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 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
   8 ;;;
   9 ;;; This file is part of GNU Guix.
  10 ;;;
  11 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  12 ;;; under the terms of the GNU General Public License as published by
  13 ;;; the Free Software Foundation; either version 3 of the License, or (at
  14 ;;; your option) any later version.
  15 ;;;
  16 ;;; GNU Guix is distributed in the hope that it will be useful, but
  17 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  18 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  19 ;;; GNU General Public License for more details.
  20 ;;;
  21 ;;; You should have received a copy of the GNU General Public License
  22 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  23
  24 (define-module (gnu packages chemistry)
  25   #:use-module (guix packages)
  26   #:use-module (guix utils)
  27   #:use-module ((guix licenses) #:prefix license:)
  28   #:use-module (guix download)
  29   #:use-module (guix git-download)
  30   #:use-module (gnu packages)
  31   #:use-module (gnu packages algebra)
  32   #:use-module (gnu packages boost)
  33   #:use-module (gnu packages check)
  34   #:use-module (gnu packages compression)
  35   #:use-module (gnu packages documentation)
  36   #:use-module (gnu packages gl)
  37   #:use-module (gnu packages graphviz)
  38   #:use-module (gnu packages gv)
  39   #:use-module (gnu packages maths)
  40   #:use-module (gnu packages mpi)
  41   #:use-module (gnu packages perl)
  42   #:use-module (gnu packages pkg-config)
  43   #:use-module (gnu packages python)
  44   #:use-module (gnu packages python-xyz)
  45   #:use-module (gnu packages qt)
  46   #:use-module (gnu packages sphinx)
  47   #:use-module (gnu packages xml)
  48   #:use-module (guix build-system cmake)
  49   #:use-module (guix build-system gnu)
  50   #:use-module (guix build-system python))
  51
  52 (define-public avogadro
  53   (package
  54     (name "avogadro")
  55     (version "1.2.0")
  56     (source
  57      (origin
  58        (method git-fetch)
  59        (uri (git-reference
  60              (url "https://github.com/cryos/avogadro")
  61              (commit version)))
  62        (sha256
  63         (base32 "0258py3lkba85qhs5ynancinyym61vlp0zaq9yrfs3hhnhpzv9n2"))
  64        (file-name (git-file-name name version))
  65        (patches
  66         (search-patches "avogadro-eigen3-update.patch"
  67                         "avogadro-python-eigen-lib.patch"
  68                         "avogadro-boost148.patch"))))
  69     (build-system cmake-build-system)
  70     (arguments
  71      `(#:tests? #f
  72        #:configure-flags
  73        (list "-DENABLE_GLSL=ON"
  74              (string-append "-DPYTHON_LIBRARIES="
  75                             (assoc-ref %build-inputs "python")
  76                             "/lib")
  77              (string-append "-DPYTHON_INCLUDE_DIRS="
  78                             (assoc-ref %build-inputs "python")
  79                             "/include/python"
  80                             ,(version-major+minor
  81                                (package-version python))))
  82        #:phases
  83        (modify-phases %standard-phases
  84          (add-after 'unpack 'patch-python-lib-path
  85            (lambda* (#:key outputs #:allow-other-keys)
  86              ;; This is necessary to install the Python module in the correct
  87              ;; directory.
  88              (substitute* "libavogadro/src/python/CMakeLists.txt"
  89                (("^EXECUTE_PROCESS.*$") "")
  90                (("^.*from sys import stdout.*$") "")
  91                (("^.*OUTPUT_VARIABLE.*")
  92                 (string-append "set(PYTHON_LIB_PATH \""
  93                                (assoc-ref outputs "out")
  94                                "/lib/python"
  95                                ,(version-major+minor
  96                                   (package-version python))
  97                                "/site-packages\")")))
  98              #t))
  99          (add-after 'install 'wrap-program
 100            (lambda* (#:key inputs outputs #:allow-other-keys)
 101              ;; Make sure 'avogadro' runs with the correct PYTHONPATH.
