[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>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;;
;;; 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 tng
  (package
    (name "tng")
    (version "1.8.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/gromacs/tng.git")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
    (build-system cmake-build-system)
    (inputs
     `(("zlib" ,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 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>
1c560401	7	;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
73114e30 KH	8	;;;
	9	;;; This file is part of GNU Guix.
	10	;;;
	11	;;; GNU Guix is free software; you can redistribute it and/or modify it
	12	;;; under the terms of the GNU General Public License as published by
	13	;;; the Free Software Foundation; either version 3 of the License, or (at
	14	;;; your option) any later version.
	15	;;;
	16	;;; GNU Guix is distributed in the hope that it will be useful, but
	17	;;; WITHOUT ANY WARRANTY; without even the implied warranty of
	18	;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	19	;;; GNU General Public License for more details.
	20	;;;
	21	;;; You should have received a copy of the GNU General Public License
	22	;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
	23
	24	(define-module (gnu packages chemistry)
	25	#:use-module (guix packages)
4ae16f9c	26	#:use-module (guix utils)
73114e30 KH	27	#:use-module ((guix licenses) #:prefix license:)
73114e30 KH	28	#:use-module (guix download)
631249dd	29	#:use-module (guix git-download)
0c468cb5	30	#:use-module (gnu packages)
348edd91	31	#:use-module (gnu packages algebra)
7d01ee66	32	#:use-module (gnu packages boost)
a49eb85c	33	#:use-module (gnu packages compression)
7d01ee66 KK	34	#:use-module (gnu packages documentation)
7d01ee66 KK	35	#:use-module (gnu packages gl)
f250a868 KH	36	#:use-module (gnu packages gv)
f250a868 KH	37	#:use-module (gnu packages maths)
348edd91	38	#:use-module (gnu packages pkg-config)
73114e30	39	#:use-module (gnu packages python)
44d10b1f	40	#:use-module (gnu packages python-xyz)
7d01ee66	41	#:use-module (gnu packages qt)
348edd91 KK	42	#:use-module (gnu packages xml)
348edd91 KK	43	#:use-module (guix build-system cmake)
a49eb85c	44	#:use-module (guix build-system gnu)
73114e30 KH	45	#:use-module (guix build-system python))
73114e30 KH	46
7d01ee66 KK	47	(define-public avogadro
	48	(package
	49	(name "avogadro")
	50	(version "1.2.0")
631249dd TGR	51	(source
	52	(origin
	53	(method git-fetch)
	54	(uri (git-reference
	55	(url "https://github.com/cryos/avogadro.git")
	56	(commit version)))
	57	(sha256
	58	(base32 "0258py3lkba85qhs5ynancinyym61vlp0zaq9yrfs3hhnhpzv9n2"))
	59	(file-name (git-file-name name version))
	60	(patches
	61	(search-patches "avogadro-eigen3-update.patch"
	62	"avogadro-python-eigen-lib.patch"
	63	"avogadro-boost148.patch"))))
7d01ee66 KK	64	(build-system cmake-build-system)
7d01ee66 KK	65	(arguments
4ae16f9c	66	`(#:tests? #f
7d01ee66 KK	67	#:configure-flags
	68	(list "-DENABLE_GLSL=ON"
	69	(string-append "-DPYTHON_LIBRARIES="
	70	(assoc-ref %build-inputs "python")
	71	"/lib")
	72	(string-append "-DPYTHON_INCLUDE_DIRS="
	73	(assoc-ref %build-inputs "python")
4ae16f9c EF	74	"/include/python"
	75	,(version-major+minor
	76	(package-version python))))
7d01ee66 KK	77	#:phases
	78	(modify-phases %standard-phases
	79	(add-after 'unpack 'patch-python-lib-path
	80	(lambda* (#:key outputs #:allow-other-keys)
	81	;; This is necessary to install the Python module in the correct
	82	;; directory.
	83	(substitute* "libavogadro/src/python/CMakeLists.txt"
	84	(("^EXECUTE_PROCESS.*$") "")
	85	(("^.from sys import stdout.$") "")
	86	(("^.OUTPUT_VARIABLE.")
