7a18bd9e74
TEXLIVE-UPDMAP.CFG and TEXLIVE-TINY should only be used as native inputs. Also remove texlive packages already provided by them. * doc/build.scm (pdf-manual): * gnu/packages/algebra.scm (pari-gp): * gnu/packages/bioinformatics.scm (discrover): (phyml): (velvet): * gnu/packages/chemistry.scm (yaehmop): * gnu/packages/chez.scm (stex-bootstrap): (chez-web): (chez-sockets): * gnu/packages/cran.scm (r-prereg): * gnu/packages/docbook.scm (dblatex): * gnu/packages/emacs-xyz.scm (emacs-auctex): * gnu/packages/engineering.scm (fastcap): * gnu/packages/fsf.scm (book-faif): * gnu/packages/graphviz.scm (dot2tex): * gnu/packages/maths.scm (hypre): * gnu/packages/ocaml.scm (unison): (ocaml-bibtex2html): * gnu/packages/plotutils.scm (asymptote): * gnu/packages/python-xyz.scm (python-nbconvert): (python-pypandoc): * gnu/packages/radio.scm (gnuradio): (libosmo-dsp): * gnu/packages/statistics.scm (r-with-tests): * gnu/packages/tex.scm (texlive-makecmds): (texlive-innerscript): (teximpatient): (texlive-xkeyval): Remove texlive packages already provided by TEXLIVE-UPDMAP.CFG. Don't add TEXLIVE-TINY or TEXLIVE-UPDMAP.CFG as inputs.
1230 lines
51 KiB
Scheme
1230 lines
51 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
|
|
;;; Copyright © 2018, 2021 Kei Kebreau <kkebreau@posteo.net>
|
|
;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
|
|
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
|
|
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
|
|
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
|
|
;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
|
|
;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
|
|
;;;
|
|
;;; 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 packages)
|
|
#:use-module (guix utils)
|
|
#:use-module ((guix licenses) #:prefix license:)
|
|
#:use-module (guix download)
|
|
#:use-module (guix gexp)
|
|
#:use-module (guix git-download)
|
|
#: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 check)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages c)
|
|
#: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 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 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-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 (guix build-system cmake)
|
|
#:use-module (guix build-system gnu)
|
|
#:use-module (guix build-system python))
|
|
|
|
(define-public avogadrolibs
|
|
(package
|
|
(name "avogadrolibs")
|
|
(version "1.93.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/OpenChemistry/avogadrolibs")
|
|
(commit version)))
|
|
(sha256
|
|
(base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39"))
|
|
(file-name (git-file-name name version))))
|
|
(build-system cmake-build-system)
|
|
(native-inputs
|
|
(list eigen
|
|
mmtf-cpp
|
|
msgpack
|
|
googletest
|
|
pkg-config
|
|
pybind11))
|
|
(inputs
|
|
(list glew
|
|
libarchive
|
|
libmsym
|
|
molequeue
|
|
python
|
|
spglib
|
|
qtbase-5))
|
|
(arguments
|
|
'(#:configure-flags (list "-DENABLE_TESTING=ON"
|
|
(string-append "-DSPGLIB_INCLUDE_DIR="
|
|
(assoc-ref %build-inputs "spglib")
|
|
"/include"))))
|
|
(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,
|
|
bioinformatics, materials science, and related areas.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public avogadro2
|
|
(package
|
|
(name "avogadro2")
|
|
(version "1.93.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/OpenChemistry/avogadroapp")
|
|
(commit version)))
|
|
(sha256
|
|
(base32
|
|
"1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
|
|
(file-name (git-file-name name version))))
|
|
(build-system cmake-build-system)
|
|
(native-inputs
|
|
(list eigen pkg-config))
|
|
(inputs
|
|
(list avogadrolibs hdf5 molequeue qtbase-5))
|
|
;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
|
|
(arguments
|
|
'(#:tests? #f))
|
|
(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 "1.06")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://www.inchi-trust.org/download/"
|
|
(string-join (string-split version #\.) "")
|
|
"/INCHI-1-SRC.zip"))
|
|
(sha256
|
|
(base32
|
|
"1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28"))
|
|
(file-name (string-append name "-" version ".zip"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
'(#:tests? #f ; no check target
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(delete 'configure) ; no configure script
|
|
(add-before 'build 'chdir-to-build-directory
|
|
(lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
|
|
(add-after 'build 'build-library
|
|
(lambda _
|
|
(chdir "../../../INCHI_API/libinchi/gcc")
|
|
(invoke "make")))
|
|
(replace 'install
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(bin (string-append out "/bin"))
|
|
(doc (string-append out "/share/doc/inchi"))
|
|
(include-dir (string-append out "/include/inchi"))
|
|
(lib (string-append out "/lib/inchi"))
|
|
(inchi-doc (assoc-ref inputs "inchi-doc"))
|
|
(unzip (search-input-file inputs "/bin/unzip")))
|
|
(chdir "../../..")