 102              (let* ((out (assoc-ref outputs "out")))
 103                (setenv "PYTHONPATH"
 104                        (string-append
 105                         (assoc-ref outputs "out")
 106                         "/lib/python"
 107                         ,(version-major+minor
 108                            (package-version python))
 109                         "/site-packages:"
 110                         (getenv "PYTHONPATH")))
 111                (wrap-program (string-append out "/bin/avogadro")
 112                  `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
 113              #t)))))
 114     (native-inputs
 115      `(("doxygen" ,doxygen)
 116        ("pkg-config" ,pkg-config)))
 117     (inputs
 118      `(("boost" ,boost)
 119        ("eigen" ,eigen)
 120        ("glew" ,glew)
 121        ("openbabel" ,openbabel)
 122        ("python" ,python-2)
 123        ("python-numpy" ,python2-numpy)
 124        ("python-pyqt" ,python2-pyqt-4)
 125        ("python-sip" ,python2-sip)
 126        ("qt" ,qt-4)
 127        ("zlib" ,zlib)))
 128     (home-page "https://avogadro.cc")
 129     (synopsis "Advanced molecule editor")
 130     (description
 131      "Avogadro is an advanced molecule editor and visualizer designed for use
 132 in computational chemistry, molecular modeling, bioinformatics, materials
 133 science, and related areas.  It offers flexible high quality rendering and a
 134 powerful plugin architecture.")
 135     (license license:gpl2+)))
 136
 137 (define-public domainfinder
 138   (package
 139     (name "domainfinder")
 140     (version "2.0.5")
 141     (source
 142      (origin
 143        (method url-fetch)
 144        (uri (string-append "https://bitbucket.org/khinsen/"
 145                            "domainfinder/downloads/DomainFinder-"
 146                            version ".tar.gz"))
 147        (sha256
 148         (base32
 149          "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
 150     (build-system python-build-system)
 151     (inputs
 152      `(("python-mmtk" ,python2-mmtk)))
 153     (arguments
 154      `(#:python ,python-2
 155        ;; No test suite
 156        #:tests? #f))
 157     (home-page "http://dirac.cnrs-orleans.fr/DomainFinder.html")
 158     (synopsis "Analysis of dynamical domains in proteins")
 159     (description "DomainFinder is an interactive program for the determination
 160 and characterization of dynamical domains in proteins.  It can infer dynamical
 161 domains by comparing two protein structures, or from normal mode analysis on a
 162 single structure.  The software is currently not actively maintained and works
 163 only with Python 2 and NumPy < 1.9.")
 164     (license license:cecill-c)))
 165
 166 (define-public inchi
 167   (package
 168     (name "inchi")
 169     (version "1.05")
 170     (source (origin
 171               (method url-fetch)
 172               (uri (string-append "http://www.inchi-trust.org/download/"
 173                                   (string-join (string-split version #\.) "")
 174                                   "/INCHI-1-SRC.zip"))
 175               (sha256
 176                (base32
 177                 "081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
 178               (file-name (string-append name "-" version ".zip"))))
 179     (build-system gnu-build-system)
 180     (arguments
 181      '(#:tests? #f ; no check target
 182        #:phases
 183        (modify-phases %standard-phases
 184          (delete 'configure) ; no configure script
 185          (add-before 'build 'chdir-to-build-directory
 186            (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
 187          (add-after 'build 'build-library
 188            (lambda _
 189              (chdir "../../../INCHI_API/libinchi/gcc")
 190              (invoke "make")))
 191          (replace 'install
 192            (lambda* (#:key inputs outputs #:allow-other-keys)
 193              (let* ((out (assoc-ref outputs "out"))
 194                     (bin (string-append out "/bin"))
 195                     (doc (string-append out "/share/doc/inchi"))
 196                     (include-dir (string-append out "/include/inchi"))
 197                     (lib (string-append out "/lib/inchi"))
 198                     (inchi-doc (assoc-ref inputs "inchi-doc"))
 199                     (unzip (string-append (assoc-ref inputs "unzip")
 200                                           "/bin/unzip")))
 201                (chdir "../../..")