	87	(string-append "set(PYTHON_LIB_PATH \""
	88	(assoc-ref outputs "out")
4ae16f9c EF	89	"/lib/python"
	90	,(version-major+minor
	91	(package-version python))
	92	"/site-packages\")")))
7d01ee66 KK	93	#t))
	94	(add-after 'install 'wrap-program
	95	(lambda* (#:key inputs outputs #:allow-other-keys)
	96	;; Make sure 'avogadro' runs with the correct PYTHONPATH.
	97	(let* ((out (assoc-ref outputs "out")))
	98	(setenv "PYTHONPATH"
	99	(string-append
	100	(assoc-ref outputs "out")
4ae16f9c EF	101	"/lib/python"
	102	,(version-major+minor
	103	(package-version python))
	104	"/site-packages:"
7d01ee66 KK	105	(getenv "PYTHONPATH")))
	106	(wrap-program (string-append out "/bin/avogadro")
	107	`("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
	108	#t)))))
	109	(native-inputs
	110	`(("doxygen" ,doxygen)
	111	("pkg-config" ,pkg-config)))
	112	(inputs
	113	`(("boost" ,boost)
	114	("eigen" ,eigen)
	115	("glew" ,glew)
	116	("openbabel" ,openbabel)
	117	("python" ,python-2)
	118	("python-numpy" ,python2-numpy)
	119	("python-pyqt" ,python2-pyqt-4)
	120	("python-sip" ,python2-sip)
	121	("qt" ,qt-4)
	122	("zlib" ,zlib)))
	123	(home-page "https://avogadro.cc")
	124	(synopsis "Advanced molecule editor")
	125	(description
	126	"Avogadro is an advanced molecule editor and visualizer designed for use
	127	in computational chemistry, molecular modeling, bioinformatics, materials
	128	science, and related areas. It offers flexible high quality rendering and a
	129	powerful plugin architecture.")
	130	(license license:gpl2+)))
	131
73114e30 KH	132	(define-public domainfinder
	133	(package
	134	(name "domainfinder")
	135	(version "2.0.5")
	136	(source
	137	(origin
	138	(method url-fetch)
	139	(uri (string-append "https://bitbucket.org/khinsen/"
	140	"domainfinder/downloads/DomainFinder-"
	141	version ".tar.gz"))
	142	(sha256
	143	(base32
	144	"1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
	145	(build-system python-build-system)
	146	(inputs
	147	`(("python-mmtk" ,python2-mmtk)))
	148	(arguments
	149	`(#:python ,python-2
	150	;; No test suite
	151	#:tests? #f))
7f489c56	152	(home-page "http://dirac.cnrs-orleans.fr/DomainFinder.html")
73114e30 KH	153	(synopsis "Analysis of dynamical domains in proteins")
	154	(description "DomainFinder is an interactive program for the determination
	155	and characterization of dynamical domains in proteins. It can infer dynamical
	156	domains by comparing two protein structures, or from normal mode analysis on a
	157	single structure. The software is currently not actively maintained and works
	158	only with Python 2 and NumPy < 1.9.")
	159	(license license:cecill-c)))
f250a868	160
a49eb85c KK	161	(define-public inchi
	162	(package
	163	(name "inchi")
	164	(version "1.05")
	165	(source (origin
	166	(method url-fetch)
	167	(uri (string-append "http://www.inchi-trust.org/download/"
	168	(string-join (string-split version #\.) "")
	169	"/INCHI-1-SRC.zip"))
	170	(sha256
	171	(base32
	172	"081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
	173	(file-name (string-append name "-" version ".zip"))))
	174	(build-system gnu-build-system)
	175	(arguments
	176	'(#:tests? #f ; no check target
	177	#:phases
	178	(modify-phases %standard-phases
	179	(delete 'configure) ; no configure script
	180	(add-before 'build 'chdir-to-build-directory
	181	(lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
	182	(add-after 'build 'build-library
	183	(lambda _
	184	(chdir "../../../INCHI_API/libinchi/gcc")
	185	(invoke "make")))
	186	(replace 'install
	187	(lambda* (#:key inputs outputs #:allow-other-keys)
	188	(let* ((out (assoc-ref outputs "out"))
	189	(bin (string-append out "/bin"))
	190	(doc (string-append out "/share/doc/inchi"))
	191	(include-dir (string-append out "/include/inchi"))
	192	(lib (string-append out "/lib/inchi"))
	193	(inchi-doc (assoc-ref inputs "inchi-doc"))
	194	(unzip (string-append (assoc-ref inputs "unzip")
	195	"/bin/unzip")))
	196	(chdir "../../..")
