[jackhill/guix/guix.git] / gnu / packages / chemistry.scm

;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
;;; Copyright © 2018 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>
;;;
;;; 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 git-download)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages documentation)
  #:use-module (gnu packages gl)
  #: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 python-xyz)
  #:use-module (gnu packages qt)
  #: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 avogadro
  (package
    (name "avogadro")
    (version "1.2.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/cryos/avogadro.git")
             (commit version)))
       (sha256
        (base32 "0258py3lkba85qhs5ynancinyym61vlp0zaq9yrfs3hhnhpzv9n2"))
       (file-name (git-file-name name version))
       (patches
        (search-patches "avogadro-eigen3-update.patch"
                        "avogadro-python-eigen-lib.patch"
                        "avogadro-boost148.patch"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f
       #:configure-flags
       (list "-DENABLE_GLSL=ON"
             (string-append "-DPYTHON_LIBRARIES="
                            (assoc-ref %build-inputs "python")
                            "/lib")
             (string-append "-DPYTHON_INCLUDE_DIRS="
                            (assoc-ref %build-inputs "python")
                            "/include/python"
                            ,(version-major+minor
                               (package-version python))))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-python-lib-path
           (lambda* (#:key outputs #:allow-other-keys)
             ;; This is necessary to install the Python module in the correct
             ;; directory.
             (substitute* "libavogadro/src/python/CMakeLists.txt"
               (("^EXECUTE_PROCESS.*$") "")
               (("^.*from sys import stdout.*$") "")
               (("^.*OUTPUT_VARIABLE.*")
                (string-append "set(PYTHON_LIB_PATH \""
                               (assoc-ref outputs "out")
                               "/lib/python"
                               ,(version-major+minor
                                  (package-version python))
                               "/site-packages\")")))
             #t))
         (add-after 'install 'wrap-program
           (lambda* (#:key inputs outputs #:allow-other-keys)
             ;; Make sure 'avogadro' runs with the correct PYTHONPATH.
             (let* ((out (assoc-ref outputs "out")))
               (setenv "PYTHONPATH"
                       (string-append
                        (assoc-ref outputs "out")
                        "/lib/python"
                        ,(version-major+minor
                           (package-version python))
                        "/site-packages:"
                        (getenv "PYTHONPATH")))
               (wrap-program (string-append out "/bin/avogadro")
                 `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
             #t)))))
    (native-inputs
     `(("doxygen" ,doxygen)
       ("pkg-config" ,pkg-config)))
    (inputs
     `(("boost" ,boost)
       ("eigen" ,eigen)
       ("glew" ,glew)
       ("openbabel" ,openbabel)
       ("python" ,python-2)
       ("python-numpy" ,python2-numpy)
       ("python-pyqt" ,python2-pyqt-4)
       ("python-sip" ,python2-sip)
       ("qt" ,qt-4)
       ("zlib" ,zlib)))
    (home-page "https://avogadro.cc")
    (synopsis "Advanced molecule editor")
    (description
     "Avogadro 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:gpl2+)))

(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.html")
    (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 git-fetch)
       (uri (git-reference
             (url "https://github.com/khinsen/nMOLDYN3")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r"))))
    (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 #f "PREFERENCES['acroread_path'] = '~a'"
                        (which "gv")))
               (("PREFERENCES\\['ncdump_path'\\] = ''")
                (format #f "PREFERENCES['ncdump_path'] = '~a'"
                        (which "ncdump")))
               (("PREFERENCES\\['ncgen_path'\\] = ''")
                (format #f "PREFERENCES['ncgen_path'] = '~a'"
                        (which "ncgen3")))
               (("PREFERENCES\\['task_manager_path'\\] = ''")
                (format #f "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.html")
    (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)))
Commit	Line	Data
73114e30 KH	1	;;; GNU Guix --- Functional package management for GNU
73114e30 KH	2	;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
a49eb85c	3	;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
4ae16f9c	4	;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
631249dd	5	;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
357328d2	6	;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
73114e30 KH	7	;;;
	8	;;; This file is part of GNU Guix.
	9	;;;
	10	;;; GNU Guix is free software; you can redistribute it and/or modify it
	11	;;; under the terms of the GNU General Public License as published by
	12	;;; the Free Software Foundation; either version 3 of the License, or (at
	13	;;; your option) any later version.
	14	;;;
	15	;;; GNU Guix is distributed in the hope that it will be useful, but
	16	;;; WITHOUT ANY WARRANTY; without even the implied warranty of
	17	;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	18	;;; GNU General Public License for more details.
