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 ;;;
   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 autotools)
  33   #:use-module (gnu packages backup)
  34   #:use-module (gnu packages boost)
  35   #:use-module (gnu packages check)
  36   #:use-module (gnu packages compression)
  37   #:use-module (gnu packages documentation)
  38   #:use-module (gnu packages gl)
  39   #:use-module (gnu packages graphviz)
  40   #:use-module (gnu packages gv)
  41   #:use-module (gnu packages maths)
  42   #:use-module (gnu packages mpi)
  43   #:use-module (gnu packages perl)
  44   #:use-module (gnu packages pkg-config)
  45   #:use-module (gnu packages python)
  46   #:use-module (gnu packages python-xyz)
  47   #:use-module (gnu packages qt)
  48   #:use-module (gnu packages serialization)
  49   #:use-module (gnu packages sphinx)
  50   #:use-module (gnu packages xml)
  51   #:use-module (guix build-system cmake)
  52   #:use-module (guix build-system gnu)
  53   #:use-module (guix build-system python))
  54
  55 (define-public avogadrolibs
  56   (package
  57     (name "avogadrolibs")
  58     (version "1.93.0")
  59     (source
  60      (origin
  61        (method git-fetch)
  62        (uri (git-reference
  63              (url "https://github.com/OpenChemistry/avogadrolibs")
  64              (commit version)))
  65        (sha256
  66         (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39"))
  67        (file-name (git-file-name name version))))
  68     (build-system cmake-build-system)
  69     (native-inputs
  70      `(("eigen" ,eigen)
  71        ("mmtf-cpp" ,mmtf-cpp)
  72        ("msgpack" ,msgpack)
  73        ("googletest" ,googletest)
  74        ("pkg-config" ,pkg-config)
  75        ("pybind11" ,pybind11)))
  76     (inputs
  77      `(("glew" ,glew)
  78        ("libarchive" ,libarchive)
  79        ("libmsym" ,libmsym)
  80        ("molequeue" ,molequeue)
  81        ("python" ,python)
  82        ("spglib" ,spglib)
  83        ("qtbase" ,qtbase)))
  84     (arguments
  85      '(#:configure-flags (list "-DENABLE_TESTING=ON"
  86                                (string-append "-DSPGLIB_INCLUDE_DIR="
  87                                               (assoc-ref %build-inputs "spglib")
  88                                               "/include"))))
  89     (home-page "https://www.openchemistry.org/projects/avogadro2/")
  90     (synopsis "Libraries for chemistry, bioinformatics, and related areas")
  91     (description
  92      "Avogadro libraries provide 3D rendering, visualization, analysis and data
  93 processing useful in computational chemistry, molecular modeling,
  94 bioinformatics, materials science, and related areas.")
  95     (license license:bsd-3)))
  96
  97 (define-public avogadro2
  98   (package
  99     (name "avogadro2")
 100     (version "1.93.0")
 101     (source
 102      (origin
 103        (method git-fetch)
 104        (uri (git-reference
 105              (url "https://github.com/OpenChemistry/avogadroapp")
 106              (commit version)))
 107        (sha256
 108         (base32
 109          "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
 110        (file-name (git-file-name name version))))
 111     (build-system cmake-build-system)
 112     (native-inputs
 113      `(("eigen" ,eigen)
 114        ("pkg-config" ,pkg-config)))
 115     (inputs
 116      `(("avogadrolibs" ,avogadrolibs)
 117        ("hdf5" ,hdf5)
 118        ("molequeue" ,molequeue)
 119        ("qtbase" ,qtbase)))
 120     ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
 121     (arguments
 122      '(#:tests? #f))
 123     (home-page "https://www.openchemistry.org/projects/avogadro2/")
 124     (synopsis "Advanced molecule editor")
 125     (description
 126      "Avogadro 2 is an advanced molecule editor and visualizer designed for use
 127 in computational chemistry, molecular modeling, bioinformatics, materials
 128 science, and related areas.  It offers flexible high quality rendering and a
 129 powerful plugin architecture.")
