gnu/packages/chemistry.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
   3 ;;; Copyright © 2018, 2021 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 ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
   9 ;;;
  10 ;;; This file is part of GNU Guix.
  11 ;;;
  12 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  13 ;;; under the terms of the GNU General Public License as published by
  14 ;;; the Free Software Foundation; either version 3 of the License, or (at
  15 ;;; your option) any later version.
  16 ;;;
  17 ;;; GNU Guix is distributed in the hope that it will be useful, but
  18 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  19 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  20 ;;; GNU General Public License for more details.
  21 ;;;
  22 ;;; You should have received a copy of the GNU General Public License
  23 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  24
  25 (define-module (gnu packages chemistry)
  26   #:use-module (guix packages)
  27   #:use-module (guix utils)
  28   #:use-module ((guix licenses) #:prefix license:)
  29   #:use-module (guix download)
  30   #:use-module (guix git-download)
  31   #:use-module (gnu packages)
  32   #:use-module (gnu packages algebra)
  33   #:use-module (gnu packages autotools)
  34   #:use-module (gnu packages backup)
  35   #:use-module (gnu packages boost)
  36   #:use-module (gnu packages check)
  37   #:use-module (gnu packages compression)
  38   #:use-module (gnu packages documentation)
  39   #:use-module (gnu packages fontutils)
  40   #:use-module (gnu packages gl)
  41   #:use-module (gnu packages graphviz)
  42   #:use-module (gnu packages gv)
  43   #:use-module (gnu packages image)
  44   #:use-module (gnu packages maths)
  45   #:use-module (gnu packages mpi)
  46   #:use-module (gnu packages perl)
  47   #:use-module (gnu packages pkg-config)
  48   #:use-module (gnu packages python)
  49   #:use-module (gnu packages python-xyz)
  50   #:use-module (gnu packages qt)
  51   #:use-module (gnu packages serialization)
  52   #:use-module (gnu packages sphinx)
  53   #:use-module (gnu packages xml)
  54   #:use-module (guix build-system cmake)
  55   #:use-module (guix build-system gnu)
  56   #:use-module (guix build-system python))
  57
  58 (define-public avogadrolibs
  59   (package
  60     (name "avogadrolibs")
  61     (version "1.93.0")
  62     (source
  63      (origin
  64        (method git-fetch)
  65        (uri (git-reference
  66              (url "https://github.com/OpenChemistry/avogadrolibs")
  67              (commit version)))
  68        (sha256
  69         (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39"))
  70        (file-name (git-file-name name version))))
  71     (build-system cmake-build-system)
  72     (native-inputs
  73      (list eigen
  74            mmtf-cpp
  75            msgpack
  76            googletest
  77            pkg-config
  78            pybind11))
  79     (inputs
  80      (list glew
  81            libarchive
  82            libmsym
  83            molequeue
  84            python
  85            spglib
  86            qtbase-5))
  87     (arguments
  88      '(#:configure-flags (list "-DENABLE_TESTING=ON"
  89                                (string-append "-DSPGLIB_INCLUDE_DIR="
  90                                               (assoc-ref %build-inputs "spglib")
  91                                               "/include"))))
  92     (home-page "https://www.openchemistry.org/projects/avogadro2/")
  93     (synopsis "Libraries for chemistry, bioinformatics, and related areas")
  94     (description
  95      "Avogadro libraries provide 3D rendering, visualization, analysis and data
  96 processing useful in computational chemistry, molecular modeling,
  97 bioinformatics, materials science, and related areas.")
  98     (license license:bsd-3)))
  99
 100 (define-public avogadro2
 101   (package
 102     (name "avogadro2")
 103     (version "1.93.0")
 104     (source
 105      (origin
 106        (method git-fetch)
 107        (uri (git-reference
 108              (url "https://github.com/OpenChemistry/avogadroapp")
 109              (commit version)))
 110        (sha256
 111         (base32
 112          "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
 113        (file-name (git-file-name name version))))
 114     (build-system cmake-build-system)
 115     (native-inputs
 116      (list eigen pkg-config))
 117     (inputs
 118      (list avogadrolibs hdf5 molequeue qtbase-5))
 119     ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
 120     (arguments
 121      '(#:tests? #f))
 122     (home-page "https://www.openchemistry.org/projects/avogadro2/")
 123     (synopsis "Advanced molecule editor")
 124     (description
 125      "Avogadro 2 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:bsd-3)))
 130
 131 (define-public inchi
 132   (package
 133     (name "inchi")
 134     ;; Update the inchi-doc native input when updating inchi.
