pkgs/applications/science/chemistry/pymol/default.nix

   1 { stdenv
   2 , lib
   3 , fetchFromGitHub
   4 , makeDesktopItem
   5 , python3
   6 , python3Packages
   7 , netcdf
   8 , glew
   9 , glm
  10 , libpng
  11 , libxml2
  12 , freetype
  13 , msgpack
  14 , qt5
  15 }:
  16 let
  17   pname = "pymol";
  18   description = "A Python-enhanced molecular graphics tool";
  19
  20   desktopItem = makeDesktopItem {
  21     name = pname;
  22     exec = pname;
  23     desktopName = "PyMol Molecular Graphics System";
  24     genericName = "Molecular Modeler";
  25     comment = description;
  26     icon = pname;
  27     mimeTypes = [
  28       "chemical/x-pdb"
  29       "chemical/x-mdl-molfile"
  30       "chemical/x-mol2"
  31       "chemical/seq-aa-fasta"
  32       "chemical/seq-na-fasta"
  33       "chemical/x-xyz"
  34       "chemical/x-mdl-sdf"
  35     ];
  36     categories = [ "Graphics" "Education" "Science" "Chemistry" ];
  37   };
  38 in
  39 python3Packages.buildPythonApplication rec {
  40   inherit pname;
  41   version = "2.5.0";
  42   src = fetchFromGitHub {
  43     owner = "schrodinger";
  44     repo = "pymol-open-source";
  45     rev = "v${version}";
  46     sha256 = "sha256-JdsgcVF1w1xFPZxVcyS+GcWg4a1Bd4SvxFOuSdlz9SM=";
  47   };
  48
  49   nativeBuildInputs = [ qt5.wrapQtAppsHook ];
  50   buildInputs = [ python3Packages.numpy python3Packages.pyqt5 glew glm libpng libxml2 freetype msgpack netcdf ];
  51   env.NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";
  52   hardeningDisable = [ "format" ];
  53
  54   installPhase = ''
  55     python setup.py install --home="$out"
  56     runHook postInstall
  57   '';
  58
  59   postInstall = with python3Packages; ''
  60     wrapProgram $out/bin/pymol \
  61       --prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3.sitePackages [ pyqt5 pyqt5.pyqt5_sip ]}
  62
  63     mkdir -p "$out/share/icons/"
  64     ln -s ../../lib/python/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg"
  65     cp -r "${desktopItem}/share/applications/" "$out/share/"
  66   '';
  67
  68   preFixup = ''
  69     wrapQtApp "$out/bin/pymol"
  70   '';
  71
  72   meta = with lib; {
  73     inherit description;
  74     homepage = "https://www.pymol.org/";
  75     license = licenses.mit;
  76     maintainers = with maintainers; [ samlich ];
  77   };
  78 }