	197	;; Install binary.
	198	(with-directory-excursion "INCHI_EXE/bin/Linux"
	199	(rename-file "inchi-1" "inchi")
	200	(install-file "inchi" bin))
	201	;; Install libraries.
	202	(with-directory-excursion "INCHI_API/bin/Linux"
	203	(for-each (lambda (file)
	204	(install-file file lib))
	205	(find-files "." "libinchi\\.so\\.1\\.*")))
	206	;; Install header files.
	207	(with-directory-excursion "INCHI_BASE/src"
	208	(for-each (lambda (file)
	209	(install-file file include-dir))
	210	(find-files "." "\\.h$")))
	211	;; Install documentation.
	212	(mkdir-p doc)
	213	(invoke unzip "-j" "-d" doc inchi-doc)
	214	#t))))))
	215	(native-inputs
	216	`(("unzip" ,unzip)
	217	("inchi-doc"
	218	,(origin
	219	(method url-fetch)
	220	(uri (string-append "http://www.inchi-trust.org/download/"
	221	(string-join (string-split version #\.) "")
	222	"/INCHI-1-DOC.zip"))
	223	(sha256
	224	(base32
225	"1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
226	(file-name (string-append name "-" version ".zip"))))))
227	(home-page "https://www.inchi-trust.org")
228	(synopsis "Utility for manipulating machine-readable chemical structures")
229	(description
230	"The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
231	chemical structures into machine-readable strings of information. InChIs are
232	unique to the compound they describe and can encode absolute stereochemistry
233	making chemicals and chemistry machine-readable and discoverable. A simple
234	analogy is that InChI is the bar-code for chemistry and chemical structures.")
235	(license (license:non-copyleft
236	"file://LICENCE"
237	"See LICENCE in the distribution."))))
238
f250a868 KH	239	(define with-numpy-1.8
	240	(package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
	241
	242	(define-public nmoldyn
	243	(package
	244	(name "nmoldyn")
	245	(version "3.0.11")
	246	(source
	247	(origin
e2293cbb KH	248	(method git-fetch)
	249	(uri (git-reference
	250	(url "https://github.com/khinsen/nMOLDYN3")
	251	(commit (string-append "v" version))))
	252	(file-name (git-file-name name version))
f250a868 KH	253	(sha256
f250a868 KH	254	(base32
e2293cbb	255	"016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r"))))
f250a868 KH	256	(build-system python-build-system)
	257	(inputs
	258	`(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
c695fb76 TGR	259	("python-scientific" ,python2-scientific)
c695fb76 TGR	260	("netcdf" ,netcdf)
f250a868 KH	261	("gv" ,gv)))
	262	(propagated-inputs
	263	`(("python-mmtk" ,python2-mmtk)))
	264	(arguments
	265	`(#:python ,python-2
	266	#:tests? #f ; No test suite
	267	#:phases
	268	(modify-phases %standard-phases
	269	(add-before 'build 'create-linux2-directory
	270	(lambda _
	271	(mkdir-p "nMOLDYN/linux2")))
	272	(add-before 'build 'change-PDF-viewer
	273	(lambda* (#:key inputs #:allow-other-keys)
	274	(substitute* "nMOLDYN/Preferences.py"
	275	;; Set the paths for external executables, substituting
	276	;; gv for acroread.
	277	;; There is also vmd_path, but VMD is not free software
	278	;; and Guix contains currently no free molecular viewer that
	279	;; could be substituted.