 130     (license license:bsd-3)))
 131
 132 (define-public domainfinder
 133   (package
 134     (name "domainfinder")
 135     (version "2.0.5")
 136     (source
 137      (origin
 138        (method url-fetch)
 139        (uri (string-append "https://bitbucket.org/khinsen/"
 140                            "domainfinder/downloads/DomainFinder-"
 141                            version ".tar.gz"))
 142        (sha256
 143         (base32
 144          "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
 145     (build-system python-build-system)
 146     (inputs
 147      `(("python-mmtk" ,python2-mmtk)))
 148     (arguments
 149      `(#:python ,python-2
 150        ;; No test suite
 151        #:tests? #f))
 152     (home-page "http://dirac.cnrs-orleans.fr/DomainFinder.html")
 153     (synopsis "Analysis of dynamical domains in proteins")
 154     (description "DomainFinder is an interactive program for the determination
 155 and characterization of dynamical domains in proteins.  It can infer dynamical
 156 domains by comparing two protein structures, or from normal mode analysis on a
 157 single structure.  The software is currently not actively maintained and works
 158 only with Python 2 and NumPy < 1.9.")
 159     (license license:cecill-c)))
 160
 161 (define-public inchi
 162   (package
 163     (name "inchi")
 164     ;; Update the inchi-doc native input when updating inchi.
 165     (version "1.06")
 166     (source (origin
 167               (method url-fetch)
 168               (uri (string-append "https://www.inchi-trust.org/download/"
 169                                   (string-join (string-split version #\.) "")
 170                                   "/INCHI-1-SRC.zip"))
 171               (sha256
 172                (base32
 173                 "1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28"))
 174               (file-name (string-append name "-" version ".zip"))))
 175     (build-system gnu-build-system)
 176     (arguments
 177      '(#:tests? #f ; no check target
 178        #:phases
 179        (modify-phases %standard-phases
 180          (delete 'configure) ; no configure script
 181          (add-before 'build 'chdir-to-build-directory
 182            (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
 183          (add-after 'build 'build-library
 184            (lambda _
 185              (chdir "../../../INCHI_API/libinchi/gcc")
 186              (invoke "make")))
 187          (replace 'install
 188            (lambda* (#:key inputs outputs #:allow-other-keys)
 189              (let* ((out (assoc-ref outputs "out"))
 190                     (bin (string-append out "/bin"))
 191                     (doc (string-append out "/share/doc/inchi"))
 192                     (include-dir (string-append out "/include/inchi"))
 193                     (lib (string-append out "/lib/inchi"))
 194                     (inchi-doc (assoc-ref inputs "inchi-doc"))
 195                     (unzip (string-append (assoc-ref inputs "unzip")
 196                                           "/bin/unzip")))
 197                (chdir "../../..")
 198                ;; Install binary.
 199                (with-directory-excursion "INCHI_EXE/bin/Linux"
 200                  (rename-file "inchi-1" "inchi")
 201                  (install-file "inchi" bin))
 202                ;; Install libraries.
 203                (with-directory-excursion "INCHI_API/bin/Linux"
 204                  (for-each (lambda (file)
 205                              (install-file file lib))
 206                            (find-files "." "libinchi\\.so\\.1\\.*")))
 207                ;; Install header files.
 208                (with-directory-excursion "INCHI_BASE/src"
 209                  (for-each (lambda (file)
 210                              (install-file file include-dir))
 211                            (find-files "." "\\.h$")))
 212                ;; Install documentation.
 213                (mkdir-p doc)
 214                (invoke unzip "-j" "-d" doc inchi-doc)
 215                #t))))))
 216     (native-inputs
 217      `(("unzip" ,unzip)
 218        ("inchi-doc"
 219         ,(origin
 220            (method url-fetch)
 221            (uri (string-append "http://www.inchi-trust.org/download/"
 222                                   (string-join (string-split version #\.) "")
 223                                   "/INCHI-1-DOC.zip"))
 224            (sha256
 225             (base32
 226              "1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f"))
 227            (file-name (string-append name "-" version ".zip"))))))
 228     (home-page "https://www.inchi-trust.org")
 229     (synopsis "Utility for manipulating machine-readable chemical structures")
 230     (description
 231      "The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
 232 chemical structures into machine-readable strings of information.  InChIs are
 233 unique to the compound they describe and can encode absolute stereochemistry
 234 making chemicals and chemistry machine-readable and discoverable.  A simple
 235 analogy is that InChI is the bar-code for chemistry and chemical structures.")
