pkgs/development/python-modules/rdkit/default.nix

   1 {
   2   lib,
   3   stdenv,
   4   buildPythonPackage,
   5   fetchFromGitHub,
   6   cmake,
   7   comic-neue,
   8   boost,
   9   catch2_3,
  10   inchi,
  11   cairo,
  12   eigen,
  13   python,
  14   rapidjson,
  15   maeparser,
  16   coordgenlibs,
  17   numpy,
  18   pandas,
  19   pillow,
  20   memorymappingHook,
  21 }:
  22 let
  23   external = {
  24     avalon = fetchFromGitHub {
  25       owner = "rdkit";
  26       repo = "ava-formake";
  27       rev = "AvalonToolkit_2.0.5-pre.3";
  28       hash = "sha256-2MuFZgRIHXnkV7Nc1da4fa7wDx57VHUtwLthrmjk+5o=";
  29     };
  30     yaehmop = fetchFromGitHub {
  31       owner = "greglandrum";
  32       repo = "yaehmop";
  33       rev = "v2024.03.1";
  34       hash = "sha256-rhR7Ev+9Fk/Ks7R2x2SjWu1L/48a4zHDHUBohx1Dw/M=";
  35     };
  36     freesasa = fetchFromGitHub {
  37       owner = "mittinatten";
  38       repo = "freesasa";
  39       rev = "2.0.3";
  40       hash = "sha256-7E+imvfDAJFnXQRWb5hNaSu+Xrf9NXeIKc9fl+o3yHQ=";
  41     };
  42     pubchem-align3d = fetchFromGitHub {
  43       owner = "ncbi";
  44       repo = "pubchem-align3d";
  45       rev = "daefab3dd0c90ca56da9d3d5e375fe4d651e6be3";
  46       hash = "sha256-tQB4wqza9rlSoy4Uj9bA99ddawjxGyN9G7DYbcv/Qdo=";
  47     };
  48   };
  49   boost' = boost.override { enableNumpy = true; };
  50 in
  51 buildPythonPackage rec {
  52   pname = "rdkit";
  53   version = "2024.09.1";
  54   pyproject = false;
  55
  56   src =
  57     let
  58       versionTag = lib.replaceStrings [ "." ] [ "_" ] version;
  59     in
  60     fetchFromGitHub {
  61       owner = "rdkit";
  62       repo = "rdkit";
  63       rev = "Release_${versionTag}";
  64       hash = "sha256-UsyPlAJ8FISblF8szEmRqWansunIhW/gbEBZx13YM+A=";
  65     };
  66
  67   unpackPhase = ''
  68     cp -r $src/* .
  69     find . -type d -exec chmod +w {} +
  70
  71     mkdir External/AvalonTools/avalon
  72     # In buildPhase, CMake patches the file in this directory
  73     # see https://github.com/rdkit/rdkit/pull/5928
  74     cp -r ${external.avalon}/* External/AvalonTools/avalon
  75
  76     mkdir External/YAeHMOP/yaehmop
  77     ln -s ${external.yaehmop}/* External/YAeHMOP/yaehmop
  78
  79     mkdir -p External/FreeSASA/freesasa
  80     cp -r ${external.freesasa}/* External/FreeSASA/freesasa
  81     chmod +w External/FreeSASA/freesasa/src
  82     cp External/FreeSASA/freesasa2.c External/FreeSASA/freesasa/src
  83
  84     ln -s ${external.pubchem-align3d} External/pubchem_shape/pubchem-align3d
  85     ln -s ${rapidjson} External/rapidjson-1.1.0
  86     ln -s ${comic-neue}/share/fonts/truetype/ComicNeue-Regular.ttf Data/Fonts/
  87   '';
  88
  89   nativeBuildInputs = [ cmake ];
  90
  91   buildInputs = [
  92     boost'
  93     cairo
  94     catch2_3
  95     coordgenlibs
  96     eigen
  97     inchi
  98     maeparser
  99   ] ++ lib.optionals (stdenv.system == "x86_64-darwin") [ memorymappingHook ];
 100
 101   dependencies = [
 102     numpy
 103     pandas
 104     pillow
 105   ];
 106
 107   hardeningDisable = [ "format" ]; # required by yaehmop
 108
 109   cmakeFlags = [
 110     (lib.cmakeBool "Boost_NO_BOOST_CMAKE" true)
 111     (lib.cmakeBool "Boost_NO_SYSTEM_PATHS" true)
 112     (lib.cmakeBool "CMAKE_SKIP_BUILD_RPATH" true) # fails to find libs in pythonImportsCheckPhase otherwise
 113     (lib.cmakeBool "RDK_BUILD_AVALON_SUPPORT" true)
 114     (lib.cmakeBool "RDK_BUILD_CAIRO_SUPPORT" true)
 115     (lib.cmakeBool "RDK_BUILD_COORDGEN_SUPPORT" true)
 116     (lib.cmakeBool "RDK_BUILD_CPP_TESTS" true)
 117     (lib.cmakeBool "RDK_BUILD_FREESASA_SUPPORT" true)
 118     (lib.cmakeBool "RDK_BUILD_INCHI_SUPPORT" true)
 119     (lib.cmakeBool "RDK_BUILD_MAEPARSER_SUPPORT" true)
 120     (lib.cmakeBool "RDK_BUILD_THREADSAFE_SSS" true)
 121     (lib.cmakeBool "RDK_BUILD_YAEHMOP_SUPPORT" true)
 122     (lib.cmakeBool "RDK_INSTALL_INTREE" false)
 123     (lib.cmakeBool "RDK_INSTALL_STATIC_LIBS" false)
 124     (lib.cmakeBool "RDK_TEST_MULTITHREADED" true)
 125     (lib.cmakeBool "RDK_TEST_MULTITHREADED" true)
 126     (lib.cmakeBool "RDK_USE_FLEXBISON" false)
 127     (lib.cmakeBool "RDK_USE_URF" false)
 128     (lib.cmakeFeature "AVALONTOOLS_DIR" "avalon")
 129     (lib.cmakeFeature "FREESASA_SRC_DIR" "freesasa")
 130     (lib.cmakeFeature "INCHI_INCLUDE_DIR" "${inchi}/include/inchi")
 131     (lib.cmakeFeature "PUBCHEMSHAPE_DIR" "External/pubchem_shape/pubchem-align3d")
 132   ];
 133
 134   checkPhase = ''
 135     export QT_QPA_PLATFORM='offscreen'
 136     export RDBASE=$(realpath ..)
 137     export PYTHONPATH="$out/${python.sitePackages}:$PYTHONPATH"
 138     (cd $RDBASE/rdkit/Chem && python $RDBASE/rdkit/TestRunner.py test_list.py)
 139   '';
 140
 141   pythonImportsCheck = [
 142     "rdkit"
 143     "rdkit.Chem"
 144     "rdkit.Chem.AllChem"
 145   ];
 146
 147   meta = with lib; {
 148     description = "Open source toolkit for cheminformatics";
 149     maintainers = with maintainers; [
 150       rmcgibbo
 151       natsukium
 152     ];
 153     license = licenses.bsd3;
 154     homepage = "https://www.rdkit.org";
 155     changelog = "https://github.com/rdkit/rdkit/releases/tag/${src.rev}";
 156   };
 157 }