| 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 compression) |
| 34 | #:use-module (gnu packages documentation) |
| 35 | #:use-module (gnu packages gl) |
| 36 | #:use-module (gnu packages gv) |
| 37 | #:use-module (gnu packages maths) |
| 38 | #:use-module (gnu packages pkg-config) |
| 39 | #:use-module (gnu packages python) |
| 40 | #:use-module (gnu packages python-xyz) |
| 41 | #:use-module (gnu packages qt) |
| 42 | #:use-module (gnu packages xml) |
| 43 | #:use-module (guix build-system cmake) |
| 44 | #:use-module (guix build-system gnu) |
| 45 | #:use-module (guix build-system python)) |
| 46 | |
| 47 | (define-public avogadro |
| 48 | (package |
| 49 | (name "avogadro") |
| 50 | (version "1.2.0") |
| 51 | (source |
| 52 | (origin |
| 53 | (method git-fetch) |
| 54 | (uri (git-reference |
| 55 | (url "https://github.com/cryos/avogadro.git") |
| 56 | (commit version))) |
| 57 | (sha256 |
| 58 | (base32 "0258py3lkba85qhs5ynancinyym61vlp0zaq9yrfs3hhnhpzv9n2")) |
| 59 | (file-name (git-file-name name version)) |
| 60 | (patches |
| 61 | (search-patches "avogadro-eigen3-update.patch" |
| 62 | "avogadro-python-eigen-lib.patch" |
| 63 | "avogadro-boost148.patch")))) |
| 64 | (build-system cmake-build-system) |
| 65 | (arguments |
| 66 | `(#:tests? #f |
| 67 | #:configure-flags |
| 68 | (list "-DENABLE_GLSL=ON" |
| 69 | (string-append "-DPYTHON_LIBRARIES=" |
| 70 | (assoc-ref %build-inputs "python") |
| 71 | "/lib") |
| 72 | (string-append "-DPYTHON_INCLUDE_DIRS=" |
| 73 | (assoc-ref %build-inputs "python") |
| 74 | "/include/python" |
| 75 | ,(version-major+minor |
| 76 | (package-version python)))) |
| 77 | #:phases |
| 78 | (modify-phases %standard-phases |
| 79 | (add-after 'unpack 'patch-python-lib-path |
| 80 | (lambda* (#:key outputs #:allow-other-keys) |
| 81 | ;; This is necessary to install the Python module in the correct |
| 82 | ;; directory. |
| 83 | (substitute* "libavogadro/src/python/CMakeLists.txt" |
| 84 | (("^EXECUTE_PROCESS.*$") "") |
| 85 | (("^.*from sys import stdout.*$") "") |
| 86 | (("^.*OUTPUT_VARIABLE.*") |
| 87 | (string-append "set(PYTHON_LIB_PATH \"" |
| 88 | (assoc-ref outputs "out") |
| 89 | "/lib/python" |
| 90 | ,(version-major+minor |
| 91 | (package-version python)) |
| 92 | "/site-packages\")"))) |
| 93 | #t)) |
| 94 | (add-after 'install 'wrap-program |
| 95 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 96 | ;; Make sure 'avogadro' runs with the correct PYTHONPATH. |
| 97 | (let* ((out (assoc-ref outputs "out"))) |
| 98 | (setenv "PYTHONPATH" |
| 99 | (string-append |
| 100 | (assoc-ref outputs "out") |
| 101 | "/lib/python" |
| 102 | ,(version-major+minor |
| 103 | (package-version python)) |
| 104 | "/site-packages:" |
| 105 | (getenv "PYTHONPATH"))) |
| 106 | (wrap-program (string-append out "/bin/avogadro") |
| 107 | `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH"))))) |
| 108 | #t))))) |
| 109 | (native-inputs |
| 110 | `(("doxygen" ,doxygen) |
| 111 | ("pkg-config" ,pkg-config))) |
| 112 | (inputs |
| 113 | `(("boost" ,boost) |
| 114 | ("eigen" ,eigen) |
| 115 | ("glew" ,glew) |
| 116 | ("openbabel" ,openbabel) |
| 117 | ("python" ,python-2) |
| 118 | ("python-numpy" ,python2-numpy) |
| 119 | ("python-pyqt" ,python2-pyqt-4) |
| 120 | ("python-sip" ,python2-sip) |
| 121 | ("qt" ,qt-4) |
| 122 | ("zlib" ,zlib))) |
| 123 | (home-page "https://avogadro.cc") |
| 124 | (synopsis "Advanced molecule editor") |
| 125 | (description |
| 126 | "Avogadro 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:gpl2+))) |
| 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 | (version "1.05") |
| 165 | (source (origin |
| 166 | (method url-fetch) |
| 167 | (uri (string-append "http://www.inchi-trust.org/download/" |
| 168 | (string-join (string-split version #\.) "") |
| 169 | "/INCHI-1-SRC.zip")) |
| 170 | (sha256 |
| 171 | (base32 |
| 172 | "081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa")) |
| 173 | (file-name (string-append name "-" version ".zip")))) |
| 174 | (build-system gnu-build-system) |
| 175 | (arguments |
| 176 | '(#:tests? #f ; no check target |
| 177 | #:phases |
| 178 | (modify-phases %standard-phases |
| 179 | (delete 'configure) ; no configure script |
