The files in the corpora folders (i.e. the folders ending in _fuzzer) can not be directly used for purposes other than fuzzing. This is because the fuzzer uses parts of the content for generating different information. Consider the example [OH3+]0. The first part [OH3+] will be used as a smiles formula, but the last part 0 will for example be used to determine whether the fuzzer should set a certain flag to true or it will be used to derive an integral value.

Compiling

To fuzz rdkit you need to have clang installed. If you have built the fuzzers you can invoke them like this: ./smiles_string_to_mol_fuzzer -dict=smiles_string_to_mol_fuzzer.dict smiles_string_to_mol_fuzzer/ For possible options that you can pass to the fuzzer see the libFuzzer docs.

Clang

export CC="clang"
export CXX="clang++"
export SANITIZER_FLAGS_address="-fsanitize=address -fsanitize-address-use-after-scope"
export COVERAGE_FLAGS="-fsanitize=fuzzer-no-link"
export CFLAGS="-O1 -fno-omit-frame-pointer -gline-tables-only -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION $COVERAGE_FLAGS $SANITIZER_FLAGS_address"
export CXXFLAGS="$CFLAGS"
export LIB_FUZZING_ENGINE="-fsanitize=fuzzer"

mkdir build && cd build && \
    cmake .. \
    -DCMAKE_BUILD_TYPE=Release \
    -DRDK_INSTALL_INTREE=ON \
    -DRDK_BUILD_PYTHON_WRAPPERS=OFF \
    -DLIB_FUZZING_ENGINE=${LIB_FUZZING_ENGINE} \
    -DRDK_BUILD_FUZZ_TARGETS=ON \
    -DRDK_INSTALL_STATIC_LIBS=ON \
    -DBoost_USE_STATIC_LIBS=ON \
    -DRDK_BUILD_CPP_TESTS=OFF \
    -DBoost_NO_SYSTEM_PATHS=ON \
make

GCC (non-fuzzing mode)

In this mode the resulting fuzzers take a list of files as argument and invoke the fuzz target on each file. No actual fuzzing will be done, since no new test cases are generated.

export CC="gcc"
export CXX="g++"
export SANITIZER_FLAGS_address="-fsanitize=address -fsanitize-address-use-after-scope"
export COVERAGE_FLAGS=""
export CFLAGS="-O1 -fno-omit-frame-pointer -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION $COVERAGE_FLAGS $SANITIZER_FLAGS_address"
export CXXFLAGS="$CFLAGS"
export LIB_FUZZING_ENGINE=""

mkdir build && cd build && \
    cmake .. \
    -DCMAKE_BUILD_TYPE=Release \
    -DRDK_INSTALL_INTREE=ON \
    -DRDK_BUILD_PYTHON_WRAPPERS=OFF \
    -DLIB_FUZZING_ENGINE=${LIB_FUZZING_ENGINE} \
    -DRDK_BUILD_FUZZ_TARGETS=ON \
    -DRDK_INSTALL_STATIC_LIBS=ON \
    -DBoost_USE_STATIC_LIBS=ON \
    -DRDK_BUILD_CPP_TESTS=OFF \
    -DBoost_NO_SYSTEM_PATHS=ON \
make

GCC (fuzzing mode)

This does not seem to be possible.