|
||
cairo
|
||
coordgenlibs
|
||
font-comic-neue
|
||
freetype
|
||
inchi
|
||
maeparser
|
||
pubchem-align3d
|
||
python
|
||
ringdecomposerlib
|
||
sqlite
|
||
yaehmop))
|
||
(native-inputs
|
||
(list bison
|
||
boost-numpy
|
||
catch2-3
|
||
eigen
|
||
flex
|
||
freesasa
|
||
pkg-config
|
||
python-pytest
|
||
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.")
|
||
;; 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)
|
||
(license license:bsd-3)))
|
||
|
||
(define-public xcfun
|
||
(package
|
||
(name "xcfun")
|
||
(version "2.1.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/dftlibs/xcfun")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1bj70cnhbh6ziy02x988wwl7cbwaq17ld7qwhswqkgnnx8rpgxid"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; Remove bundled and generated code
|
||
(delete-file-recursively "external")
|
||
(delete-file-recursively "cmake/autocmake")
|
||
(delete-file-recursively "cmake/downloaded")
|
||
(delete-file-recursively "CMakeLists.txt")
|
||
(delete-file "cmake/update.py")))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'generate-cmake-file
|
||
(lambda _
|
||
(let ((autocmake-path
|
||
#$(this-package-native-input "autocmake-src")))
|
||
(with-directory-excursion "cmake"
|
||
(substitute* "autocmake.yml"
|
||
(("^url_root:.*")
|
||
(string-append "url_root: "
|
||
(string-append autocmake-path "/") "\n")))
|
||
(invoke "python3"
|
||
(string-append autocmake-path "/update.py") "..")))))
|
||
(add-after 'generate-cmake-file 'set-libtaylor-path
|
||
(lambda _
|
||
(substitute* "src/CMakeLists.txt"
|
||
(("\\$\\{PROJECT_SOURCE_DIR\\}/external/upstream/taylor")
|
||
(string-append #$(this-package-native-input "libtaylor")
|
||
"/include/taylor"))))))))
|
||
(native-inputs
|
||
`(("libtaylor" ,libtaylor)
|
||
;; The Autocmake script copies files from its source repository (or ;;
|
||
;; directory) and there are no packaging scripts, so the source is used
|
||
;; directly.
|
||
("autocmake-src"
|
||
,(let* ((commit "77a1f851f08af1cbe0d95fd7dba4a16a14264412")
|
||
(revision "0")
|
||
(version (git-version "1.0.0" revision commit)))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/dev-cafe/autocmake")
|
||
(commit commit)))
|
||
(file-name (git-file-name "autocmake" version))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
(delete-file-recursively "autocmake/external")))
|
||
(sha256
|
||
(base32
|
||
"0rq5hyaj6c3yv4357a2p317cqv22gngw5085aansii69h063d0a4")))))
|
||
("python" ,python)
|
||
("python-pyyaml" ,python-pyyaml)))
|
||
(home-page "https://github.com/dftlibs/xcfun")
|
||
(synopsis
|
||
"Library of exchange-correlation functionals with automatic differentiation")
|
||
(description
|
||
"@code{XCFun} is a library of exchange-correlation functionals with
|
||
arbitrary-order derivatives for density functional theory.")
|
||
(license license:mpl2.0)))
|
||
|
||
;;;
|
||
;;; Avoid adding new packages to the end of this file. To reduce the chances
|
||
;;; of a merge conflict, place them above in alphabetical order.
|
||
;;;
|