[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 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)
348edd91	24	#:use-module (gnu packages algebra)
a49eb85c	25	#:use-module (gnu packages compression)
f250a868 KH	26	#:use-module (gnu packages gv)
f250a868 KH	27	#:use-module (gnu packages maths)
348edd91	28	#:use-module (gnu packages pkg-config)
73114e30	29	#:use-module (gnu packages python)
348edd91 KK	30	#:use-module (gnu packages xml)
348edd91 KK	31	#:use-module (guix build-system cmake)
a49eb85c	32	#:use-module (guix build-system gnu)
73114e30 KH	33	#:use-module (guix build-system python))
	34
	35	(define-public domainfinder
	36	(package
	37	(name "domainfinder")
	38	(version "2.0.5")
	39	(source
	40	(origin
	41	(method url-fetch)
	42	(uri (string-append "https://bitbucket.org/khinsen/"
	43	"domainfinder/downloads/DomainFinder-"
	44	version ".tar.gz"))
	45	(sha256
	46	(base32
	47	"1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
	48	(build-system python-build-system)
	49	(inputs
	50	`(("python-mmtk" ,python2-mmtk)))
	51	(arguments
	52	`(#:python ,python-2
	53	;; No test suite
	54	#:tests? #f))
	55	(home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
	56	(synopsis "Analysis of dynamical domains in proteins")
	57	(description "DomainFinder is an interactive program for the determination
	58	and characterization of dynamical domains in proteins. It can infer dynamical
	59	domains by comparing two protein structures, or from normal mode analysis on a
	60	single structure. The software is currently not actively maintained and works
	61	only with Python 2 and NumPy < 1.9.")
	62	(license license:cecill-c)))
f250a868	63
a49eb85c KK	64	(define-public inchi
	65	(package
	66	(name "inchi")
	67	(version "1.05")
	68	(source (origin
	69	(method url-fetch)
	70	(uri (string-append "http://www.inchi-trust.org/download/"
	71	(string-join (string-split version #\.) "")
	72	"/INCHI-1-SRC.zip"))
	73	(sha256
	74	(base32
	75	"081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
	76	(file-name (string-append name "-" version ".zip"))))
	77	(build-system gnu-build-system)
	78	(arguments
	79	'(#:tests? #f ; no check target
	80	#:phases
	81	(modify-phases %standard-phases
	82	(delete 'configure) ; no configure script
	83	(add-before 'build 'chdir-to-build-directory
	84	(lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
	85	(add-after 'build 'build-library
	86	(lambda _
	87	(chdir "../../../INCHI_API/libinchi/gcc")
	88	(invoke "make")))
	89	(replace 'install
	90	(lambda* (#:key inputs outputs #:allow-other-keys)
	91	(let* ((out (assoc-ref outputs "out"))
	92	(bin (string-append out "/bin"))
	93	(doc (string-append out "/share/doc/inchi"))
	94	(include-dir (string-append out "/include/inchi"))
	95	(lib (string-append out "/lib/inchi"))
	96	(inchi-doc (assoc-ref inputs "inchi-doc"))
	97	(unzip (string-append (assoc-ref inputs "unzip")
	98	"/bin/unzip")))
	99	(chdir "../../..")
	100	;; Install binary.
	101	(with-directory-excursion "INCHI_EXE/bin/Linux"
	102	(rename-file "inchi-1" "inchi")
	103	(install-file "inchi" bin))
	104	;; Install libraries.
	105	(with-directory-excursion "INCHI_API/bin/Linux"
	106	(for-each (lambda (file)
	107	(install-file file lib))
	108	(find-files "." "libinchi\\.so\\.1\\.*")))
	109	;; Install header files.
	110	(with-directory-excursion "INCHI_BASE/src"
	111	(for-each (lambda (file)
	112	(install-file file include-dir))
	113	(find-files "." "\\.h$")))
	114	;; Install documentation.
	115	(mkdir-p doc)
	116	(invoke unzip "-j" "-d" doc inchi-doc)
	117	#t))))))
	118	(native-inputs
	119	`(("unzip" ,unzip)
	120	("inchi-doc"
	121	,(origin
	122	(method url-fetch)
	123	(uri (string-append "http://www.inchi-trust.org/download/"
	124	(string-join (string-split version #\.) "")
	125	"/INCHI-1-DOC.zip"))
	126	(sha256
	127	(base32
128	"1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
129	(file-name (string-append name "-" version ".zip"))))))
130	(home-page "https://www.inchi-trust.org")
131	(synopsis "Utility for manipulating machine-readable chemical structures")
132	(description
133	"The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
134	chemical structures into machine-readable strings of information. InChIs are
135	unique to the compound they describe and can encode absolute stereochemistry
136	making chemicals and chemistry machine-readable and discoverable. A simple
137	analogy is that InChI is the bar-code for chemistry and chemical structures.")
