[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>
;;;
;;; 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)))
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>
73114e30 KH	4	;;;
	5	;;; This file is part of GNU Guix.
	6	;;;
	7	;;; GNU Guix is free software; you can redistribute it and/or modify it
	8	;;; under the terms of the GNU General Public License as published by
	9	;;; the Free Software Foundation; either version 3 of the License, or (at
	10	;;; your option) any later version.
	11	;;;
	12	;;; GNU Guix is distributed in the hope that it will be useful, but
	13	;;; WITHOUT ANY WARRANTY; without even the implied warranty of
	14	;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	15	;;; GNU General Public License for more details.
	16	;;;
	17	;;; You should have received a copy of the GNU General Public License
	18	;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
	19
	20	(define-module (gnu packages chemistry)
	21	#:use-module (guix packages)
	22	#:use-module ((guix licenses) #:prefix license:)
	23	#:use-module (guix download)
0c468cb5	24	#:use-module (gnu packages)
348edd91	25	#:use-module (gnu packages algebra)
a49eb85c	26	#:use-module (gnu packages compression)
f250a868 KH	27	#:use-module (gnu packages gv)
f250a868 KH	28	#:use-module (gnu packages maths)
348edd91	29	#:use-module (gnu packages pkg-config)
73114e30	30	#:use-module (gnu packages python)
348edd91 KK	31	#:use-module (gnu packages xml)
348edd91 KK	32	#:use-module (guix build-system cmake)
a49eb85c	33	#:use-module (guix build-system gnu)
73114e30 KH	34	#:use-module (guix build-system python))
	35
	36	(define-public domainfinder
	37	(package
	38	(name "domainfinder")
	39	(version "2.0.5")
	40	(source
	41	(origin
	42	(method url-fetch)
	43	(uri (string-append "https://bitbucket.org/khinsen/"
	44	"domainfinder/downloads/DomainFinder-"
	45	version ".tar.gz"))
	46	(sha256
	47	(base32
	48	"1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
	49	(build-system python-build-system)
	50	(inputs
	51	`(("python-mmtk" ,python2-mmtk)))
	52	(arguments
	53	`(#:python ,python-2
	54	;; No test suite
	55	#:tests? #f))
	56	(home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
	57	(synopsis "Analysis of dynamical domains in proteins")
	58	(description "DomainFinder is an interactive program for the determination
	59	and characterization of dynamical domains in proteins. It can infer dynamical
	60	domains by comparing two protein structures, or from normal mode analysis on a
	61	single structure. The software is currently not actively maintained and works
	62	only with Python 2 and NumPy < 1.9.")
	63	(license license:cecill-c)))
f250a868	64
a49eb85c KK	65	(define-public inchi
	66	(package
	67	(name "inchi")
	68	(version "1.05")
	69	(source (origin
	70	(method url-fetch)
	71	(uri (string-append "http://www.inchi-trust.org/download/"
	72	(string-join (string-split version #\.) "")
	73	"/INCHI-1-SRC.zip"))
	74	(sha256
	75	(base32
	76	"081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
	77	(file-name (string-append name "-" version ".zip"))))
	78	(build-system gnu-build-system)
	79	(arguments
	80	'(#:tests? #f ; no check target
	81	#:phases
	82	(modify-phases %standard-phases
	83	(delete 'configure) ; no configure script
	84	(add-before 'build 'chdir-to-build-directory
	85	(lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
	86	(add-after 'build 'build-library
	87	(lambda _
	88	(chdir "../../../INCHI_API/libinchi/gcc")
	89	(invoke "make")))
	90	(replace 'install
	91	(lambda* (#:key inputs outputs #:allow-other-keys)
	92	(let* ((out (assoc-ref outputs "out"))
	93	(bin (string-append out "/bin"))
	94	(doc (string-append out "/share/doc/inchi"))
	95	(include-dir (string-append out "/include/inchi"))
	96	(lib (string-append out "/lib/inchi"))
	97	(inchi-doc (assoc-ref inputs "inchi-doc"))
	98	(unzip (string-append (assoc-ref inputs "unzip")
	99	"/bin/unzip")))
	100	(chdir "../../..")
	101	;; Install binary.
	102	(with-directory-excursion "INCHI_EXE/bin/Linux"
	103	(rename-file "inchi-1" "inchi")
	104	(install-file "inchi" bin))
	105	;; Install libraries.
	106	(with-directory-excursion "INCHI_API/bin/Linux"
	107	(for-each (lambda (file)
	108	(install-file file lib))
	109	(find-files "." "libinchi\\.so\\.1\\.*")))
	110	;; Install header files.
	111	(with-directory-excursion "INCHI_BASE/src"
	112	(for-each (lambda (file)
	113	(install-file file include-dir))
	114	(find-files "." "\\.h$")))
	115	;; Install documentation.