 202                ;; Install binary.
 203                (with-directory-excursion "INCHI_EXE/bin/Linux"
 204                  (rename-file "inchi-1" "inchi")
 205                  (install-file "inchi" bin))
 206                ;; Install libraries.
 207                (with-directory-excursion "INCHI_API/bin/Linux"
 208                  (for-each (lambda (file)
 209                              (install-file file lib))
 210                            (find-files "." "libinchi\\.so\\.1\\.*")))
 211                ;; Install header files.
 212                (with-directory-excursion "INCHI_BASE/src"
 213                  (for-each (lambda (file)
 214                              (install-file file include-dir))
 215                            (find-files "." "\\.h$")))
 216                ;; Install documentation.
 217                (mkdir-p doc)
 218                (invoke unzip "-j" "-d" doc inchi-doc)
 219                #t))))))
 220     (native-inputs
 221      `(("unzip" ,unzip)
 222        ("inchi-doc"
 223         ,(origin
 224            (method url-fetch)
 225            (uri (string-append "http://www.inchi-trust.org/download/"
 226                                   (string-join (string-split version #\.) "")
 227                                   "/INCHI-1-DOC.zip"))
 228            (sha256
 229             (base32
 230              "1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
 231            (file-name (string-append name "-" version ".zip"))))))
 232     (home-page "https://www.inchi-trust.org")
 233     (synopsis "Utility for manipulating machine-readable chemical structures")
 234     (description
 235      "The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
 236 chemical structures into machine-readable strings of information.  InChIs are
 237 unique to the compound they describe and can encode absolute stereochemistry
 238 making chemicals and chemistry machine-readable and discoverable.  A simple
 239 analogy is that InChI is the bar-code for chemistry and chemical structures.")
 240     (license (license:non-copyleft
 241               "file://LICENCE"
 242               "See LICENCE in the distribution."))))
 243
 244 (define with-numpy-1.8
 245   (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
 246
 247 (define-public nmoldyn
 248   (package
 249     (name "nmoldyn")
 250     (version "3.0.11")
 251     (source
 252      (origin
 253        (method git-fetch)
 254        (uri (git-reference
 255              (url "https://github.com/khinsen/nMOLDYN3")
 256              (commit (string-append "v" version))))
 257        (file-name (git-file-name name version))
 258        (sha256
 259         (base32
 260          "016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r"))))
 261     (build-system python-build-system)
 262     (inputs
 263      `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
 264        ("python-scientific" ,python2-scientific)
 265        ("netcdf" ,netcdf)
 266        ("gv" ,gv)))
 267     (propagated-inputs
 268      `(("python-mmtk" ,python2-mmtk)))
 269     (arguments
 270      `(#:python ,python-2
 271        #:tests? #f  ; No test suite
 272        #:phases
 273        (modify-phases %standard-phases
 274          (add-before 'build 'create-linux2-directory
 275            (lambda _
 276              (mkdir-p "nMOLDYN/linux2")))
 277          (add-before 'build 'change-PDF-viewer
 278            (lambda* (#:key inputs #:allow-other-keys)
 279              (substitute* "nMOLDYN/Preferences.py"
 280                ;; Set the paths for external executables, substituting
 281                ;; gv for acroread.
 282                ;; There is also vmd_path, but VMD is not free software
 283                ;; and Guix contains currently no free molecular viewer that
 284                ;; could be substituted.