 135     (version "1.06")
 136     (source (origin
 137               (method url-fetch)
 138               (uri (string-append "https://www.inchi-trust.org/download/"
 139                                   (string-join (string-split version #\.) "")
 140                                   "/INCHI-1-SRC.zip"))
 141               (sha256
 142                (base32
 143                 "1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28"))
 144               (file-name (string-append name "-" version ".zip"))))
 145     (build-system gnu-build-system)
 146     (arguments
 147      '(#:tests? #f ; no check target
 148        #:phases
 149        (modify-phases %standard-phases
 150          (delete 'configure) ; no configure script
 151          (add-before 'build 'chdir-to-build-directory
 152            (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
 153          (add-after 'build 'build-library
 154            (lambda _
 155              (chdir "../../../INCHI_API/libinchi/gcc")
 156              (invoke "make")))
 157          (replace 'install
 158            (lambda* (#:key inputs outputs #:allow-other-keys)
 159              (let* ((out (assoc-ref outputs "out"))
 160                     (bin (string-append out "/bin"))
 161                     (doc (string-append out "/share/doc/inchi"))
 162                     (include-dir (string-append out "/include/inchi"))
 163                     (lib (string-append out "/lib/inchi"))
 164                     (inchi-doc (assoc-ref inputs "inchi-doc"))
 165                     (unzip (search-input-file inputs "/bin/unzip")))
 166                (chdir "../../..")
 167                ;; Install binary.
 168                (with-directory-excursion "INCHI_EXE/bin/Linux"
 169                  (rename-file "inchi-1" "inchi")
 170                  (install-file "inchi" bin))
 171                ;; Install libraries.
 172                (with-directory-excursion "INCHI_API/bin/Linux"
 173                  (for-each (lambda (file)
 174                              (install-file file lib))
 175                            (find-files "." "libinchi\\.so\\.1\\.*")))
 176                ;; Install header files.
 177                (with-directory-excursion "INCHI_BASE/src"
 178                  (for-each (lambda (file)
 179                              (install-file file include-dir))
 180                            (find-files "." "\\.h$")))
 181                ;; Install documentation.
 182                (mkdir-p doc)
 183                (invoke unzip "-j" "-d" doc inchi-doc)
 184                #t))))))
 185     (native-inputs
 186      `(("unzip" ,unzip)
 187        ("inchi-doc"
 188         ,(origin
 189            (method url-fetch)
 190            (uri (string-append "http://www.inchi-trust.org/download/"
 191                                   (string-join (string-split version #\.) "")
 192                                   "/INCHI-1-DOC.zip"))
 193            (sha256
 194             (base32
 195              "1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f"))
 196            (file-name (string-append name "-" version ".zip"))))))
 197     (home-page "https://www.inchi-trust.org")
 198     (synopsis "Utility for manipulating machine-readable chemical structures")
 199     (description
 200      "The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
 201 chemical structures into machine-readable strings of information.  InChIs are
 202 unique to the compound they describe and can encode absolute stereochemistry
 203 making chemicals and chemistry machine-readable and discoverable.  A simple
 204 analogy is that InChI is the bar-code for chemistry and chemical structures.")
 205     (license (license:non-copyleft
 206               "file://LICENCE"
 207               "See LICENCE in the distribution."))))
 208
 209 (define-public libmsym
 210   (package
 211     (name "libmsym")
 212     (version "0.2.3")
 213     (source
 214      (origin
 215        (method git-fetch)
 216        (uri (git-reference
 217              (url "https://github.com/mcodev31/libmsym")
 218              (commit (string-append "v" version))))
 219        (sha256
 220         (base32
 221          "0a9j28irdsr461qpzlc9z1yjyb9kp64fh5zw7ylspc9zn3189qwk"))
 222        (file-name (git-file-name name version))))
 223     (build-system cmake-build-system)
 224     (arguments
 225      '(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")
 226        #:tests? #f))                    ; no check target
 227     (home-page "https://github.com/mcodev31/libmsym")
 228     (synopsis "C library dealing with point group symmetry in molecules")
 229     (description "libmsym is a C library dealing with point group symmetry in
 230 molecules.")
 231     (license license:expat)))
 232
 233 (define-public mmtf-cpp
 234   (package
 235     (name "mmtf-cpp")
 236     (version "1.0.0")
 237     (source
 238      (origin
 239        (method git-fetch)
 240        (uri (git-reference
 241              (url "https://github.com/rcsb/mmtf-cpp")
 242              (commit (string-append "v" version))))
 243        (file-name (git-file-name name version))
 244        (sha256
 245         (base32
 246          "17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l"))))
 247     (build-system cmake-build-system)
 248     ;; Tests require the soon-to-be-deprecated version 1 of the catch-framework.
