gnu/packages/chemistry.scm

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