	280	(("PREFERENCES\\['acroread_path'\\] = ''")
30d0f7fa	281	(format #f "PREFERENCES['acroread_path'] = '~a'"
f250a868 KH	282	(which "gv")))
f250a868 KH	283	(("PREFERENCES\\['ncdump_path'\\] = ''")
30d0f7fa	284	(format #f "PREFERENCES['ncdump_path'] = '~a'"
f250a868 KH	285	(which "ncdump")))
f250a868 KH	286	(("PREFERENCES\\['ncgen_path'\\] = ''")
30d0f7fa	287	(format #f "PREFERENCES['ncgen_path'] = '~a'"
f250a868 KH	288	(which "ncgen3")))
f250a868 KH	289	(("PREFERENCES\\['task_manager_path'\\] = ''")
30d0f7fa	290	(format #f "PREFERENCES['task_manager_path'] = '~a'"
f250a868 KH	291	(which "task_manager")))
	292	;; Show documentation as PDF
	293	(("PREFERENCES\\['documentation_style'\\] = 'html'")
	294	"PREFERENCES['documentation_style'] = 'pdf'") ))))))
357328d2	295	(home-page "http://dirac.cnrs-orleans.fr/nMOLDYN.html")
f250a868 KH	296	(synopsis "Analysis software for Molecular Dynamics trajectories")
	297	(description "nMOLDYN is an interactive analysis program for Molecular Dynamics
	298	simulations. It is especially designed for the computation and decomposition of
	299	neutron scattering spectra, but also computes other quantities. The software
	300	is currently not actively maintained and works only with Python 2 and
	301	NumPy < 1.9.")
	302	(license license:cecill)))
348edd91	303
1c560401 VL	304	(define-public tng
	305	(package
	306	(name "tng")
	307	(version "1.8.2")
	308	(source (origin
	309	(method git-fetch)
	310	(uri (git-reference
	311	(url "https://github.com/gromacs/tng.git")
	312	(commit (string-append "v" version))))
	313	(file-name (git-file-name name version))
	314	(sha256
	315	(base32
	316	"1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
	317	(build-system cmake-build-system)
	318	(inputs
	319	`(("zlib" ,zlib)))
	320	(arguments
	321	`(#:phases
	322	(modify-phases %standard-phases
	323	(add-after 'unpack 'remove-bundled-zlib
	324	(lambda _
	325	(delete-file-recursively "external")
	326	#t))
	327	(replace 'check
	328	(lambda _
	329	(invoke "../build/bin/tests/tng_testing")
	330	#t)))))
	331	(home-page "https://github.com/gromacs/tng")
	332	(synopsis "Trajectory Next Generation binary format manipulation library")
	333	(description "TRAJNG (Trajectory next generation) is a program library for
	334	handling molecular dynamics (MD) trajectories. It can store coordinates, and
	335	optionally velocities and the H-matrix. Coordinates and velocities are
	336	stored with user-specified precision.")
	337	(license license:bsd-3)))
	338
348edd91 KK	339	(define-public openbabel
	340	(package
	341	(name "openbabel")
	342	(version "2.4.1")
	343	(source (origin
	344	(method url-fetch)
	345	(uri (string-append "mirror://sourceforge/" name "/" name "/"
	346	version "/" name "-" version ".tar.gz"))
	347	(sha256
	348	(base32
eb5ece73 KK	349	"1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
	350	(patches
	351	(search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
348edd91 KK	352	(build-system cmake-build-system)
	353	(arguments
	354	`(#:configure-flags
	355	(list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
	356	(string-append "-DINCHI_LIBRARY="
	357	(assoc-ref %build-inputs "inchi")
	358	"/lib/inchi/libinchi.so.1")
	359	(string-append "-DINCHI_INCLUDE_DIR="
	360	(assoc-ref %build-inputs "inchi") "/include/inchi"))
	361	#:test-target "test"))
	362	(native-inputs
	363	`(("pkg-config" ,pkg-config)))
	364	(inputs
	365	`(("eigen" ,eigen)
	366	("inchi" ,inchi)
	367	("libxml2" ,libxml2)
	368	("zlib" ,zlib)))
	369	(home-page "http://openbabel.org/wiki/Main_Page")
	370	(synopsis "Chemistry data manipulation toolbox")
	371	(description
	372	"Open Babel is a chemical toolbox designed to speak the many languages of
	373	chemical data. It's a collaborative project allowing anyone to search, convert,
	374	analyze, or store data from molecular modeling, chemistry, solid-state
	375	materials, biochemistry, or related areas.")
	376	(license license:gpl2)))