	19	;;;
	20	;;; You should have received a copy of the GNU General Public License
	21	;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
	22
	23	(define-module (gnu packages chemistry)
	24	#:use-module (guix packages)
4ae16f9c	25	#:use-module (guix utils)
73114e30 KH	26	#:use-module ((guix licenses) #:prefix license:)
73114e30 KH	27	#:use-module (guix download)
631249dd	28	#:use-module (guix git-download)
0c468cb5	29	#:use-module (gnu packages)
348edd91	30	#:use-module (gnu packages algebra)
7d01ee66	31	#:use-module (gnu packages boost)
a49eb85c	32	#:use-module (gnu packages compression)
7d01ee66 KK	33	#:use-module (gnu packages documentation)
7d01ee66 KK	34	#:use-module (gnu packages gl)
f250a868 KH	35	#:use-module (gnu packages gv)
f250a868 KH	36	#:use-module (gnu packages maths)
348edd91	37	#:use-module (gnu packages pkg-config)
73114e30	38	#:use-module (gnu packages python)
44d10b1f	39	#:use-module (gnu packages python-xyz)
7d01ee66	40	#:use-module (gnu packages qt)
348edd91 KK	41	#:use-module (gnu packages xml)
348edd91 KK	42	#:use-module (guix build-system cmake)
a49eb85c	43	#:use-module (guix build-system gnu)
73114e30 KH	44	#:use-module (guix build-system python))
73114e30 KH	45
7d01ee66 KK	46	(define-public avogadro
	47	(package
	48	(name "avogadro")
	49	(version "1.2.0")
631249dd TGR	50	(source
	51	(origin
	52	(method git-fetch)
	53	(uri (git-reference
	54	(url "https://github.com/cryos/avogadro.git")
	55	(commit version)))
	56	(sha256
	57	(base32 "0258py3lkba85qhs5ynancinyym61vlp0zaq9yrfs3hhnhpzv9n2"))
	58	(file-name (git-file-name name version))
	59	(patches
	60	(search-patches "avogadro-eigen3-update.patch"
	61	"avogadro-python-eigen-lib.patch"
	62	"avogadro-boost148.patch"))))
7d01ee66 KK	63	(build-system cmake-build-system)
7d01ee66 KK	64	(arguments
4ae16f9c	65	`(#:tests? #f
7d01ee66 KK	66	#:configure-flags
	67	(list "-DENABLE_GLSL=ON"
	68	(string-append "-DPYTHON_LIBRARIES="
	69	(assoc-ref %build-inputs "python")
	70	"/lib")
	71	(string-append "-DPYTHON_INCLUDE_DIRS="
	72	(assoc-ref %build-inputs "python")
4ae16f9c EF	73	"/include/python"
	74	,(version-major+minor
	75	(package-version python))))
7d01ee66 KK	76	#:phases
	77	(modify-phases %standard-phases
	78	(add-after 'unpack 'patch-python-lib-path
	79	(lambda* (#:key outputs #:allow-other-keys)
	80	;; This is necessary to install the Python module in the correct
	81	;; directory.
	82	(substitute* "libavogadro/src/python/CMakeLists.txt"
	83	(("^EXECUTE_PROCESS.*$") "")
	84	(("^.from sys import stdout.$") "")
	85	(("^.OUTPUT_VARIABLE.")
	86	(string-append "set(PYTHON_LIB_PATH \""
	87	(assoc-ref outputs "out")
4ae16f9c EF	88	"/lib/python"
	89	,(version-major+minor
	90	(package-version python))
	91	"/site-packages\")")))
7d01ee66 KK	92	#t))
	93	(add-after 'install 'wrap-program
	94	(lambda* (#:key inputs outputs #:allow-other-keys)
	95	;; Make sure 'avogadro' runs with the correct PYTHONPATH.
	96	(let* ((out (assoc-ref outputs "out")))
	97	(setenv "PYTHONPATH"
	98	(string-append
	99	(assoc-ref outputs "out")
4ae16f9c EF	100	"/lib/python"
	101	,(version-major+minor
	102	(package-version python))
	103	"/site-packages:"
7d01ee66 KK	104	(getenv "PYTHONPATH")))
	105	(wrap-program (string-append out "/bin/avogadro")
	106	`("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
	107	#t)))))
	108	(native-inputs
	109	`(("doxygen" ,doxygen)
	110	("pkg-config" ,pkg-config)))
	111	(inputs
	112	`(("boost" ,boost)
	113	("eigen" ,eigen)
	114	("glew" ,glew)
	115	("openbabel" ,openbabel)
	116	("python" ,python-2)
	117	("python-numpy" ,python2-numpy)
	118	("python-pyqt" ,python2-pyqt-4)
	119	("python-sip" ,python2-sip)
	120	("qt" ,qt-4)
	121	("zlib" ,zlib)))
	122	(home-page "https://avogadro.cc")
	123	(synopsis "Advanced molecule editor")
	124	(description
	125	"Avogadro is an advanced molecule editor and visualizer designed for use
	126	in computational chemistry, molecular modeling, bioinformatics, materials
	127	science, and related areas. It offers flexible high quality rendering and a
	128	powerful plugin architecture.")