138	(license (license:non-copyleft
139	"file://LICENCE"
140	"See LICENCE in the distribution."))))
141
f250a868 KH	142	(define with-numpy-1.8
	143	(package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
	144
	145	(define-public nmoldyn
	146	(package
	147	(name "nmoldyn")
	148	(version "3.0.11")
	149	(source
	150	(origin
	151	(method url-fetch)
	152	(uri (string-append "https://bitbucket.org/khinsen/"
	153	"nmoldyn3/downloads/nMOLDYN-"
	154	version ".tar.gz"))
	155	(sha256
	156	(base32
	157	"1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a"))))
	158	(build-system python-build-system)
	159	(inputs
	160	`(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
c695fb76 TGR	161	("python-scientific" ,python2-scientific)
c695fb76 TGR	162	("netcdf" ,netcdf)
f250a868 KH	163	("gv" ,gv)))
	164	(propagated-inputs
	165	`(("python-mmtk" ,python2-mmtk)))
	166	(arguments
	167	`(#:python ,python-2
	168	#:tests? #f ; No test suite
	169	#:phases
	170	(modify-phases %standard-phases
	171	(add-before 'build 'create-linux2-directory
	172	(lambda _
	173	(mkdir-p "nMOLDYN/linux2")))
	174	(add-before 'build 'change-PDF-viewer
	175	(lambda* (#:key inputs #:allow-other-keys)
	176	(substitute* "nMOLDYN/Preferences.py"
	177	;; Set the paths for external executables, substituting
	178	;; gv for acroread.
	179	;; There is also vmd_path, but VMD is not free software
	180	;; and Guix contains currently no free molecular viewer that
	181	;; could be substituted.
	182	(("PREFERENCES\\['acroread_path'\\] = ''")
	183	(format "PREFERENCES['acroread_path'] = '~a'"
	184	(which "gv")))
	185	(("PREFERENCES\\['ncdump_path'\\] = ''")
	186	(format "PREFERENCES['ncdump_path'] = '~a'"
	187	(which "ncdump")))
	188	(("PREFERENCES\\['ncgen_path'\\] = ''")
	189	(format "PREFERENCES['ncgen_path'] = '~a'"
	190	(which "ncgen3")))
	191	(("PREFERENCES\\['task_manager_path'\\] = ''")
	192	(format "PREFERENCES['task_manager_path'] = '~a'"
	193	(which "task_manager")))
	194	;; Show documentation as PDF
	195	(("PREFERENCES\\['documentation_style'\\] = 'html'")
	196	"PREFERENCES['documentation_style'] = 'pdf'") ))))))
	197	(home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/")
	198	(synopsis "Analysis software for Molecular Dynamics trajectories")
	199	(description "nMOLDYN is an interactive analysis program for Molecular Dynamics
	200	simulations. It is especially designed for the computation and decomposition of
	201	neutron scattering spectra, but also computes other quantities. The software
	202	is currently not actively maintained and works only with Python 2 and
	203	NumPy < 1.9.")
	204	(license license:cecill)))
348edd91 KK	205
	206	(define-public openbabel
	207	(package
	208	(name "openbabel")
	209	(version "2.4.1")
	210	(source (origin
	211	(method url-fetch)
	212	(uri (string-append "mirror://sourceforge/" name "/" name "/"
	213	version "/" name "-" version ".tar.gz"))
	214	(sha256
	215	(base32
eb5ece73 KK	216	"1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
	217	(patches
	218	(search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
348edd91 KK	219	(build-system cmake-build-system)
	220	(arguments
	221	`(#:configure-flags
	222	(list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
	223	(string-append "-DINCHI_LIBRARY="
	224	(assoc-ref %build-inputs "inchi")
	225	"/lib/inchi/libinchi.so.1")
	226	(string-append "-DINCHI_INCLUDE_DIR="
	227	(assoc-ref %build-inputs "inchi") "/include/inchi"))
	228	#:test-target "test"))
	229	(native-inputs
	230	`(("pkg-config" ,pkg-config)))
	231	(inputs
	232	`(("eigen" ,eigen)
	233	("inchi" ,inchi)
	234	("libxml2" ,libxml2)
	235	("zlib" ,zlib)))
	236	(home-page "http://openbabel.org/wiki/Main_Page")
	237	(synopsis "Chemistry data manipulation toolbox")
	238	(description
	239	"Open Babel is a chemical toolbox designed to speak the many languages of
	240	chemical data. It's a collaborative project allowing anyone to search, convert,
	241	analyze, or store data from molecular modeling, chemistry, solid-state
	242	materials, biochemistry, or related areas.")
	243	(license license:gpl2)))