| 180 | (add-before 'build 'chdir-to-build-directory |
| 181 | (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t)) |
| 182 | (add-after 'build 'build-library |
| 183 | (lambda _ |
| 184 | (chdir "../../../INCHI_API/libinchi/gcc") |
| 185 | (invoke "make"))) |
| 186 | (replace 'install |
| 187 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 188 | (let* ((out (assoc-ref outputs "out")) |
| 189 | (bin (string-append out "/bin")) |
| 190 | (doc (string-append out "/share/doc/inchi")) |
| 191 | (include-dir (string-append out "/include/inchi")) |
| 192 | (lib (string-append out "/lib/inchi")) |
| 193 | (inchi-doc (assoc-ref inputs "inchi-doc")) |
| 194 | (unzip (string-append (assoc-ref inputs "unzip") |
| 195 | "/bin/unzip"))) |
| 196 | (chdir "../../..") |
| 197 | ;; Install binary. |
| 198 | (with-directory-excursion "INCHI_EXE/bin/Linux" |
| 199 | (rename-file "inchi-1" "inchi") |
| 200 | (install-file "inchi" bin)) |
| 201 | ;; Install libraries. |
| 202 | (with-directory-excursion "INCHI_API/bin/Linux" |
| 203 | (for-each (lambda (file) |
| 204 | (install-file file lib)) |
| 205 | (find-files "." "libinchi\\.so\\.1\\.*"))) |
| 206 | ;; Install header files. |
| 207 | (with-directory-excursion "INCHI_BASE/src" |
| 208 | (for-each (lambda (file) |
| 209 | (install-file file include-dir)) |
| 210 | (find-files "." "\\.h$"))) |
| 211 | ;; Install documentation. |
| 212 | (mkdir-p doc) |
| 213 | (invoke unzip "-j" "-d" doc inchi-doc) |
| 214 | #t)))))) |
| 215 | (native-inputs |
| 216 | `(("unzip" ,unzip) |
| 217 | ("inchi-doc" |
| 218 | ,(origin |
| 219 | (method url-fetch) |
| 220 | (uri (string-append "http://www.inchi-trust.org/download/" |
| 221 | (string-join (string-split version #\.) "") |
| 222 | "/INCHI-1-DOC.zip")) |
| 223 | (sha256 |
| 224 | (base32 |
| 225 | "1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6")) |
| 226 | (file-name (string-append name "-" version ".zip")))))) |
| 227 | (home-page "https://www.inchi-trust.org") |
| 228 | (synopsis "Utility for manipulating machine-readable chemical structures") |
| 229 | (description |
| 230 | "The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns |
| 231 | chemical structures into machine-readable strings of information. InChIs are |
| 232 | unique to the compound they describe and can encode absolute stereochemistry |
| 233 | making chemicals and chemistry machine-readable and discoverable. A simple |
| 234 | analogy is that InChI is the bar-code for chemistry and chemical structures.") |
| 235 | (license (license:non-copyleft |
| 236 | "file://LICENCE" |
| 237 | "See LICENCE in the distribution.")))) |
| 238 | |
| 239 | (define with-numpy-1.8 |
| 240 | (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8)))) |
| 241 | |
| 242 | (define-public nmoldyn |
| 243 | (package |
| 244 | (name "nmoldyn") |
| 245 | (version "3.0.11") |
| 246 | (source |
| 247 | (origin |
| 248 | (method git-fetch) |
| 249 | (uri (git-reference |
| 250 | (url "https://github.com/khinsen/nMOLDYN3") |
| 251 | (commit (string-append "v" version)))) |
| 252 | (file-name (git-file-name name version)) |
| 253 | (sha256 |
| 254 | (base32 |
| 255 | "016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r")))) |
| 256 | (build-system python-build-system) |
| 257 | (inputs |
| 258 | `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib)) |
| 259 | ("python-scientific" ,python2-scientific) |
| 260 | ("netcdf" ,netcdf) |
| 261 | ("gv" ,gv))) |
| 262 | (propagated-inputs |
| 263 | `(("python-mmtk" ,python2-mmtk))) |
| 264 | (arguments |
| 265 | `(#:python ,python-2 |
| 266 | #:tests? #f ; No test suite |
| 267 | #:phases |
| 268 | (modify-phases %standard-phases |
| 269 | (add-before 'build 'create-linux2-directory |
| 270 | (lambda _ |
| 271 | (mkdir-p "nMOLDYN/linux2"))) |
| 272 | (add-before 'build 'change-PDF-viewer |
| 273 | (lambda* (#:key inputs #:allow-other-keys) |
| 274 | (substitute* "nMOLDYN/Preferences.py" |
| 275 | ;; Set the paths for external executables, substituting |
| 276 | ;; gv for acroread. |
| 277 | ;; There is also vmd_path, but VMD is not free software |
| 278 | ;; and Guix contains currently no free molecular viewer that |
| 279 | ;; could be substituted. |