	129	(license license:gpl2+)))
	130
73114e30 KH	131	(define-public domainfinder
	132	(package
	133	(name "domainfinder")
	134	(version "2.0.5")
	135	(source
	136	(origin
	137	(method url-fetch)
	138	(uri (string-append "https://bitbucket.org/khinsen/"
	139	"domainfinder/downloads/DomainFinder-"
	140	version ".tar.gz"))
	141	(sha256
	142	(base32
	143	"1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
	144	(build-system python-build-system)
	145	(inputs
	146	`(("python-mmtk" ,python2-mmtk)))
	147	(arguments
	148	`(#:python ,python-2
	149	;; No test suite
	150	#:tests? #f))
7f489c56	151	(home-page "http://dirac.cnrs-orleans.fr/DomainFinder.html")
73114e30 KH	152	(synopsis "Analysis of dynamical domains in proteins")
	153	(description "DomainFinder is an interactive program for the determination
	154	and characterization of dynamical domains in proteins. It can infer dynamical
	155	domains by comparing two protein structures, or from normal mode analysis on a
	156	single structure. The software is currently not actively maintained and works
	157	only with Python 2 and NumPy < 1.9.")
	158	(license license:cecill-c)))
f250a868	159
a49eb85c KK	160	(define-public inchi
	161	(package
	162	(name "inchi")
	163	(version "1.05")
	164	(source (origin
	165	(method url-fetch)
	166	(uri (string-append "http://www.inchi-trust.org/download/"
	167	(string-join (string-split version #\.) "")
	168	"/INCHI-1-SRC.zip"))
	169	(sha256
	170	(base32
	171	"081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
	172	(file-name (string-append name "-" version ".zip"))))
	173	(build-system gnu-build-system)
	174	(arguments
	175	'(#:tests? #f ; no check target
	176	#:phases
	177	(modify-phases %standard-phases
	178	(delete 'configure) ; no configure script
	179	(add-before 'build 'chdir-to-build-directory
	180	(lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
	181	(add-after 'build 'build-library
	182	(lambda _
	183	(chdir "../../../INCHI_API/libinchi/gcc")
	184	(invoke "make")))
	185	(replace 'install
	186	(lambda* (#:key inputs outputs #:allow-other-keys)
	187	(let* ((out (assoc-ref outputs "out"))
	188	(bin (string-append out "/bin"))
	189	(doc (string-append out "/share/doc/inchi"))
	190	(include-dir (string-append out "/include/inchi"))
	191	(lib (string-append out "/lib/inchi"))
	192	(inchi-doc (assoc-ref inputs "inchi-doc"))
	193	(unzip (string-append (assoc-ref inputs "unzip")
	194	"/bin/unzip")))
	195	(chdir "../../..")
	196	;; Install binary.
	197	(with-directory-excursion "INCHI_EXE/bin/Linux"
	198	(rename-file "inchi-1" "inchi")
	199	(install-file "inchi" bin))
	200	;; Install libraries.
	201	(with-directory-excursion "INCHI_API/bin/Linux"
	202	(for-each (lambda (file)
	203	(install-file file lib))
	204	(find-files "." "libinchi\\.so\\.1\\.*")))
	205	;; Install header files.
	206	(with-directory-excursion "INCHI_BASE/src"
	207	(for-each (lambda (file)
	208	(install-file file include-dir))
	209	(find-files "." "\\.h$")))
	210	;; Install documentation.
	211	(mkdir-p doc)
	212	(invoke unzip "-j" "-d" doc inchi-doc)
	213	#t))))))
	214	(native-inputs
	215	`(("unzip" ,unzip)
	216	("inchi-doc"
	217	,(origin
	218	(method url-fetch)
	219	(uri (string-append "http://www.inchi-trust.org/download/"
	220	(string-join (string-split version #\.) "")
	221	"/INCHI-1-DOC.zip"))
	222	(sha256
	223	(base32
224	"1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
225	(file-name (string-append name "-" version ".zip"))))))
226	(home-page "https://www.inchi-trust.org")
227	(synopsis "Utility for manipulating machine-readable chemical structures")
228	(description
229	"The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
230	chemical structures into machine-readable strings of information. InChIs are
231	unique to the compound they describe and can encode absolute stereochemistry
232	making chemicals and chemistry machine-readable and discoverable. A simple
233	analogy is that InChI is the bar-code for chemistry and chemical structures.")
234	(license (license:non-copyleft
235	"file://LICENCE"
236	"See LICENCE in the distribution."))))