 236     (license (license:non-copyleft
 237               "file://LICENCE"
 238               "See LICENCE in the distribution."))))
 239
 240 (define-public libmsym
 241   (package
 242     (name "libmsym")
 243     (version "0.2.3")
 244     (source
 245      (origin
 246        (method git-fetch)
 247        (uri (git-reference
 248              (url "https://github.com/mcodev31/libmsym")
 249              (commit (string-append "v" version))))
 250        (sha256
 251         (base32
 252          "0a9j28irdsr461qpzlc9z1yjyb9kp64fh5zw7ylspc9zn3189qwk"))
 253        (file-name (git-file-name name version))))
 254     (build-system cmake-build-system)
 255     (arguments
 256      '(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")
 257        #:tests? #f))                    ; no check target
 258     (home-page "https://github.com/mcodev31/libmsym")
 259     (synopsis "C library dealing with point group symmetry in molecules")
 260     (description "libmsym is a C library dealing with point group symmetry in
 261 molecules.")
 262     (license license:expat)))
 263
 264 (define-public mmtf-cpp
 265   (package
 266     (name "mmtf-cpp")
 267     (version "1.0.0")
 268     (source
 269      (origin
 270        (method git-fetch)
 271        (uri (git-reference
 272              (url "https://github.com/rcsb/mmtf-cpp")
 273              (commit (string-append "v" version))))
 274        (file-name (git-file-name name version))
 275        (sha256
 276         (base32
 277          "17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l"))))
 278     (build-system cmake-build-system)
 279     ;; Tests require the soon-to-be-deprecated version 1 of the catch-framework.
 280     (arguments
 281      '(#:tests? #f))
 282     (home-page "https://mmtf.rcsb.org/")
 283     (synopsis "C++ API for the Macromolecular Transmission Format")
 284     (description "This package is a library for the
 285 @acronym{MMTF,macromolecular transmission format}, a binary encoding of
 286 biological structures.")
 287     (license license:expat)))
 288
 289 (define-public molequeue
 290   (package
 291     (name "molequeue")
 292     (version "0.9.0")
 293     (source
 294      (origin
 295        (method url-fetch)
 296        (uri (string-append "https://github.com/OpenChemistry/molequeue/"
 297                            "releases/download/" version "/molequeue-"
 298                            version ".tar.bz2"))
 299        (sha256
 300         (base32
 301          "1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998"))))
 302     (build-system cmake-build-system)
 303     (inputs
 304      `(("qtbase" ,qtbase)))
 305     (arguments
 306      '(#:configure-flags '("-DENABLE_TESTING=ON")
 307        #:phases
 308        (modify-phases %standard-phases
 309          (add-after 'unpack 'patch-tests
 310            (lambda _
 311              ;; TODO: Fix/enable the failing message and clientserver tests.
 312              ;; In the message test, the floating-point value "5.36893473232" on
 313              ;; line 165 of molequeue/app/testing/messagetest.cpp should
 314              ;; (apparently) be truncated, but it is not.
 315              (substitute* "molequeue/app/testing/messagetest.cpp"
 316                (("5\\.36893473232") "5.36893"))
 317              ;; It is unclear why the clientserver test fails, so it is
 318              ;; completely disabled.
 319              (substitute* "molequeue/app/testing/CMakeLists.txt"
 320                ((".*clientserver.*") ""))
 321              #t))
 322          (add-before 'check 'set-display
 323            (lambda _
 324              ;; Make Qt render "offscreen" for the sake of tests.
 325              (setenv "QT_QPA_PLATFORM" "offscreen")
 326              #t)))))
 327     (home-page "https://www.openchemistry.org/projects/molequeue/")
 328     (synopsis "Application for coordinating computational jobs")
 329     (description "MoleQueue is a system-tray resident desktop application for
 330 abstracting, managing, and coordinating the execution of tasks both locally and
 331  on remote computational resources.  Users can set up local and remote queues
 332 that describe where the task will be executed.  Each queue can have programs,
 333 with templates to facilitate the execution of the program.  Input files can be
 334 staged, and output files collected using a standard interface.")
