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