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Diffstat (limited to 'gnu/packages/chemistry.scm')
| -rw-r--r-- | gnu/packages/chemistry.scm | 96 |
1 files changed, 96 insertions, 0 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 3b06d56711..54d9d9b79b 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -36,6 +37,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages c) #:use-module (gnu packages cpp) #:use-module (gnu packages documentation) #:use-module (gnu packages fontutils) @@ -570,3 +572,97 @@ symmetries written in C. Spglib can be used to: used to prepare publication-quality figures, to share interactive results with your colleagues, or to generate pre-rendered animations.") (license license:bsd-3))) + +(define-public gemmi + (package + (name "gemmi") + (version "0.5.7") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/project-gemmi/gemmi") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a")) + (patches + (search-patches "gemmi-fix-sajson-types.patch" + "gemmi-fix-pegtl-usage.patch")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "include/gemmi/third_party") + (delete-file-recursively "third_party"))))) + (outputs '("out" "bin" "python")) + (build-system cmake-build-system) + (arguments + (list + #:modules '((guix build cmake-build-system) + (guix build utils) + ((guix build python-build-system) + #:select (site-packages))) + #:imported-modules (append %cmake-build-system-modules + '((guix build python-build-system))) + #:configure-flags + #~(list "-DUSE_PYTHON=ON" + (string-append "-DPYTHON_INSTALL_DIR=" + (site-packages %build-inputs %outputs))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-includes + (lambda _ + (substitute* (list "include/gemmi/sprintf.hpp" + "include/gemmi/dirwalk.hpp" + "include/gemmi/cif.hpp" + "include/gemmi/json.hpp" + "python/gemmi.cpp" + "include/gemmi/atof.hpp" + "include/gemmi/numb.hpp" + "include/gemmi/fourier.hpp") + (("<stb/stb_sprintf.h>") "<stb_sprintf.h>") + (("\"third_party/tinydir.h\"") "<tinydir.h>") + (("\"third_party/tao/pegtl.hpp\"") "<tao/pegtl.hpp>") + (("\"third_party/sajson.h\"") "<sajson.h>") + (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"") + "<tao/pegtl/parse_error.hpp>") + (("\"third_party/fast_float.h\"") + "<fast_float/fast_float.h>") + (("\"third_party/pocketfft_hdronly.h\"") + "<pocketfft_hdronly.h>")))) + (add-after 'unpack 'change-bin-prefix + (lambda _ + (substitute* "CMakeLists.txt" + (("install\\(TARGETS program DESTINATION bin\\)") + (string-append + "install(TARGETS program DESTINATION " + #$output:bin "/bin)"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "../source" + (setenv "PYTHONPATH" "../build") + (invoke "python3" "-m" "unittest" "discover" "-v" + "-s" "tests")))))))) + (inputs (list python zlib)) + (native-inputs + (list fast-float + optionparser + pegtl + pocketfft-cpp + pybind11 + sajson-for-gemmi + stb-sprintf + tinydir)) + (home-page "https://gemmi.readthedocs.io/en/latest/") + (synopsis "Macromolecular crystallography library and utilities") + (description "GEMMI is a C++ library for macromolecular crystallography. +It can be used for working with +@enumerate +@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files), +@item refinement restraints (CIF files), +@item reflection data (MTZ and mmCIF formats), +@item data on a 3D grid (electron density maps, masks, MRC/CCP4 format) +@item crystallographic symmetry. +@end enumerate") + (license license:mpl2.0))) |