 335     (license license:bsd-3)))
 336
 337 (define with-numpy-1.8
 338   (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
 339
 340 (define-public nmoldyn
 341   (package
 342     (name "nmoldyn")
 343     (version "3.0.11")
 344     (source
 345      (origin
 346        (method git-fetch)
 347        (uri (git-reference
 348              (url "https://github.com/khinsen/nMOLDYN3")
 349              (commit (string-append "v" version))))
 350        (file-name (git-file-name name version))
 351        (sha256
 352         (base32
 353          "016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r"))))
 354     (build-system python-build-system)
 355     (inputs
 356      `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
 357        ("python-scientific" ,python2-scientific)
 358        ("netcdf" ,netcdf)
 359        ("gv" ,gv)))
 360     (propagated-inputs
 361      `(("python-mmtk" ,python2-mmtk)))
 362     (arguments
 363      `(#:python ,python-2
 364        #:tests? #f  ; No test suite
 365        #:phases
 366        (modify-phases %standard-phases
 367          (add-before 'build 'create-linux2-directory
 368            (lambda _
 369              (mkdir-p "nMOLDYN/linux2")))
 370          (add-before 'build 'change-PDF-viewer
 371            (lambda* (#:key inputs #:allow-other-keys)
 372              (substitute* "nMOLDYN/Preferences.py"
 373                ;; Set the paths for external executables, substituting
 374                ;; gv for acroread.
 375                ;; There is also vmd_path, but VMD is not free software
 376                ;; and Guix contains currently no free molecular viewer that
 377                ;; could be substituted.
 378                (("PREFERENCES\\['acroread_path'\\] = ''")
 379                 (format #f "PREFERENCES['acroread_path'] = '~a'"
 380                         (which "gv")))
 381                (("PREFERENCES\\['ncdump_path'\\] = ''")
 382                 (format #f "PREFERENCES['ncdump_path'] = '~a'"
 383                         (which "ncdump")))
 384                (("PREFERENCES\\['ncgen_path'\\] = ''")
 385                 (format #f "PREFERENCES['ncgen_path'] = '~a'"
 386                         (which "ncgen3")))
 387                (("PREFERENCES\\['task_manager_path'\\] = ''")
 388                 (format #f "PREFERENCES['task_manager_path'] = '~a'"
 389                         (which "task_manager")))
 390                ;; Show documentation as PDF
 391                (("PREFERENCES\\['documentation_style'\\] = 'html'")
 392                 "PREFERENCES['documentation_style'] = 'pdf'") ))))))
 393     (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN.html")
 394     (synopsis "Analysis software for Molecular Dynamics trajectories")
 395     (description "nMOLDYN is an interactive analysis program for Molecular Dynamics
 396 simulations.  It is especially designed for the computation and decomposition of
 397 neutron scattering spectra, but also computes other quantities.  The software
 398 is currently not actively maintained and works only with Python 2 and
 399 NumPy < 1.9.")
 400     (license license:cecill)))
 401
 402 (define-public tng
 403   (package
 404     (name "tng")
 405     (version "1.8.2")
 406     (source (origin
 407               (method git-fetch)
 408               (uri (git-reference
 409                     (url "https://github.com/gromacs/tng")
 410                     (commit (string-append "v" version))))
 411               (file-name (git-file-name name version))
 412               (sha256
 413                (base32
 414                 "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
 415     (build-system cmake-build-system)
 416     (inputs
 417      `(("zlib" ,zlib)))
 418     (arguments
 419      `(#:phases
 420        (modify-phases %standard-phases
 421          (add-after 'unpack 'remove-bundled-zlib
 422            (lambda _
 423              (delete-file-recursively "external")
 424              #t))
 425          (replace 'check
 426            (lambda _
 427              (invoke "../build/bin/tests/tng_testing")
 428              #t)))))
 429     (home-page "https://github.com/gromacs/tng")
 430     (synopsis "Trajectory Next Generation binary format manipulation library")
 431     (description "TRAJNG (Trajectory next generation) is a program library for
 432 handling molecular dynamics (MD) trajectories.  It can store coordinates, and
 433 optionally velocities and the H-matrix.  Coordinates and velocities are
 434 stored with user-specified precision.")