|
|
;; Install binary.
|
|
(with-directory-excursion "INCHI_EXE/bin/Linux"
|
|
(rename-file "inchi-1" "inchi")
|
|
(install-file "inchi" bin))
|
|
;; Install libraries.
|
|
(with-directory-excursion "INCHI_API/bin/Linux"
|
|
(for-each (lambda (file)
|
|
(install-file file lib))
|
|
(find-files "." "libinchi\\.so\\.1\\.*")))
|
|
;; Install header files.
|
|
(with-directory-excursion "INCHI_BASE/src"
|
|
(for-each (lambda (file)
|
|
(install-file file include-dir))
|
|
(find-files "." "\\.h$")))
|
|
;; Install documentation.
|
|
(mkdir-p doc)
|
|
(invoke unzip "-j" "-d" doc inchi-doc)
|
|
#t))))))
|
|
(native-inputs
|
|
`(("unzip" ,unzip)
|
|
("inchi-doc"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://www.inchi-trust.org/download/"
|
|
(string-join (string-split version #\.) "")
|
|
"/INCHI-1-DOC.zip"))
|
|
(sha256
|
|
(base32
|
|
"1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f"))
|
|
(file-name (string-append name "-" version ".zip"))))))
|
|
(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:non-copyleft
|
|
"file://LICENCE"
|
|
"See LICENCE in the distribution."))))
|
|
|
|
(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 "1.0.0")
|
|
(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
|
|
"17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l"))))
|
|
(build-system cmake-build-system)
|
|
;; Tests require the soon-to-be-deprecated version 1 of the catch-framework.
|
|
(arguments
|
|
'(#:tests? #f))
|
|
(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 url-fetch)
|
|
(uri (string-append "https://github.com/openbabel/openbabel/"
|
|
"releases/download/openbabel-"
|
|
(string-replace-substring version "." "-")
|
|
"/openbabel-" version "-source.tar.bz2"))
|
|
(sha256
|
|
(base32
|
|
"0s0f4zib8vshfaywsr5bjjz55jwsg6yiz2qw4i5jm8wysn0q7v56"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
`(;; 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="
|
|
(assoc-ref %build-inputs "inchi")
|
|
"/lib/inchi/libinchi.so.1")
|
|
(string-append "-DINCHI_INCLUDE_DIR="
|
|
(assoc-ref %build-inputs "inchi") "/include/inchi"))
|
|
#:test-target "test"))
|
|
(native-inputs
|
|
(list pkg-config))
|
|
(inputs
|
|
(list eigen inchi libxml2 zlib))
|
|
(home-page "http://openbabel.org/wiki/Main_Page")
|
|
(synopsis "Chemistry data manipulation toolbox")
|
|
(description
|
|
"Open Babel is a chemical toolbox designed to speak the many languages of
|
|
chemical data. It's a collaborative project allowing anyone to search, convert,
|
|
analyze, or store data from molecular modeling, chemistry, solid-state
|
|
materials, biochemistry, or related areas.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public spglib
|
|
(package
|
|
(name "spglib")
|
|
(version "1.16.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/spglib/spglib")
|
|
(commit (string-append "v" version))))
|
|
(sha256
|
|
(base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
|
|
(file-name (git-file-name name version))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
'(#:test-target "check"
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'patch-header-install-dir
|
|
(lambda _
|
|
;; As of the writing of this package, CMake and GNU build systems
|
|
;; install the header to two different location. This patch makes
|
|
;; the CMake build system's choice of header directory compatible
|
|
;; with the GNU build system's choice and with what avogadrolibs
|
|
;; expects.
|
|
;; See https://github.com/spglib/spglib/issues/75 and the relevant
|
|
;; part of https://github.com/OpenChemistry/avogadroapp/issues/97.