237
f250a868 KH	238	(define with-numpy-1.8
	239	(package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
	240
	241	(define-public nmoldyn
	242	(package
	243	(name "nmoldyn")
	244	(version "3.0.11")
	245	(source
	246	(origin
e2293cbb KH	247	(method git-fetch)
	248	(uri (git-reference
	249	(url "https://github.com/khinsen/nMOLDYN3")
	250	(commit (string-append "v" version))))
	251	(file-name (git-file-name name version))
f250a868 KH	252	(sha256
f250a868 KH	253	(base32
e2293cbb	254	"016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r"))))
f250a868 KH	255	(build-system python-build-system)
	256	(inputs
	257	`(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
c695fb76 TGR	258	("python-scientific" ,python2-scientific)
c695fb76 TGR	259	("netcdf" ,netcdf)
f250a868 KH	260	("gv" ,gv)))
	261	(propagated-inputs
	262	`(("python-mmtk" ,python2-mmtk)))
	263	(arguments
	264	`(#:python ,python-2
	265	#:tests? #f ; No test suite
	266	#:phases
	267	(modify-phases %standard-phases
	268	(add-before 'build 'create-linux2-directory
	269	(lambda _
	270	(mkdir-p "nMOLDYN/linux2")))
	271	(add-before 'build 'change-PDF-viewer
	272	(lambda* (#:key inputs #:allow-other-keys)
	273	(substitute* "nMOLDYN/Preferences.py"
	274	;; Set the paths for external executables, substituting
	275	;; gv for acroread.
	276	;; There is also vmd_path, but VMD is not free software
	277	;; and Guix contains currently no free molecular viewer that
	278	;; could be substituted.
	279	(("PREFERENCES\\['acroread_path'\\] = ''")
30d0f7fa	280	(format #f "PREFERENCES['acroread_path'] = '~a'"
f250a868 KH	281	(which "gv")))
f250a868 KH	282	(("PREFERENCES\\['ncdump_path'\\] = ''")
30d0f7fa	283	(format #f "PREFERENCES['ncdump_path'] = '~a'"
f250a868 KH	284	(which "ncdump")))
f250a868 KH	285	(("PREFERENCES\\['ncgen_path'\\] = ''")
30d0f7fa	286	(format #f "PREFERENCES['ncgen_path'] = '~a'"
f250a868 KH	287	(which "ncgen3")))
f250a868 KH	288	(("PREFERENCES\\['task_manager_path'\\] = ''")
30d0f7fa	289	(format #f "PREFERENCES['task_manager_path'] = '~a'"
f250a868 KH	290	(which "task_manager")))
	291	;; Show documentation as PDF
	292	(("PREFERENCES\\['documentation_style'\\] = 'html'")
	293	"PREFERENCES['documentation_style'] = 'pdf'") ))))))
357328d2	294	(home-page "http://dirac.cnrs-orleans.fr/nMOLDYN.html")
f250a868 KH	295	(synopsis "Analysis software for Molecular Dynamics trajectories")
	296	(description "nMOLDYN is an interactive analysis program for Molecular Dynamics
	297	simulations. It is especially designed for the computation and decomposition of
	298	neutron scattering spectra, but also computes other quantities. The software
	299	is currently not actively maintained and works only with Python 2 and
	300	NumPy < 1.9.")
	301	(license license:cecill)))
348edd91 KK	302
	303	(define-public openbabel
	304	(package
	305	(name "openbabel")
	306	(version "2.4.1")
	307	(source (origin
	308	(method url-fetch)
	309	(uri (string-append "mirror://sourceforge/" name "/" name "/"
	310	version "/" name "-" version ".tar.gz"))
	311	(sha256
	312	(base32
eb5ece73 KK	313	"1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
	314	(patches
	315	(search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
348edd91 KK	316	(build-system cmake-build-system)
	317	(arguments
	318	`(#:configure-flags
	319	(list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
	320	(string-append "-DINCHI_LIBRARY="
	321	(assoc-ref %build-inputs "inchi")
	322	"/lib/inchi/libinchi.so.1")
	323	(string-append "-DINCHI_INCLUDE_DIR="
	324	(assoc-ref %build-inputs "inchi") "/include/inchi"))
	325	#:test-target "test"))
	326	(native-inputs
	327	`(("pkg-config" ,pkg-config)))
	328	(inputs
	329	`(("eigen" ,eigen)
	330	("inchi" ,inchi)
	331	("libxml2" ,libxml2)
	332	("zlib" ,zlib)))
	333	(home-page "http://openbabel.org/wiki/Main_Page")
	334	(synopsis "Chemistry data manipulation toolbox")
	335	(description
	336	"Open Babel is a chemical toolbox designed to speak the many languages of
	337	chemical data. It's a collaborative project allowing anyone to search, convert,
	338	analyze, or store data from molecular modeling, chemistry, solid-state
	339	materials, biochemistry, or related areas.")
	340	(license license:gpl2)))