 435     (license license:bsd-3)))
 436
 437 (define-public gromacs
 438   (package
 439     (name "gromacs")
 440     (version "2020.2")
 441     (source (origin
 442               (method url-fetch)
 443               (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
 444                                   version ".tar.gz"))
 445               (sha256
 446                (base32
 447                 "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
 448               ;; Our version of tinyxml2 is far newer than the bundled one and
 449               ;; require fixing `testutils' code. See patch header for more info
 450               (patches (search-patches "gromacs-tinyxml2.patch"))))
 451     (build-system cmake-build-system)
 452     (arguments
 453      `(#:configure-flags
 454        (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
 455              ;; Unbundling
 456              "-DGMX_USE_LMFIT=EXTERNAL"
 457              "-DGMX_BUILD_OWN_FFTW=off"
 458              "-DGMX_EXTERNAL_BLAS=on"
 459              "-DGMX_EXTERNAL_LAPACK=on"
 460              "-DGMX_EXTERNAL_TNG=on"
 461              "-DGMX_EXTERNAL_ZLIB=on"
 462              "-DGMX_EXTERNAL_TINYXML2=on"
 463              (string-append "-DTinyXML2_DIR="
 464                             (assoc-ref %build-inputs "tinyxml2"))
 465              ;; Workaround for cmake/FindSphinx.cmake version parsing that does
 466              ;; not understand the guix-wrapped `sphinx-build --version' answer
 467              (string-append "-DSPHINX_EXECUTABLE_VERSION="
 468                             ,(package-version python-sphinx)))
 469        #:phases
 470        (modify-phases %standard-phases
 471          (add-after 'unpack 'fixes
 472            (lambda* (#:key inputs #:allow-other-keys)
 473              ;; Still bundled: part of gromacs, source behind registration
 474              ;; but free software anyways
 475              ;;(delete-file-recursively "src/external/vmd_molfile")
 476              ;; Still bundled: threads-based OpenMPI-compatible fallback
 477              ;; designed to be bundled like that
 478              ;;(delete-file-recursively "src/external/thread_mpi")
 479              ;; Unbundling
 480              (delete-file-recursively "src/external/lmfit")
 481              (delete-file-recursively "src/external/clFFT")
 482              (delete-file-recursively "src/external/fftpack")
 483              (delete-file-recursively "src/external/build-fftw")
 484              (delete-file-recursively "src/external/tng_io")
 485              (delete-file-recursively "src/external/tinyxml2")
 486              (delete-file-recursively "src/external/googletest")
 487              (copy-recursively (assoc-ref inputs "googletest-source")
 488                                "src/external/googletest")
 489              ;; This test warns about the build host hardware, disable
 490              (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
 491                (("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
 492                 "void __guix_disabled()"))
 493              #t)))))
 494     (native-inputs
 495      `(("doxygen" ,doxygen)
 496        ("googletest-source" ,(package-source googletest))
 497        ("graphviz" ,graphviz)
 498        ("pkg-config" ,pkg-config)
 499        ("python" ,python)
 500        ("python-pygments" ,python-pygments)
 501        ("python-sphinx" ,python-sphinx)))
 502     (inputs
 503      `(("fftwf" ,fftwf)
 504        ("hwloc" ,hwloc-2 "lib")
 505        ("lmfit" ,lmfit)
 506        ("openblas" ,openblas)
 507        ("perl" ,perl)
 508        ("tinyxml2" ,tinyxml2)
 509        ("tng" ,tng)))
 510     (home-page "http://www.gromacs.org/")
 511     (synopsis "Molecular dynamics software package")
 512     (description "GROMACS is a versatile package to perform molecular dynamics,
 513 i.e. simulate the Newtonian equations of motion for systems with hundreds to
 514 millions of particles.  It is primarily designed for biochemical molecules like
 515 proteins, lipids and nucleic acids that have a lot of complicated bonded
 516 interactions, but since GROMACS is extremely fast at calculating the nonbonded
 517 interactions (that usually dominate simulations) many groups are also using it
 518 for research on non-biological systems, e.g. polymers.  GROMACS supports all the
 519 usual algorithms you expect from a modern molecular dynamics implementation.")
