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{ lib
, stdenv
, buildPythonPackage
, fetchFromGitHub
, cmake
, comic-neue
, boost
, catch2
, inchi
, cairo
, eigen
, python
, rapidjson
, maeparser
, coordgenlibs
, numpy
, pandas
, pillow
, memorymappingHook
}:
let
external = {
avalon = fetchFromGitHub {
owner = "rdkit";
repo = "ava-formake";
rev = "AvalonToolkit_2.0.5-pre.3";
hash = "sha256-2MuFZgRIHXnkV7Nc1da4fa7wDx57VHUtwLthrmjk+5o=";
};
yaehmop = fetchFromGitHub {
owner = "greglandrum";
repo = "yaehmop";
rev = "v2023.03.1";
hash = "sha256-K9//cDN69U4sLETfIZq9NUaBE3RXOReH53qfiCzutqM=";
};
freesasa = fetchFromGitHub {
owner = "mittinatten";
repo = "freesasa";
rev = "2.0.3";
hash = "sha256-7E+imvfDAJFnXQRWb5hNaSu+Xrf9NXeIKc9fl+o3yHQ=";
};
};
in
buildPythonPackage rec {
pname = "rdkit";
version = "2023.09.1";
format = "other";
src =
let
versionTag = lib.replaceStrings [ "." ] [ "_" ] version;
in
fetchFromGitHub {
owner = pname;
repo = pname;
rev = "Release_${versionTag}";
hash = "sha256-qaYD/46oCTnso1FbD08zr2JuatKmSSqNBhOYlfeIiAA=";
};
unpackPhase = ''
cp -r $src/* .
find . -type d -exec chmod +w {} +
mkdir External/AvalonTools/avalon
# In buildPhase, CMake patches the file in this directory
# see https://github.com/rdkit/rdkit/pull/5928
cp -r ${external.avalon}/* External/AvalonTools/avalon
mkdir External/YAeHMOP/yaehmop
ln -s ${external.yaehmop}/* External/YAeHMOP/yaehmop
mkdir -p External/FreeSASA/freesasa
cp -r ${external.freesasa}/* External/FreeSASA/freesasa
chmod +w External/FreeSASA/freesasa/src
cp External/FreeSASA/freesasa2.c External/FreeSASA/freesasa/src
ln -s ${rapidjson} External/rapidjson-1.1.0
ln -s ${comic-neue}/share/fonts/truetype/ComicNeue-Regular.ttf Data/Fonts/
'';
nativeBuildInputs = [
cmake
];
buildInputs = [
boost
cairo
] ++ lib.optionals (stdenv.system == "x86_64-darwin") [
memorymappingHook
];
propagatedBuildInputs = [
numpy
pandas
pillow
];
hardeningDisable = [ "format" ]; # required by yaehmop
dontUseSetuptoolsBuild = true;
dontUsePipInstall = true;
dontUseSetuptoolsCheck = true;
preConfigure = ''
# Since we can't expand with bash in cmakeFlags
cmakeFlags="$cmakeFlags -DPYTHON_NUMPY_INCLUDE_PATH=$(${python}/bin/python -c 'import numpy; print(numpy.get_include())')"
cmakeFlags="$cmakeFlags -DFREESASA_DIR=$PWD/External/FreeSASA/freesasa"
cmakeFlags="$cmakeFlags -DFREESASA_SRC_DIR=$PWD/External/FreeSASA/freesasa"
cmakeFlags="$cmakeFlags -DAVALONTOOLS_DIR=$PWD/External/AvalonTools/avalon"
'';
cmakeFlags = [
"-DCATCH_DIR=${catch2}/include/catch2"
"-DINCHI_LIBRARY=${inchi}/lib/libinchi.so"
"-DINCHI_LIBRARIES=${inchi}/lib/libinchi.so"
"-DINCHI_INCLUDE_DIR=${inchi}/include/inchi"
"-DEIGEN3_INCLUDE_DIR=${eigen}/include/eigen3"
"-DRDK_INSTALL_INTREE=OFF"
"-DRDK_INSTALL_STATIC_LIBS=OFF"
"-DRDK_BUILD_INCHI_SUPPORT=ON"
"-DRDK_BUILD_AVALON_SUPPORT=ON"
"-DRDK_BUILD_FREESASA_SUPPORT=ON"
"-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
"-DRDK_BUILD_MAEPARSER_SUPPORT=ON"
"-DMAEPARSER_DIR=${maeparser}"
"-DRDK_BUILD_COORDGEN_SUPPORT=ON"
"-DCOORDGEN_DIR=${coordgenlibs}"
"-DRDK_USE_URF=OFF"
"-DRDK_USE_FLEXBISON=OFF"
"-DRDK_BUILD_CAIRO_SUPPORT=ON"
"-DRDK_BUILD_THREADSAFE_SSS=ON"
"-DRDK_TEST_MULTITHREADED=ON"
"-DRDK_BUILD_CPP_TESTS=ON"
"-DRDK_TEST_MULTITHREADED=ON"
"-DPYTHON_EXECUTABLE=${python}/bin/python"
"-DBOOST_ROOT=${boost}"
"-DBoost_NO_SYSTEM_PATHS=ON"
"-DBoost_NO_BOOST_CMAKE=TRUE"
"-DCMAKE_SKIP_BUILD_RPATH=ON" # fails to find libs in pythonImportsCheckPhase otherwise
];
checkPhase = ''
export QT_QPA_PLATFORM='offscreen'
export RDBASE=$(realpath ..)
export PYTHONPATH="$out/lib/${python.libPrefix}/site-packages:$PYTHONPATH"
(cd $RDBASE/rdkit/Chem && python $RDBASE/rdkit/TestRunner.py test_list.py)
'';
pythonImportsCheck = [
"rdkit"
"rdkit.Chem"
"rdkit.Chem.AllChem"
];
meta = with lib; {
description = "Open source toolkit for cheminformatics";
maintainers = with maintainers; [ rmcgibbo natsukium ];
license = licenses.bsd3;
homepage = "https://www.rdkit.org";
changelog = "https://github.com/rdkit/rdkit/releases/tag/${src.rev}";
};
}
|