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 ;;;
   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)
  24   #:use-module (gnu packages)
  25   #:use-module (gnu packages algebra)
  26   #:use-module (gnu packages boost)
  27   #:use-module (gnu packages compression)
  28   #:use-module (gnu packages documentation)
  29   #:use-module (gnu packages gl)
  30   #:use-module (gnu packages gv)
  31   #:use-module (gnu packages maths)
  32   #:use-module (gnu packages pkg-config)
  33   #:use-module (gnu packages python)
  34   #:use-module (gnu packages qt)
  35   #:use-module (gnu packages xml)
  36   #:use-module (guix build-system cmake)
  37   #:use-module (guix build-system gnu)
  38   #:use-module (guix build-system python))
  39
  40 (define-public avogadro
  41   (package
  42     (name "avogadro")
  43     (version "1.2.0")
  44     (source (origin
  45               (method url-fetch)
  46               (uri (string-append "https://github.com/cryos/avogadro/archive/"
  47                                   version ".tar.gz"))
  48               (sha256
  49                (base32
  50                 "02v4h6hi1m7ilv0apdf74a8l1cm6dxnxyqp0rdaidrp3i9pf6lv4"))
  51               (file-name (string-append name "-" version ".tar.gz"))
  52               (patches
  53                (search-patches "avogadro-eigen3-update.patch"
  54                                "avogadro-python-eigen-lib.patch"
  55                                "avogadro-boost148.patch"))))
  56     (build-system cmake-build-system)
  57     (arguments
  58      '(#:tests? #f
  59        #:configure-flags
  60        (list "-DENABLE_GLSL=ON"
  61              (string-append "-DPYTHON_LIBRARIES="
  62                             (assoc-ref %build-inputs "python")
  63                             "/lib")
  64              (string-append "-DPYTHON_INCLUDE_DIRS="
  65                             (assoc-ref %build-inputs "python")
  66                             "/include/python2.7"))
  67        #:phases
  68        (modify-phases %standard-phases
  69          (add-after 'unpack 'patch-python-lib-path
  70            (lambda* (#:key outputs #:allow-other-keys)
  71              ;; This is necessary to install the Python module in the correct
  72              ;; directory.
  73              (substitute* "libavogadro/src/python/CMakeLists.txt"
  74                (("^EXECUTE_PROCESS.*$") "")
  75                (("^.*from sys import stdout.*$") "")
  76                (("^.*OUTPUT_VARIABLE.*")
  77                 (string-append "set(PYTHON_LIB_PATH \""
  78                                (assoc-ref outputs "out")
  79                                "/lib/python2.7/site-packages\")")))
  80              #t))
  81          (add-after 'install 'wrap-program
  82            (lambda* (#:key inputs outputs #:allow-other-keys)
  83              ;; Make sure 'avogadro' runs with the correct PYTHONPATH.
  84              (let* ((out (assoc-ref outputs "out")))
  85                (setenv "PYTHONPATH"
  86                        (string-append
  87                         (assoc-ref outputs "out")
  88                         "/lib/python2.7/site-packages:"
  89                         (getenv "PYTHONPATH")))
  90                (wrap-program (string-append out "/bin/avogadro")
  91                  `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
  92              #t)))))
  93     (native-inputs
  94      `(("doxygen" ,doxygen)
  95        ("pkg-config" ,pkg-config)))
  96     (inputs
  97      `(("boost" ,boost)
  98        ("eigen" ,eigen)
  99        ("glew" ,glew)
 100        ("openbabel" ,openbabel)
 101        ("python" ,python-2)
 102        ("python-numpy" ,python2-numpy)
 103        ("python-pyqt" ,python2-pyqt-4)
 104        ("python-sip" ,python2-sip)
 105        ("qt" ,qt-4)
 106        ("zlib" ,zlib)))
 107     (home-page "https://avogadro.cc")
 108     (synopsis "Advanced molecule editor")
 109     (description
 110      "Avogadro is an advanced molecule editor and visualizer designed for use
 111 in computational chemistry, molecular modeling, bioinformatics, materials
 112 science, and related areas.  It offers flexible high quality rendering and a
 113 powerful plugin architecture.")