|
|
(substitute* "CMakeLists.txt"
|
|
(("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir)
|
|
(string-append include-dir "/spglib")))
|
|
#t)))))
|
|
(home-page "https://spglib.github.io/spglib/index.html")
|
|
(synopsis "Library for crystal symmetry search")
|
|
(description "Spglib is a library for finding and handling crystal
|
|
symmetries written in C. Spglib can be used to:
|
|
|
|
@enumerate
|
|
@item Find symmetry operations
|
|
@item Identify space-group type
|
|
@item Wyckoff position assignment
|
|
@item Refine crystal structure
|
|
@item Find a primitive cell
|
|
@item Search irreducible k-points
|
|
@end enumerate")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-pymol
|
|
(package
|
|
(name "python-pymol")
|
|
(version "2.5.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/schrodinger/pymol-open-source")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "08zmfgclkbjkqjpq8xs1mphs1i8rpqj76mcw7m2mrhvma5qj1nr5"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:configure-flags
|
|
(list "--glut" "--testing")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'make-reproducible
|
|
(lambda _
|
|
(substitute* "create_shadertext.py"
|
|
(("time\\.time\\(\\)") "0"))))
|
|
(add-after 'unpack 'add-include-directories
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(setenv "CPLUS_INCLUDE_PATH"
|
|
(string-append (assoc-ref inputs "freetype")
|
|
"/include/freetype2:"
|
|
(assoc-ref inputs "libxml2")
|
|
"/include/libxml2:"
|
|
(getenv "CPLUS_INCLUDE_PATH")))))
|
|
;; The setup.py script does not support one of the Python build
|
|
;; system's default flags, "--single-version-externally-managed".
|
|
(replace 'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(invoke "python" "setup.py" "install"
|
|
(string-append "--prefix=" (assoc-ref outputs "out"))
|
|
"--root=/"))))))
|
|
(inputs
|
|
(list freetype
|
|
libpng
|
|
freeglut
|
|
glew
|
|
libxml2
|
|
mmtf-cpp
|
|
msgpack
|
|
python-pyqt
|
|
glm
|
|
netcdf))
|
|
(native-inputs
|
|
(list catch2 python-setuptools))
|
|
(home-page "https://pymol.org")
|
|
(synopsis "Molecular visualization system")
|
|
(description "PyMOL is a capable molecular viewer and renderer. It can be
|
|
used to prepare publication-quality figures, to share interactive results with
|
|
your colleagues, or to generate pre-rendered animations.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public gemmi
|
|
(package
|
|
(name "gemmi")
|
|
(version "0.5.7")
|
|
(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
|
|
"00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
|
|
(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 _
|
|
(substitute* (list "include/gemmi/sprintf.hpp"
|
|
"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)))
|
|
|
|
(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")
|
|
#: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 ${libxml2_LIBS}\n"))
|
|
(("_a_SOURCES") "_la_SOURCES"))
|
|
(substitute* "configure.ac"
|
|
(("AC_PROG_INSTALL" inst)
|
|
(string-append "AM_PROG_LIBTOOL\n" inst)))
|
|
(substitute* "tests/Makefile.am"
|
|
(("libfreesasa\\.a") "libfreesasa.la"))))
|
|
(add-before 'build 'build-lexer-and-parser
|
|
(lambda _
|
|
(with-directory-excursion "src"
|
|
(invoke "make" "lexer.h" "parser.h"))))
|
|
(add-after 'install 'install-doc
|
|
(lambda _
|
|
(copy-recursively
|
|
"doc/html"
|
|
(string-append #$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 "1.3.0")
|
|
(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
|
|
"1yv4y5hn49fhylziigsg922bb244lb57p69r7vg9q899zd3l5b7l"))))
|
|
(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 "3.0.1")
|
|
(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
|
|
"0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv"))))
|
|
(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 "2022.09.1")
|
|
(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
|
|
"1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
|
|
(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 "-" #$version))))
|
|
(delete 'check)
|
|
(add-after 'install-doc 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(invoke "./test_eht")))))))
|
|
(inputs (list openblas))
|
|
(native-inputs
|
|
(list gfortran
|
|
(texlive-updmap.cfg
|
|
(list texlive-epstopdf
|
|
texlive-latexmk))))
|
|
(home-page "https://github.com/greglandrum/yaehmop")
|
|
(synopsis "Perform extended Hückel calculations")
|
|
(description "@acronym{YAeHMOP, Yet Another extended Hueckel Molecular
|
|
Orbital Package} contains a program and library for performing extended Hückel
|
|
calculations and analyzing the results.")
|
|
(license license:bsd-2)))
|
|
|
|
(define-public avalon-toolkit
|
|
(package
|
|
(name "avalon-toolkit")
|
|
(version "1.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"mirror://sourceforge/avalontoolkit/"
|
|
"AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_"
|
|
version ".source.tar"))
|
|
(sha256
|
|
(base32
|
|
"0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
|
|
(modules '((guix build utils) (ice-9 ftw)))
|
|
(snippet
|
|
#~(begin
|
|
(delete-file-recursively "../SourceDistribution/java")))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
(list
|
|
;; There are no intended tests
|
|
#:tests? #f
|
|
#:phases
|
|
#~(let ((programs '("canonizer" "matchtest" "sketch" "smi2mol" "struchk")))
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'chdir
|
|
(lambda _ (chdir "common")))
|
|
(delete 'configure)
|
|
(add-before 'build 'dont-free-static-memory
|
|
(lambda _
|
|
(substitute* "reaccsio.c"
|
|
(("MyFree\\(.*tempdir\\)" m)
|
|
(string-append "/* freeing memory from getenv is bad */"
|
|
"// " m)))))
|
|
;; The makefile has incorrect compiler flags and is missing some
|
|
;; object files, so we build it ourselves.