 249     (arguments
 250      '(#:tests? #f))
 251     (home-page "https://mmtf.rcsb.org/")
 252     (synopsis "C++ API for the Macromolecular Transmission Format")
 253     (description "This package is a library for the
 254 @acronym{MMTF,macromolecular transmission format}, a binary encoding of
 255 biological structures.")
 256     (license license:expat)))
 257
 258 (define-public molequeue
 259   (package
 260     (name "molequeue")
 261     (version "0.9.0")
 262     (source
 263      (origin
 264        (method url-fetch)
 265        (uri (string-append "https://github.com/OpenChemistry/molequeue/"
 266                            "releases/download/" version "/molequeue-"
 267                            version ".tar.bz2"))
 268        (sha256
 269         (base32
 270          "1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998"))))
 271     (build-system cmake-build-system)
 272     (inputs
 273      (list qtbase-5))
 274     (arguments
 275      '(#:configure-flags '("-DENABLE_TESTING=ON")
 276        #:phases
 277        (modify-phases %standard-phases
 278          (add-after 'unpack 'patch-tests
 279            (lambda _
 280              ;; TODO: Fix/enable the failing message and clientserver tests.
 281              ;; In the message test, the floating-point value "5.36893473232" on
 282              ;; line 165 of molequeue/app/testing/messagetest.cpp should
 283              ;; (apparently) be truncated, but it is not.
 284              (substitute* "molequeue/app/testing/messagetest.cpp"
 285                (("5\\.36893473232") "5.36893"))
 286              ;; It is unclear why the clientserver test fails, so it is
 287              ;; completely disabled.
 288              (substitute* "molequeue/app/testing/CMakeLists.txt"
 289                ((".*clientserver.*") ""))
 290              #t))
 291          (add-before 'check 'set-display
 292            (lambda _
 293              ;; Make Qt render "offscreen" for the sake of tests.
 294              (setenv "QT_QPA_PLATFORM" "offscreen")
 295              #t)))))
 296     (home-page "https://www.openchemistry.org/projects/molequeue/")
 297     (synopsis "Application for coordinating computational jobs")
 298     (description "MoleQueue is a system-tray resident desktop application for
 299 abstracting, managing, and coordinating the execution of tasks both locally and
 300  on remote computational resources.  Users can set up local and remote queues
 301 that describe where the task will be executed.  Each queue can have programs,
 302 with templates to facilitate the execution of the program.  Input files can be
 303 staged, and output files collected using a standard interface.")
 304     (license license:bsd-3)))
 305
 306 (define-public tng
 307   (package
 308     (name "tng")
 309     (version "1.8.2")
 310     (source (origin
 311               (method git-fetch)
 312               (uri (git-reference
 313                     (url "https://github.com/gromacs/tng")
 314                     (commit (string-append "v" version))))
 315               (file-name (git-file-name name version))
 316               (sha256
 317                (base32
 318                 "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
 319     (build-system cmake-build-system)
 320     (inputs
 321      (list zlib))
 322     (arguments
 323      `(#:phases
 324        (modify-phases %standard-phases
 325          (add-after 'unpack 'remove-bundled-zlib
 326            (lambda _
 327              (delete-file-recursively "external")
 328              #t))
 329          (replace 'check
 330            (lambda _
 331              (invoke "../build/bin/tests/tng_testing")
 332              #t)))))
 333     (home-page "https://github.com/gromacs/tng")
 334     (synopsis "Trajectory Next Generation binary format manipulation library")
 335     (description "TRAJNG (Trajectory next generation) is a program library for
 336 handling molecular dynamics (MD) trajectories.  It can store coordinates, and
 337 optionally velocities and the H-matrix.  Coordinates and velocities are
 338 stored with user-specified precision.")
