160 lines
4.2 KiB
Nix
160 lines
4.2 KiB
Nix
{ lib
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, stdenv
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, buildPythonPackage
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, fetchFromGitHub
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, cmake
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, comic-neue
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, boost
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, catch2
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, inchi
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, cairo
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, eigen
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, python
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, rapidjson
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, maeparser
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, coordgenlibs
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, numpy
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, pandas
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, pillow
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, memorymappingHook
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}:
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let
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external = {
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avalon = fetchFromGitHub {
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owner = "rohdebe1";
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repo = "ava-formake";
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rev = "AvalonToolkit_2.0.4a";
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hash = "sha256-ZyhrDBBv9XuXe1NY/Djiad86tGIJwCSTrxEMICHgSqk=";
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};
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yaehmop = fetchFromGitHub {
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owner = "greglandrum";
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repo = "yaehmop";
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rev = "v2022.09.1";
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hash = "sha256-QMnc5RyHlY3giw9QmrkGntiA+Srs7OhCIKs9GGo5DfQ=";
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};
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freesasa = fetchFromGitHub {
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owner = "mittinatten";
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repo = "freesasa";
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rev = "2.0.3";
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hash = "sha256-7E+imvfDAJFnXQRWb5hNaSu+Xrf9NXeIKc9fl+o3yHQ=";
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};
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};
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in
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buildPythonPackage rec {
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pname = "rdkit";
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version = "2023.03.1";
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format = "other";
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src =
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let
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versionTag = lib.replaceStrings [ "." ] [ "_" ] version;
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in
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fetchFromGitHub {
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owner = pname;
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repo = pname;
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rev = "Release_${versionTag}";
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hash = "sha256-hiDaPWDAWzALRf3+SAfzghu2K706rcajeZ69tMFplhU=";
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};
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unpackPhase = ''
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cp -r $src/* .
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find . -type d -exec chmod +w {} +
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mkdir External/AvalonTools/avalon
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# In buildPhase, CMake patches the file in this directory
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# see https://github.com/rdkit/rdkit/pull/5928
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cp -r ${external.avalon}/* External/AvalonTools/avalon
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mkdir External/YAeHMOP/yaehmop
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ln -s ${external.yaehmop}/* External/YAeHMOP/yaehmop
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mkdir -p External/FreeSASA/freesasa
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cp -r ${external.freesasa}/* External/FreeSASA/freesasa
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chmod +w External/FreeSASA/freesasa/src
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cp External/FreeSASA/freesasa2.c External/FreeSASA/freesasa/src
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ln -s ${rapidjson} External/rapidjson-1.1.0
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ln -s ${comic-neue}/share/fonts/truetype/ComicNeue-Regular.ttf Data/Fonts/
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'';
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nativeBuildInputs = [
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cmake
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];
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buildInputs = [
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boost
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cairo
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] ++ lib.optionals (stdenv.system == "x86_64-darwin") [
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memorymappingHook
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];
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propagatedBuildInputs = [
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numpy
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pandas
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pillow
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];
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hardeningDisable = [ "format" ]; # required by yaehmop
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dontUseSetuptoolsBuild = true;
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dontUsePipInstall = true;
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dontUseSetuptoolsCheck = true;
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preConfigure = ''
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# Since we can't expand with bash in cmakeFlags
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cmakeFlags="$cmakeFlags -DPYTHON_NUMPY_INCLUDE_PATH=$(${python}/bin/python -c 'import numpy; print(numpy.get_include())')"
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cmakeFlags="$cmakeFlags -DFREESASA_DIR=$PWD/External/FreeSASA/freesasa"
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cmakeFlags="$cmakeFlags -DFREESASA_SRC_DIR=$PWD/External/FreeSASA/freesasa"
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cmakeFlags="$cmakeFlags -DAVALONTOOLS_DIR=$PWD/External/AvalonTools/avalon"
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'';
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cmakeFlags = [
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"-DCATCH_DIR=${catch2}/include/catch2"
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"-DINCHI_LIBRARY=${inchi}/lib/libinchi.so"
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"-DINCHI_LIBRARIES=${inchi}/lib/libinchi.so"
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"-DINCHI_INCLUDE_DIR=${inchi}/include/inchi"
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"-DEIGEN3_INCLUDE_DIR=${eigen}/include/eigen3"
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"-DRDK_INSTALL_INTREE=OFF"
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"-DRDK_INSTALL_STATIC_LIBS=OFF"
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"-DRDK_BUILD_INCHI_SUPPORT=ON"
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"-DRDK_BUILD_AVALON_SUPPORT=ON"
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"-DRDK_BUILD_FREESASA_SUPPORT=ON"
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"-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
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"-DRDK_BUILD_MAEPARSER_SUPPORT=ON"
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"-DMAEPARSER_DIR=${maeparser}"
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"-DRDK_BUILD_COORDGEN_SUPPORT=ON"
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"-DCOORDGEN_DIR=${coordgenlibs}"
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"-DRDK_USE_URF=OFF"
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"-DRDK_USE_FLEXBISON=OFF"
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"-DRDK_BUILD_CAIRO_SUPPORT=ON"
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"-DRDK_BUILD_THREADSAFE_SSS=ON"
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"-DRDK_TEST_MULTITHREADED=ON"
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"-DRDK_BUILD_CPP_TESTS=ON"
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"-DRDK_TEST_MULTITHREADED=ON"
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"-DPYTHON_EXECUTABLE=${python}/bin/python"
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"-DBOOST_ROOT=${boost}"
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"-DBoost_NO_SYSTEM_PATHS=ON"
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"-DBoost_NO_BOOST_CMAKE=TRUE"
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"-DCMAKE_SKIP_BUILD_RPATH=ON" # fails to find libs in pythonImportsCheckPhase otherwise
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];
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checkPhase = ''
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export QT_QPA_PLATFORM='offscreen'
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export RDBASE=$(realpath ..)
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export PYTHONPATH="$out/lib/${python.libPrefix}/site-packages:$PYTHONPATH"
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(cd $RDBASE/rdkit/Chem && python $RDBASE/rdkit/TestRunner.py test_list.py)
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'';
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pythonImportsCheck = [
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"rdkit"
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"rdkit.Chem"
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"rdkit.Chem.AllChem"
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];
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meta = with lib; {
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description = "Open source toolkit for cheminformatics";
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maintainers = with maintainers; [ rmcgibbo natsukium ];
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license = licenses.bsd3;
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homepage = "https://www.rdkit.org";
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};
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}
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