|
|
(replace 'build
|
|
(lambda _
|
|
(for-each
|
|
(lambda (part)
|
|
(format #t "Compiling ~a.c ~~> ~a.o~%" part part)
|
|
(invoke #$(cc-for-target) "-c" "-fPIC" "-O2"
|
|
(string-append part ".c")
|
|
"-o" (string-append part ".o")))
|
|
(list "aacheck" "casutils" "denormal" "depictutil"
|
|
"didepict" "fixcharges" "forio" "geometry"
|
|
"graph" "hashcode" "layout" "local" "pattern"
|
|
"perceive" "reaccsio" "rtutils" "set" "shortcut"
|
|
"sketch" "ssmatch" "stereo" "symbol_lists"
|
|
"symboltable" "utilities"))
|
|
(display "Building libavalontoolkit.so\n")
|
|
(apply invoke "gcc" "-fPIC" "-shared" "-lm"
|
|
"-o" "libavalontoolkit.so" "canonizer.c" "smi2mol.c"
|
|
"struchk.c" "patclean.c" (find-files "." "\\.o$"))
|
|
;; patclean is not built here as there is an undeclared
|
|
;; variable in main().
|
|
(for-each
|
|
(lambda (program)
|
|
(display (string-append "Building " program "\n"))
|
|
(invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2"
|
|
(string-append "-Wl,-rpath=" #$output "/lib")
|
|
"-DMAIN" (string-append program ".c") "-o" program))
|
|
programs)))
|
|
(replace 'install
|
|
(lambda _
|
|
;; Executables
|
|
(for-each
|
|
(lambda (program)
|
|
(install-file program (string-append #$output "/bin")))
|
|
programs)
|
|
(for-each
|
|
(lambda (name)
|
|
(symlink (string-append #$output "/bin/smi2mol")
|
|
(string-append #$output "/bin/" name)))
|
|
'("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
|
|
;; Library
|
|
(install-file "libavalontoolkit.so"
|
|
(string-append #$output "/lib"))
|
|
(for-each
|
|
(lambda (file)
|
|
(install-file file (string-append #$output
|
|
"/include/avalontoolkit")))
|
|
(find-files "." "\\.h$"))
|
|
(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 "-" #$version "/html"))))
|
|
(delete 'check)
|
|
(add-after 'install 'check
|
|
(assoc-ref %standard-phases 'check))
|
|
(add-before 'check 'set-pythonpath
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(add-installed-pythonpath inputs outputs))))))
|
|
(inputs (list python))
|
|
(native-inputs (list doxygen python python-cython python-sphinx))
|
|
(home-page "https://github.com/rareylab/RingDecomposerLib")
|
|
(synopsis "Calculate ring topology descriptions")
|
|
(description "RingDecomposerLib is a library for the calculation of
|
|
unique ring families, relevant cycles, the smallest set of smallest rings and
|
|
other ring topology descriptions.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public rdkit
|
|
(package
|
|
(name "rdkit")
|
|
(version "2022.03.5")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/rdkit/rdkit")
|
|
(commit
|
|
(string-append
|
|
"Release_" (string-replace-substring version "." "_")))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
|
|
(patches
|
|
(search-patches "rdkit-unbundle-external-dependencies.patch"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
#~(begin
|
|
;; Remove pickle files (only used in tests),
|
|
;; as they are compiled programs
|
|
(for-each
|
|
(lambda (name)
|
|
(display (string-append name "\n"))
|
|
(delete-file name))
|
|
(find-files "." "\\.pkl(\\.gz)?$"))
|
|
;; 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
|
|
"pyRanker") "|")
|
|
")")))))))))
|
|
(inputs
|
|
(list avalon-toolkit
|
|
cairo
|
|
coordgenlibs
|
|
font-comic-neue
|
|
freetype
|
|
inchi
|
|
maeparser
|
|
python
|
|
ringdecomposerlib
|
|
sqlite
|
|
yaehmop))
|
|
(native-inputs
|
|
(list bison
|
|
boost
|
|
catch2
|
|
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.")
|
|
(license license:bsd-3)))
|