 339     (license license:bsd-3)))
 340
 341 (define-public gromacs
 342   (package
 343     (name "gromacs")
 344     (version "2020.2")
 345     (source (origin
 346               (method url-fetch)
 347               (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
 348                                   version ".tar.gz"))
 349               (sha256
 350                (base32
 351                 "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
 352               ;; Our version of tinyxml2 is far newer than the bundled one and
 353               ;; require fixing `testutils' code. See patch header for more info
 354               (patches (search-patches "gromacs-tinyxml2.patch"))))
 355     (build-system cmake-build-system)
 356     (arguments
 357      `(#:configure-flags
 358        (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
 359              ;; Unbundling
 360              "-DGMX_USE_LMFIT=EXTERNAL"
 361              "-DGMX_BUILD_OWN_FFTW=off"
 362              "-DGMX_EXTERNAL_BLAS=on"
 363              "-DGMX_EXTERNAL_LAPACK=on"
 364              "-DGMX_EXTERNAL_TNG=on"
 365              "-DGMX_EXTERNAL_ZLIB=on"
 366              "-DGMX_EXTERNAL_TINYXML2=on"
 367              (string-append "-DTinyXML2_DIR="
 368                             (assoc-ref %build-inputs "tinyxml2"))
 369              ;; Workaround for cmake/FindSphinx.cmake version parsing that does
 370              ;; not understand the guix-wrapped `sphinx-build --version' answer
 371              (string-append "-DSPHINX_EXECUTABLE_VERSION="
 372                             ,(package-version python-sphinx)))
 373        #:phases
 374        (modify-phases %standard-phases
 375          (add-after 'unpack 'fixes
 376            (lambda* (#:key inputs #:allow-other-keys)
 377              ;; Still bundled: part of gromacs, source behind registration
 378              ;; but free software anyways
 379              ;;(delete-file-recursively "src/external/vmd_molfile")
 380              ;; Still bundled: threads-based OpenMPI-compatible fallback
 381              ;; designed to be bundled like that
 382              ;;(delete-file-recursively "src/external/thread_mpi")
 383              ;; Unbundling
 384              (delete-file-recursively "src/external/lmfit")
 385              (delete-file-recursively "src/external/clFFT")
 386              (delete-file-recursively "src/external/fftpack")
 387              (delete-file-recursively "src/external/build-fftw")
 388              (delete-file-recursively "src/external/tng_io")
 389              (delete-file-recursively "src/external/tinyxml2")
 390              (delete-file-recursively "src/external/googletest")
 391              (copy-recursively (assoc-ref inputs "googletest-source")
 392                                "src/external/googletest")
 393              ;; This test warns about the build host hardware, disable
 394              (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
 395                (("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
 396                 "void __guix_disabled()"))
 397              #t)))))
 398     (native-inputs
 399      `(("doxygen" ,doxygen)
 400        ("googletest-source" ,(package-source googletest))
 401        ("graphviz" ,graphviz)
 402        ("pkg-config" ,pkg-config)
 403        ("python" ,python)
 404        ("python-pygments" ,python-pygments)
 405        ("python-sphinx" ,python-sphinx)))
 406     (inputs
 407      (list fftwf
 408            `(,hwloc-2 "lib")
 409            lmfit
 410            openblas
 411            perl
 412            tinyxml2
 413            tng))
 414     (home-page "http://www.gromacs.org/")
 415     (synopsis "Molecular dynamics software package")
 416     (description "GROMACS is a versatile package to perform molecular dynamics,
 417 i.e. simulate the Newtonian equations of motion for systems with hundreds to
 418 millions of particles.  It is primarily designed for biochemical molecules like
 419 proteins, lipids and nucleic acids that have a lot of complicated bonded
 420 interactions, but since GROMACS is extremely fast at calculating the nonbonded
 421 interactions (that usually dominate simulations) many groups are also using it
 422 for research on non-biological systems, e.g. polymers.  GROMACS supports all the
 423 usual algorithms you expect from a modern molecular dynamics implementation.")
 424     (license license:lgpl2.1+)))
 425
 426 (define-public openbabel
 427   (package
 428     (name "openbabel")
 429     (version "3.1.1")
 430     (source (origin
 431               (method url-fetch)
 432               (uri (string-append "https://github.com/openbabel/openbabel/"
 433                                   "releases/download/openbabel-"
 434                                   (string-replace-substring version "." "-")
 435                                   "/openbabel-" version "-source.tar.bz2"))
 436               (sha256
 437                (base32
 438                 "0s0f4zib8vshfaywsr5bjjz55jwsg6yiz2qw4i5jm8wysn0q7v56"))))
 439     (build-system cmake-build-system)
 440     (arguments
 441      `(;; FIXME: Disable tests on i686 to work around
 442        ;; https://github.com/openbabel/openbabel/issues/2041.
 443        #:tests? ,(or (%current-target-system)
 444                      (not (string=? "i686-linux" (%current-system))))
 445        #:configure-flags
 446        (list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
 447              (string-append "-DINCHI_LIBRARY="
 448                             (assoc-ref %build-inputs "inchi")
 449                             "/lib/inchi/libinchi.so.1")
 450              (string-append "-DINCHI_INCLUDE_DIR="
 451                             (assoc-ref %build-inputs "inchi") "/include/inchi"))
 452        #:test-target "test"))
 453     (native-inputs
 454      (list pkg-config))
 455     (inputs
 456      (list eigen inchi libxml2 zlib))
 457     (home-page "http://openbabel.org/wiki/Main_Page")
 458     (synopsis "Chemistry data manipulation toolbox")
 459     (description
 460      "Open Babel is a chemical toolbox designed to speak the many languages of
 461 chemical data.  It's a collaborative project allowing anyone to search, convert,
 462 analyze, or store data from molecular modeling, chemistry, solid-state
 463 materials, biochemistry, or related areas.")