 520     (license license:lgpl2.1+)))
 521
 522 (define-public openbabel
 523   (package
 524     (name "openbabel")
 525     (version "3.1.1")
 526     (source (origin
 527               (method url-fetch)
 528               (uri (string-append "https://github.com/openbabel/openbabel/"
 529                                   "releases/download/openbabel-"
 530                                   (string-replace-substring version "." "-")
 531                                   "/openbabel-" version "-source.tar.bz2"))
 532               (sha256
 533                (base32
 534                 "0s0f4zib8vshfaywsr5bjjz55jwsg6yiz2qw4i5jm8wysn0q7v56"))))
 535     (build-system cmake-build-system)
 536     (arguments
 537      `(;; FIXME: Disable tests on i686 to work around
 538        ;; https://github.com/openbabel/openbabel/issues/2041.
 539        #:tests? ,(or (%current-target-system)
 540                      (not (string=? "i686-linux" (%current-system))))
 541        #:configure-flags
 542        (list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
 543              (string-append "-DINCHI_LIBRARY="
 544                             (assoc-ref %build-inputs "inchi")
 545                             "/lib/inchi/libinchi.so.1")
 546              (string-append "-DINCHI_INCLUDE_DIR="
 547                             (assoc-ref %build-inputs "inchi") "/include/inchi"))
 548        #:test-target "test"))
 549     (native-inputs
 550      `(("pkg-config" ,pkg-config)))
 551     (inputs
 552      `(("eigen" ,eigen)
 553        ("inchi" ,inchi)
 554        ("libxml2" ,libxml2)
 555        ("zlib" ,zlib)))
 556     (home-page "http://openbabel.org/wiki/Main_Page")
 557     (synopsis "Chemistry data manipulation toolbox")
 558     (description
 559      "Open Babel is a chemical toolbox designed to speak the many languages of
 560 chemical data.  It's a collaborative project allowing anyone to search, convert,
 561 analyze, or store data from molecular modeling, chemistry, solid-state
 562 materials, biochemistry, or related areas.")
 563     (license license:gpl2)))
 564
 565 (define-public spglib
 566   (package
 567     (name "spglib")
 568     (version "1.16.0")
 569     (source
 570      (origin
 571        (method git-fetch)
 572        (uri (git-reference
 573              (url "https://github.com/spglib/spglib")
 574              (commit (string-append "v" version))))
 575        (sha256
 576         (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
 577        (file-name (git-file-name name version))))
 578     (build-system cmake-build-system)
 579     (arguments
 580      '(#:test-target "check"
 581        #:phases
 582        (modify-phases %standard-phases
 583          (add-after 'unpack 'patch-header-install-dir
 584            (lambda _
 585              ;; As of the writing of this package, CMake and GNU build systems
 586              ;; install the header to two different location.  This patch makes
 587              ;; the CMake build system's choice of header directory compatible
 588              ;; with the GNU build system's choice and with what avogadrolibs
 589              ;; expects.
 590              ;; See https://github.com/spglib/spglib/issues/75 and the relevant
 591              ;; part of https://github.com/OpenChemistry/avogadroapp/issues/97.
 592              (substitute* "CMakeLists.txt"
 593                (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir)
 594                 (string-append include-dir "/spglib")))
 595              #t)))))
 596     (home-page "https://spglib.github.io/spglib/index.html")
 597     (synopsis "Library for crystal symmetry search")
 598     (description "Spglib is a library for finding and handling crystal
 599 symmetries written in C.  Spglib can be used to:
 600
 601 @enumerate
 602 @item Find symmetry operations
 603 @item Identify space-group type
 604 @item Wyckoff position assignment
 605 @item Refine crystal structure
 606 @item Find a primitive cell
 607 @item Search irreducible k-points
 608 @end enumerate")
 609     (license license:bsd-3)))