 285                (("PREFERENCES\\['acroread_path'\\] = ''")
 286                 (format #f "PREFERENCES['acroread_path'] = '~a'"
 287                         (which "gv")))
 288                (("PREFERENCES\\['ncdump_path'\\] = ''")
 289                 (format #f "PREFERENCES['ncdump_path'] = '~a'"
 290                         (which "ncdump")))
 291                (("PREFERENCES\\['ncgen_path'\\] = ''")
 292                 (format #f "PREFERENCES['ncgen_path'] = '~a'"
 293                         (which "ncgen3")))
 294                (("PREFERENCES\\['task_manager_path'\\] = ''")
 295                 (format #f "PREFERENCES['task_manager_path'] = '~a'"
 296                         (which "task_manager")))
 297                ;; Show documentation as PDF
 298                (("PREFERENCES\\['documentation_style'\\] = 'html'")
 299                 "PREFERENCES['documentation_style'] = 'pdf'") ))))))
 300     (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN.html")
 301     (synopsis "Analysis software for Molecular Dynamics trajectories")
 302     (description "nMOLDYN is an interactive analysis program for Molecular Dynamics
 303 simulations.  It is especially designed for the computation and decomposition of
 304 neutron scattering spectra, but also computes other quantities.  The software
 305 is currently not actively maintained and works only with Python 2 and
 306 NumPy < 1.9.")
 307     (license license:cecill)))
 308
 309 (define-public tng
 310   (package
 311     (name "tng")
 312     (version "1.8.2")
 313     (source (origin
 314               (method git-fetch)
 315               (uri (git-reference
 316                     (url "https://github.com/gromacs/tng")
 317                     (commit (string-append "v" version))))
 318               (file-name (git-file-name name version))
 319               (sha256
 320                (base32
 321                 "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
 322     (build-system cmake-build-system)
 323     (inputs
 324      `(("zlib" ,zlib)))
 325     (arguments
 326      `(#:phases
 327        (modify-phases %standard-phases
 328          (add-after 'unpack 'remove-bundled-zlib
 329            (lambda _
 330              (delete-file-recursively "external")
 331              #t))
 332          (replace 'check
 333            (lambda _
 334              (invoke "../build/bin/tests/tng_testing")
 335              #t)))))
 336     (home-page "https://github.com/gromacs/tng")
 337     (synopsis "Trajectory Next Generation binary format manipulation library")
 338     (description "TRAJNG (Trajectory next generation) is a program library for
 339 handling molecular dynamics (MD) trajectories.  It can store coordinates, and
 340 optionally velocities and the H-matrix.  Coordinates and velocities are
 341 stored with user-specified precision.")
 342     (license license:bsd-3)))
 343
 344 (define-public gromacs
 345   (package
 346     (name "gromacs")
 347     (version "2020.2")
 348     (source (origin
 349               (method url-fetch)
 350               (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
 351                                   version ".tar.gz"))
 352               (sha256
 353                (base32
 354                 "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
 355               ;; Our version of tinyxml2 is far newer than the bundled one and
 356               ;; require fixing `testutils' code. See patch header for more info
 357               (patches (search-patches "gromacs-tinyxml2.patch"))))
 358     (build-system cmake-build-system)
 359     (arguments
 360      `(#:configure-flags
 361        (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
 362              ;; Unbundling
 363              "-DGMX_USE_LMFIT=EXTERNAL"
 364              "-DGMX_BUILD_OWN_FFTW=off"
 365              "-DGMX_EXTERNAL_BLAS=on"
 366              "-DGMX_EXTERNAL_LAPACK=on"
 367              "-DGMX_EXTERNAL_TNG=on"
 368              "-DGMX_EXTERNAL_ZLIB=on"
 369              "-DGMX_EXTERNAL_TINYXML2=on"
 370              (string-append "-DTinyXML2_DIR="
 371                             (assoc-ref %build-inputs "tinyxml2"))
 372              ;; Workaround for cmake/FindSphinx.cmake version parsing that does
 373              ;; not understand the guix-wrapped `sphinx-build --version' answer
 374              (string-append "-DSPHINX_EXECUTABLE_VERSION="
 375                             ,(package-version python-sphinx)))
 376        #:phases
 377        (modify-phases %standard-phases