	116	(mkdir-p doc)
	117	(invoke unzip "-j" "-d" doc inchi-doc)
	118	#t))))))
	119	(native-inputs
	120	`(("unzip" ,unzip)
	121	("inchi-doc"
	122	,(origin
	123	(method url-fetch)
	124	(uri (string-append "http://www.inchi-trust.org/download/"
	125	(string-join (string-split version #\.) "")
	126	"/INCHI-1-DOC.zip"))
	127	(sha256
	128	(base32
129	"1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
130	(file-name (string-append name "-" version ".zip"))))))
131	(home-page "https://www.inchi-trust.org")
132	(synopsis "Utility for manipulating machine-readable chemical structures")
133	(description
134	"The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
135	chemical structures into machine-readable strings of information. InChIs are
136	unique to the compound they describe and can encode absolute stereochemistry
137	making chemicals and chemistry machine-readable and discoverable. A simple
138	analogy is that InChI is the bar-code for chemistry and chemical structures.")
139	(license (license:non-copyleft
140	"file://LICENCE"
141	"See LICENCE in the distribution."))))
142
f250a868 KH	143	(define with-numpy-1.8
	144	(package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
	145
	146	(define-public nmoldyn
	147	(package
	148	(name "nmoldyn")
	149	(version "3.0.11")
	150	(source
	151	(origin
	152	(method url-fetch)
	153	(uri (string-append "https://bitbucket.org/khinsen/"
	154	"nmoldyn3/downloads/nMOLDYN-"
	155	version ".tar.gz"))
	156	(sha256
	157	(base32
	158	"1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a"))))
	159	(build-system python-build-system)
	160	(inputs
	161	`(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
c695fb76 TGR	162	("python-scientific" ,python2-scientific)
c695fb76 TGR	163	("netcdf" ,netcdf)
f250a868 KH	164	("gv" ,gv)))
	165	(propagated-inputs
	166	`(("python-mmtk" ,python2-mmtk)))
	167	(arguments
	168	`(#:python ,python-2
	169	#:tests? #f ; No test suite
	170	#:phases
	171	(modify-phases %standard-phases
	172	(add-before 'build 'create-linux2-directory
	173	(lambda _
	174	(mkdir-p "nMOLDYN/linux2")))
	175	(add-before 'build 'change-PDF-viewer
	176	(lambda* (#:key inputs #:allow-other-keys)
	177	(substitute* "nMOLDYN/Preferences.py"
	178	;; Set the paths for external executables, substituting
	179	;; gv for acroread.
	180	;; There is also vmd_path, but VMD is not free software
	181	;; and Guix contains currently no free molecular viewer that
	182	;; could be substituted.
	183	(("PREFERENCES\\['acroread_path'\\] = ''")
	184	(format "PREFERENCES['acroread_path'] = '~a'"
	185	(which "gv")))
	186	(("PREFERENCES\\['ncdump_path'\\] = ''")
	187	(format "PREFERENCES['ncdump_path'] = '~a'"
	188	(which "ncdump")))
	189	(("PREFERENCES\\['ncgen_path'\\] = ''")
	190	(format "PREFERENCES['ncgen_path'] = '~a'"
	191	(which "ncgen3")))
	192	(("PREFERENCES\\['task_manager_path'\\] = ''")
	193	(format "PREFERENCES['task_manager_path'] = '~a'"
	194	(which "task_manager")))
	195	;; Show documentation as PDF
	196	(("PREFERENCES\\['documentation_style'\\] = 'html'")
	197	"PREFERENCES['documentation_style'] = 'pdf'") ))))))
	198	(home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/")
	199	(synopsis "Analysis software for Molecular Dynamics trajectories")
	200	(description "nMOLDYN is an interactive analysis program for Molecular Dynamics
	201	simulations. It is especially designed for the computation and decomposition of
	202	neutron scattering spectra, but also computes other quantities. The software
	203	is currently not actively maintained and works only with Python 2 and
	204	NumPy < 1.9.")
	205	(license license:cecill)))
348edd91 KK	206
	207	(define-public openbabel
	208	(package
	209	(name "openbabel")
	210	(version "2.4.1")
	211	(source (origin
	212	(method url-fetch)
	213	(uri (string-append "mirror://sourceforge/" name "/" name "/"
	214	version "/" name "-" version ".tar.gz"))
	215	(sha256
	216	(base32
eb5ece73 KK	217	"1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
	218	(patches
	219	(search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
348edd91 KK	220	(build-system cmake-build-system)
	221	(arguments
	222	`(#:configure-flags
	223	(list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
	224	(string-append "-DINCHI_LIBRARY="
	225	(assoc-ref %build-inputs "inchi")
	226	"/lib/inchi/libinchi.so.1")
	227	(string-append "-DINCHI_INCLUDE_DIR="
	228	(assoc-ref %build-inputs "inchi") "/include/inchi"))
	229	#:test-target "test"))
	230	(native-inputs
	231	`(("pkg-config" ,pkg-config)))
	232	(inputs
	233	`(("eigen" ,eigen)
	234	("inchi" ,inchi)
	235	("libxml2" ,libxml2)
	236	("zlib" ,zlib)))
	237	(home-page "http://openbabel.org/wiki/Main_Page")
	238	(synopsis "Chemistry data manipulation toolbox")
	239	(description
	240	"Open Babel is a chemical toolbox designed to speak the many languages of
	241	chemical data. It's a collaborative project allowing anyone to search, convert,
	242	analyze, or store data from molecular modeling, chemistry, solid-state
	243	materials, biochemistry, or related areas.")
	244	(license license:gpl2)))