 114     (license license:gpl2+)))
 115
 116 (define-public domainfinder
 117   (package
 118     (name "domainfinder")
 119     (version "2.0.5")
 120     (source
 121      (origin
 122        (method url-fetch)
 123        (uri (string-append "https://bitbucket.org/khinsen/"
 124                            "domainfinder/downloads/DomainFinder-"
 125                            version ".tar.gz"))
 126        (sha256
 127         (base32
 128          "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
 129     (build-system python-build-system)
 130     (inputs
 131      `(("python-mmtk" ,python2-mmtk)))
 132     (arguments
 133      `(#:python ,python-2
 134        ;; No test suite
 135        #:tests? #f))
 136     (home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
 137     (synopsis "Analysis of dynamical domains in proteins")
 138     (description "DomainFinder is an interactive program for the determination
 139 and characterization of dynamical domains in proteins.  It can infer dynamical
 140 domains by comparing two protein structures, or from normal mode analysis on a
 141 single structure.  The software is currently not actively maintained and works
 142 only with Python 2 and NumPy < 1.9.")
 143     (license license:cecill-c)))
 144
 145 (define-public inchi
 146   (package
 147     (name "inchi")
 148     (version "1.05")
 149     (source (origin
 150               (method url-fetch)
 151               (uri (string-append "http://www.inchi-trust.org/download/"
 152                                   (string-join (string-split version #\.) "")
 153                                   "/INCHI-1-SRC.zip"))
 154               (sha256
 155                (base32
 156                 "081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
 157               (file-name (string-append name "-" version ".zip"))))
 158     (build-system gnu-build-system)
 159     (arguments
 160      '(#:tests? #f ; no check target
 161        #:phases
 162        (modify-phases %standard-phases
 163          (delete 'configure) ; no configure script
 164          (add-before 'build 'chdir-to-build-directory
 165            (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
 166          (add-after 'build 'build-library
 167            (lambda _
 168              (chdir "../../../INCHI_API/libinchi/gcc")
 169              (invoke "make")))
 170          (replace 'install
 171            (lambda* (#:key inputs outputs #:allow-other-keys)
 172              (let* ((out (assoc-ref outputs "out"))
 173                     (bin (string-append out "/bin"))
 174                     (doc (string-append out "/share/doc/inchi"))
 175                     (include-dir (string-append out "/include/inchi"))
 176                     (lib (string-append out "/lib/inchi"))
 177                     (inchi-doc (assoc-ref inputs "inchi-doc"))
 178                     (unzip (string-append (assoc-ref inputs "unzip")
 179                                           "/bin/unzip")))
 180                (chdir "../../..")
 181                ;; Install binary.
 182                (with-directory-excursion "INCHI_EXE/bin/Linux"
 183                  (rename-file "inchi-1" "inchi")
 184                  (install-file "inchi" bin))
 185                ;; Install libraries.
 186                (with-directory-excursion "INCHI_API/bin/Linux"
 187                  (for-each (lambda (file)
 188                              (install-file file lib))
 189                            (find-files "." "libinchi\\.so\\.1\\.*")))
 190                ;; Install header files.
 191                (with-directory-excursion "INCHI_BASE/src"
 192                  (for-each (lambda (file)
 193                              (install-file file include-dir))
 194                            (find-files "." "\\.h$")))
 195                ;; Install documentation.
 196                (mkdir-p doc)
 197                (invoke unzip "-j" "-d" doc inchi-doc)
 198                #t))))))
 199     (native-inputs
 200      `(("unzip" ,unzip)
 201        ("inchi-doc"
 202         ,(origin
 203            (method url-fetch)
 204            (uri (string-append "http://www.inchi-trust.org/download/"
 205                                   (string-join (string-split version #\.) "")
 206                                   "/INCHI-1-DOC.zip"))
 207            (sha256
 208             (base32
 209              "1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
 210            (file-name (string-append name "-" version ".zip"))))))
 211     (home-page "https://www.inchi-trust.org")
 212     (synopsis "Utility for manipulating machine-readable chemical structures")
 213     (description
 214      "The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
 215 chemical structures into machine-readable strings of information.  InChIs are
 216 unique to the compound they describe and can encode absolute stereochemistry
 217 making chemicals and chemistry machine-readable and discoverable.  A simple
 218 analogy is that InChI is the bar-code for chemistry and chemical structures.")
 219     (license (license:non-copyleft
 220               "file://LICENCE"
 221               "See LICENCE in the distribution."))))