 464     (license license:gpl2)))
 465
 466 (define-public spglib
 467   (package
 468     (name "spglib")
 469     (version "1.16.0")
 470     (source
 471      (origin
 472        (method git-fetch)
 473        (uri (git-reference
 474              (url "https://github.com/spglib/spglib")
 475              (commit (string-append "v" version))))
 476        (sha256
 477         (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
 478        (file-name (git-file-name name version))))
 479     (build-system cmake-build-system)
 480     (arguments
 481      '(#:test-target "check"
 482        #:phases
 483        (modify-phases %standard-phases
 484          (add-after 'unpack 'patch-header-install-dir
 485            (lambda _
 486              ;; As of the writing of this package, CMake and GNU build systems
 487              ;; install the header to two different location.  This patch makes
 488              ;; the CMake build system's choice of header directory compatible
 489              ;; with the GNU build system's choice and with what avogadrolibs
 490              ;; expects.
 491              ;; See https://github.com/spglib/spglib/issues/75 and the relevant
 492              ;; part of https://github.com/OpenChemistry/avogadroapp/issues/97.
 493              (substitute* "CMakeLists.txt"
 494                (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir)
 495                 (string-append include-dir "/spglib")))
 496              #t)))))
 497     (home-page "https://spglib.github.io/spglib/index.html")
 498     (synopsis "Library for crystal symmetry search")
 499     (description "Spglib is a library for finding and handling crystal
 500 symmetries written in C.  Spglib can be used to:
 501
 502 @enumerate
 503 @item Find symmetry operations
 504 @item Identify space-group type
 505 @item Wyckoff position assignment
 506 @item Refine crystal structure
 507 @item Find a primitive cell
 508 @item Search irreducible k-points
 509 @end enumerate")
 510     (license license:bsd-3)))
 511
 512 (define-public python-pymol
 513   (package
 514     (name "python-pymol")
 515     (version "2.5.0")
 516     (source
 517      (origin
 518        (method git-fetch)
 519        (uri (git-reference
 520              (url "https://github.com/schrodinger/pymol-open-source")
 521              (commit (string-append "v" version))))
 522        (file-name (git-file-name name version))
 523        (sha256
 524         (base32 "08zmfgclkbjkqjpq8xs1mphs1i8rpqj76mcw7m2mrhvma5qj1nr5"))))
 525     (build-system python-build-system)
 526     (arguments
 527      '(#:configure-flags
 528        (list "--glut" "--testing")
 529        #:phases
 530        (modify-phases %standard-phases
 531          (add-after 'unpack 'make-reproducible
 532            (lambda _
 533              (substitute* "create_shadertext.py"
 534                (("time\\.time\\(\\)") "0"))))
 535          (add-after 'unpack 'add-include-directories
 536            (lambda* (#:key inputs #:allow-other-keys)
 537              (setenv "CPLUS_INCLUDE_PATH"
 538                      (string-append (assoc-ref inputs "freetype")
 539                                     "/include/freetype2:"
 540                                     (assoc-ref inputs "libxml2")
 541                                     "/include/libxml2:"
 542                                     (getenv "CPLUS_INCLUDE_PATH")))))
 543          ;; The setup.py script does not support one of the Python build
 544          ;; system's default flags, "--single-version-externally-managed".
 545          (replace 'install
 546            (lambda* (#:key outputs #:allow-other-keys)
 547              (invoke "python" "setup.py" "install"
 548                      (string-append "--prefix=" (assoc-ref outputs "out"))
 549                      "--root=/"))))))
 550     (inputs
 551      (list freetype
 552            libpng
 553            freeglut
 554            glew
 555            libxml2
 556            mmtf-cpp
 557            msgpack
 558            python-pyqt
 559            glm
 560            netcdf))
 561     (native-inputs
 562      (list catch2 python-setuptools))
 563     (home-page "https://pymol.org")
 564     (synopsis "Molecular visualization system")
 565     (description "PyMOL is a capable molecular viewer and renderer.  It can be
 566 used to prepare publication-quality figures, to share interactive results with
 567 your colleagues, or to generate pre-rendered animations.")
 568     (license license:bsd-3)))