 378          (add-after 'unpack 'fixes
 379            (lambda* (#:key inputs #:allow-other-keys)
 380              ;; Still bundled: part of gromacs, source behind registration
 381              ;; but free software anyways
 382              ;;(delete-file-recursively "src/external/vmd_molfile")
 383              ;; Still bundled: threads-based OpenMPI-compatible fallback
 384              ;; designed to be bundled like that
 385              ;;(delete-file-recursively "src/external/thread_mpi")
 386              ;; Unbundling
 387              (delete-file-recursively "src/external/lmfit")
 388              (delete-file-recursively "src/external/clFFT")
 389              (delete-file-recursively "src/external/fftpack")
 390              (delete-file-recursively "src/external/build-fftw")
 391              (delete-file-recursively "src/external/tng_io")
 392              (delete-file-recursively "src/external/tinyxml2")
 393              (delete-file-recursively "src/external/googletest")
 394              (copy-recursively (assoc-ref inputs "googletest-source")
 395                                "src/external/googletest")
 396              ;; This test warns about the build host hardware, disable
 397              (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
 398                (("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
 399                 "void __guix_disabled()"))
 400              #t)))))
 401     (native-inputs
 402      `(("doxygen" ,doxygen)
 403        ("googletest-source" ,(package-source googletest))
 404        ("graphviz" ,graphviz)
 405        ("pkg-config" ,pkg-config)
 406        ("python" ,python)
 407        ("python-pygments" ,python-pygments)
 408        ("python-sphinx" ,python-sphinx)))
 409     (inputs
 410      `(("fftwf" ,fftwf)
 411        ("hwloc" ,hwloc-2 "lib")
 412        ("lmfit" ,lmfit)
 413        ("openblas" ,openblas)
 414        ("perl" ,perl)
 415        ("tinyxml2" ,tinyxml2)
 416        ("tng" ,tng)))
 417     (home-page "http://www.gromacs.org/")
 418     (synopsis "Molecular dynamics software package")
 419     (description "GROMACS is a versatile package to perform molecular dynamics,
 420 i.e. simulate the Newtonian equations of motion for systems with hundreds to
 421 millions of particles.  It is primarily designed for biochemical molecules like
 422 proteins, lipids and nucleic acids that have a lot of complicated bonded
 423 interactions, but since GROMACS is extremely fast at calculating the nonbonded
 424 interactions (that usually dominate simulations) many groups are also using it
 425 for research on non-biological systems, e.g. polymers.  GROMACS supports all the
 426 usual algorithms you expect from a modern molecular dynamics implementation.")
 427     (license license:lgpl2.1+)))
 428
 429 (define-public openbabel
 430   (package
 431     (name "openbabel")
 432     (version "2.4.1")
 433     (source (origin
 434               (method url-fetch)
 435               (uri (string-append "mirror://sourceforge/" name "/" name "/"
 436                                   version "/" name "-" version ".tar.gz"))
 437               (sha256
 438                (base32
 439                 "1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
 440               (patches
 441                (search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
 442     (build-system cmake-build-system)
 443     (arguments
 444      `(#:configure-flags
 445        (list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
 446              (string-append "-DINCHI_LIBRARY="
 447                             (assoc-ref %build-inputs "inchi")
 448                             "/lib/inchi/libinchi.so.1")
 449              (string-append "-DINCHI_INCLUDE_DIR="
 450                             (assoc-ref %build-inputs "inchi") "/include/inchi"))
 451        #:test-target "test"))
 452     (native-inputs
 453      `(("pkg-config" ,pkg-config)))
 454     (inputs
 455      `(("eigen" ,eigen)
 456        ("inchi" ,inchi)
 457        ("libxml2" ,libxml2)
 458        ("zlib" ,zlib)))
 459     (home-page "http://openbabel.org/wiki/Main_Page")
 460     (synopsis "Chemistry data manipulation toolbox")
 461     (description
 462      "Open Babel is a chemical toolbox designed to speak the many languages of
 463 chemical data.  It's a collaborative project allowing anyone to search, convert,
 464 analyze, or store data from molecular modeling, chemistry, solid-state
 465 materials, biochemistry, or related areas.")
 466     (license license:gpl2)))