mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-12-26 14:28:15 -05:00
0c468cb52d
This is a follow-up to commit eb5ece73a8.
* gnu/packages/chemistry.scm: Import (gnu packages).
244 lines
10 KiB
Scheme
244 lines
10 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
|
|
;;; Copyright © 2018 Kei Kebreau <kkebreau@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 licenses) #:prefix license:)
|
|
#:use-module (guix download)
|
|
#:use-module (gnu packages)
|
|
#:use-module (gnu packages algebra)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages gv)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages pkg-config)
|
|
#:use-module (gnu packages python)
|
|
#: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 domainfinder
|
|
(package
|
|
(name "domainfinder")
|
|
(version "2.0.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://bitbucket.org/khinsen/"
|
|
"domainfinder/downloads/DomainFinder-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
|
|
(build-system python-build-system)
|
|
(inputs
|
|
`(("python-mmtk" ,python2-mmtk)))
|
|
(arguments
|
|
`(#:python ,python-2
|
|
;; No test suite
|
|
#:tests? #f))
|
|
(home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
|
|
(synopsis "Analysis of dynamical domains in proteins")
|
|
(description "DomainFinder is an interactive program for the determination
|
|
and characterization of dynamical domains in proteins. It can infer dynamical
|
|
domains by comparing two protein structures, or from normal mode analysis on a
|
|
single structure. The software is currently not actively maintained and works
|
|
only with Python 2 and NumPy < 1.9.")
|
|
(license license:cecill-c)))
|
|
|
|
(define-public inchi
|
|
(package
|
|
(name "inchi")
|
|
(version "1.05")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://www.inchi-trust.org/download/"
|
|
(string-join (string-split version #\.) "")
|
|
"/INCHI-1-SRC.zip"))
|
|
(sha256
|
|
(base32
|
|
"081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
|
|
(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 (string-append (assoc-ref inputs "unzip")
|
|
"/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
|
|
"1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
|
|
(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 with-numpy-1.8
|
|
(package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
|
|
|
|
(define-public nmoldyn
|
|
(package
|
|
(name "nmoldyn")
|
|
(version "3.0.11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://bitbucket.org/khinsen/"
|
|
"nmoldyn3/downloads/nMOLDYN-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a"))))
|
|
(build-system python-build-system)
|
|
(inputs
|
|
`(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
|
|
("python-scientific" ,python2-scientific)
|
|
("netcdf" ,netcdf)
|
|
("gv" ,gv)))
|
|
(propagated-inputs
|
|
`(("python-mmtk" ,python2-mmtk)))
|
|
(arguments
|
|
`(#:python ,python-2
|
|
#:tests? #f ; No test suite
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-before 'build 'create-linux2-directory
|
|
(lambda _
|
|
(mkdir-p "nMOLDYN/linux2")))
|
|
(add-before 'build 'change-PDF-viewer
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(substitute* "nMOLDYN/Preferences.py"
|
|
;; Set the paths for external executables, substituting
|
|
;; gv for acroread.
|
|
;; There is also vmd_path, but VMD is not free software
|
|
;; and Guix contains currently no free molecular viewer that
|
|
;; could be substituted.
|
|
(("PREFERENCES\\['acroread_path'\\] = ''")
|
|
(format "PREFERENCES['acroread_path'] = '~a'"
|
|
(which "gv")))
|
|
(("PREFERENCES\\['ncdump_path'\\] = ''")
|
|
(format "PREFERENCES['ncdump_path'] = '~a'"
|
|
(which "ncdump")))
|
|
(("PREFERENCES\\['ncgen_path'\\] = ''")
|
|
(format "PREFERENCES['ncgen_path'] = '~a'"
|
|
(which "ncgen3")))
|
|
(("PREFERENCES\\['task_manager_path'\\] = ''")
|
|
(format "PREFERENCES['task_manager_path'] = '~a'"
|
|
(which "task_manager")))
|
|
;; Show documentation as PDF
|
|
(("PREFERENCES\\['documentation_style'\\] = 'html'")
|
|
"PREFERENCES['documentation_style'] = 'pdf'") ))))))
|
|
(home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/")
|
|
(synopsis "Analysis software for Molecular Dynamics trajectories")
|
|
(description "nMOLDYN is an interactive analysis program for Molecular Dynamics
|
|
simulations. It is especially designed for the computation and decomposition of
|
|
neutron scattering spectra, but also computes other quantities. The software
|
|
is currently not actively maintained and works only with Python 2 and
|
|
NumPy < 1.9.")
|
|
(license license:cecill)))
|
|
|
|
(define-public openbabel
|
|
(package
|
|
(name "openbabel")
|
|
(version "2.4.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://sourceforge/" name "/" name "/"
|
|
version "/" name "-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
|
|
(patches
|
|
(search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
`(#: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
|
|
`(("pkg-config" ,pkg-config)))
|
|
(inputs
|
|
`(("eigen" ,eigen)
|
|
("inchi" ,inchi)
|
|
("libxml2" ,libxml2)
|
|
("zlib" ,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)))
|