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Build cuik_molmaker

Follow the instructions below to build cuik_molmaker from source.

Setup linux environment

Install eigen

sudo apt-get install libeigen3-dev

Verify eigen is installed correctly

dpkg -s libeigen3-dev

Install cmake

sudo apt install cmake
# Check cmake version
cmake --version

Setup conda environment

# Set desired python and RDKit versions as environment variables. 
# Here is an example for python 3.11, RDKit 2025.03.2.
export PYTHON_VERSION=3.11
export RDKIT_VERSION=2025.03.2

# Create conda env
conda create -n cuik_molmaker_build python=$PYTHON_VERSION conda-forge::rdkit==$RDKIT_VERSION conda-forge::pybind11==2.13.6 conda-forge::librdkit-dev==$RDKIT_VERSION conda-forge::pybind11==2.13.6  conda-forge::libboost-devel==1.86.0 conda-forge::libboost-python-devel==1.86.0

# Activate conda env
conda activate cuik_molmaker_build

Note: If you are building against an older version of RDKit, you may need to use an older version of Boost that is compatible with that RDKit release. Check the RDKit documentation for the recommended Boost version for your RDKit version.

Build cuik_molmaker

# Clone cuik_molmaker repo
git clone https://github.com/NVIDIA-Digital-Bio/cuik-molmaker
cd cuik_molmaker

# Build C++ extension for cuik_molmaker
RDKIT_VERSION=$RDKIT_VERSION PYTHON_VERSION=$PYTHON_VERSION python setup.py build_ext --inplace

# Install build
pip install build

# Build wheel
RDKIT_VERSION=$RDKIT_VERSION PYTHON_VERSION=$PYTHON_VERSION python -m build --outdir path/to/output/directory --wheel

Install cuik_molmaker from wheel

pip install path/to/output/directory/cuik_molmaker*.whl

Test installation

pip install pytest
pytest tests/python/

If the installation was successful, you should see that all tests pass. If not, please refer to the Troubleshooting section below.

Troubleshooting

  • If you see a CMake error about RDKit::GraphMol including the non-existent path $CONDA_PREFIX/include/python3.9 even though you are using a different python version, symlink it to the correct path as shown:
ln -s $CONDA_PREFIX/lib/python$PYTHON_VERSION $CONDA_PREFIX/lib/python3.9
ln -s $CONDA_PREFIX/include/python$PYTHON_VERSION $CONDA_PREFIX/include/python3.9
  • If any of the build steps fails, delete the build, cuik-molmaker.egg-info, cuik-molmaker and wheel output directories before trying again.