| 280 | (("PREFERENCES\\['acroread_path'\\] = ''") |
| 281 | (format #f "PREFERENCES['acroread_path'] = '~a'" |
| 282 | (which "gv"))) |
| 283 | (("PREFERENCES\\['ncdump_path'\\] = ''") |
| 284 | (format #f "PREFERENCES['ncdump_path'] = '~a'" |
| 285 | (which "ncdump"))) |
| 286 | (("PREFERENCES\\['ncgen_path'\\] = ''") |
| 287 | (format #f "PREFERENCES['ncgen_path'] = '~a'" |
| 288 | (which "ncgen3"))) |
| 289 | (("PREFERENCES\\['task_manager_path'\\] = ''") |
| 290 | (format #f "PREFERENCES['task_manager_path'] = '~a'" |
| 291 | (which "task_manager"))) |
| 292 | ;; Show documentation as PDF |
| 293 | (("PREFERENCES\\['documentation_style'\\] = 'html'") |
| 294 | "PREFERENCES['documentation_style'] = 'pdf'") )))))) |
| 295 | (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN.html") |
| 296 | (synopsis "Analysis software for Molecular Dynamics trajectories") |
| 297 | (description "nMOLDYN is an interactive analysis program for Molecular Dynamics |
| 298 | simulations. It is especially designed for the computation and decomposition of |
| 299 | neutron scattering spectra, but also computes other quantities. The software |
| 300 | is currently not actively maintained and works only with Python 2 and |
| 301 | NumPy < 1.9.") |
| 302 | (license license:cecill))) |
| 303 | |
| 304 | (define-public tng |
| 305 | (package |
| 306 | (name "tng") |
| 307 | (version "1.8.2") |
| 308 | (source (origin |
| 309 | (method git-fetch) |
| 310 | (uri (git-reference |
| 311 | (url "https://github.com/gromacs/tng.git") |
| 312 | (commit (string-append "v" version)))) |
| 313 | (file-name (git-file-name name version)) |
| 314 | (sha256 |
| 315 | (base32 |
| 316 | "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q")))) |
| 317 | (build-system cmake-build-system) |
| 318 | (inputs |
| 319 | `(("zlib" ,zlib))) |
| 320 | (arguments |
| 321 | `(#:phases |
| 322 | (modify-phases %standard-phases |
| 323 | (add-after 'unpack 'remove-bundled-zlib |
| 324 | (lambda _ |
| 325 | (delete-file-recursively "external") |
| 326 | #t)) |
| 327 | (replace 'check |
| 328 | (lambda _ |
| 329 | (invoke "../build/bin/tests/tng_testing") |
| 330 | #t))))) |
| 331 | (home-page "https://github.com/gromacs/tng") |
| 332 | (synopsis "Trajectory Next Generation binary format manipulation library") |
| 333 | (description "TRAJNG (Trajectory next generation) is a program library for |
| 334 | handling molecular dynamics (MD) trajectories. It can store coordinates, and |
| 335 | optionally velocities and the H-matrix. Coordinates and velocities are |
| 336 | stored with user-specified precision.") |
| 337 | (license license:bsd-3))) |
| 338 | |
| 339 | (define-public openbabel |
| 340 | (package |
| 341 | (name "openbabel") |
| 342 | (version "2.4.1") |
| 343 | (source (origin |
| 344 | (method url-fetch) |
| 345 | (uri (string-append "mirror://sourceforge/" name "/" name "/" |
| 346 | version "/" name "-" version ".tar.gz")) |
| 347 | (sha256 |
| 348 | (base32 |
| 349 | "1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90")) |
| 350 | (patches |
| 351 | (search-patches "openbabel-fix-crash-on-nwchem-output.patch")))) |
| 352 | (build-system cmake-build-system) |
| 353 | (arguments |
| 354 | `(#:configure-flags |
| 355 | (list "-DOPENBABEL_USE_SYSTEM_INCHI=ON" |
| 356 | (string-append "-DINCHI_LIBRARY=" |
| 357 | (assoc-ref %build-inputs "inchi") |
| 358 | "/lib/inchi/libinchi.so.1") |
| 359 | (string-append "-DINCHI_INCLUDE_DIR=" |
| 360 | (assoc-ref %build-inputs "inchi") "/include/inchi")) |
| 361 | #:test-target "test")) |
| 362 | (native-inputs |
| 363 | `(("pkg-config" ,pkg-config))) |
| 364 | (inputs |
| 365 | `(("eigen" ,eigen) |
| 366 | ("inchi" ,inchi) |
| 367 | ("libxml2" ,libxml2) |
| 368 | ("zlib" ,zlib))) |
| 369 | (home-page "http://openbabel.org/wiki/Main_Page") |
| 370 | (synopsis "Chemistry data manipulation toolbox") |
| 371 | (description |
| 372 | "Open Babel is a chemical toolbox designed to speak the many languages of |
| 373 | chemical data. It's a collaborative project allowing anyone to search, convert, |
| 374 | analyze, or store data from molecular modeling, chemistry, solid-state |
| 375 | materials, biochemistry, or related areas.") |
| 376 | (license license:gpl2))) |