 222
 223 (define with-numpy-1.8
 224   (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
 225
 226 (define-public nmoldyn
 227   (package
 228     (name "nmoldyn")
 229     (version "3.0.11")
 230     (source
 231      (origin
 232        (method url-fetch)
 233        (uri (string-append "https://bitbucket.org/khinsen/"
 234                            "nmoldyn3/downloads/nMOLDYN-"
 235                            version ".tar.gz"))
 236        (sha256
 237         (base32
 238          "1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a"))))
 239     (build-system python-build-system)
 240     (inputs
 241      `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
 242        ("python-scientific" ,python2-scientific)
 243        ("netcdf" ,netcdf)
 244        ("gv" ,gv)))
 245     (propagated-inputs
 246      `(("python-mmtk" ,python2-mmtk)))
 247     (arguments
 248      `(#:python ,python-2
 249        #:tests? #f  ; No test suite
 250        #:phases
 251        (modify-phases %standard-phases
 252          (add-before 'build 'create-linux2-directory
 253            (lambda _
 254              (mkdir-p "nMOLDYN/linux2")))
 255          (add-before 'build 'change-PDF-viewer
 256            (lambda* (#:key inputs #:allow-other-keys)
 257              (substitute* "nMOLDYN/Preferences.py"
 258                ;; Set the paths for external executables, substituting
 259                ;; gv for acroread.
 260                ;; There is also vmd_path, but VMD is not free software
 261                ;; and Guix contains currently no free molecular viewer that
 262                ;; could be substituted.
 263                (("PREFERENCES\\['acroread_path'\\] = ''")
 264                 (format "PREFERENCES['acroread_path'] = '~a'"
 265                         (which "gv")))
 266                (("PREFERENCES\\['ncdump_path'\\] = ''")
 267                 (format "PREFERENCES['ncdump_path'] = '~a'"
 268                         (which "ncdump")))
 269                (("PREFERENCES\\['ncgen_path'\\] = ''")
 270                 (format "PREFERENCES['ncgen_path'] = '~a'"
 271                         (which "ncgen3")))
 272                (("PREFERENCES\\['task_manager_path'\\] = ''")
 273                 (format "PREFERENCES['task_manager_path'] = '~a'"
 274                         (which "task_manager")))
 275                ;; Show documentation as PDF
 276                (("PREFERENCES\\['documentation_style'\\] = 'html'")
 277                 "PREFERENCES['documentation_style'] = 'pdf'") ))))))
 278     (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/")
 279     (synopsis "Analysis software for Molecular Dynamics trajectories")
 280     (description "nMOLDYN is an interactive analysis program for Molecular Dynamics
 281 simulations.  It is especially designed for the computation and decomposition of
 282 neutron scattering spectra, but also computes other quantities.  The software
 283 is currently not actively maintained and works only with Python 2 and
 284 NumPy < 1.9.")
 285     (license license:cecill)))
 286
 287 (define-public openbabel
 288   (package
 289     (name "openbabel")
 290     (version "2.4.1")
 291     (source (origin
 292               (method url-fetch)
 293               (uri (string-append "mirror://sourceforge/" name "/" name "/"
 294                                   version "/" name "-" version ".tar.gz"))
 295               (sha256
 296                (base32
 297                 "1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
 298               (patches
 299                (search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
 300     (build-system cmake-build-system)
 301     (arguments
 302      `(#:configure-flags
 303        (list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
 304              (string-append "-DINCHI_LIBRARY="
 305                             (assoc-ref %build-inputs "inchi")
 306                             "/lib/inchi/libinchi.so.1")
 307              (string-append "-DINCHI_INCLUDE_DIR="
 308                             (assoc-ref %build-inputs "inchi") "/include/inchi"))
 309        #:test-target "test"))
 310     (native-inputs
 311      `(("pkg-config" ,pkg-config)))
 312     (inputs
 313      `(("eigen" ,eigen)
 314        ("inchi" ,inchi)
 315        ("libxml2" ,libxml2)
 316        ("zlib" ,zlib)))
 317     (home-page "http://openbabel.org/wiki/Main_Page")
 318     (synopsis "Chemistry data manipulation toolbox")
 319     (description
 320      "Open Babel is a chemical toolbox designed to speak the many languages of
 321 chemical data.  It's a collaborative project allowing anyone to search, convert,
 322 analyze, or store data from molecular modeling, chemistry, solid-state
 323 materials, biochemistry, or related areas.")
 324     (license license:gpl2)))