Acknowledgments

We are grateful to many open source software packages, including but not limited to:

• RDKit (https://rdkit.org/)
• Constrained Embedding - Joshua Meyers' Notebook, Tim Dudgeon' example
• Grafting, Peter Schmidtke PeterSchmidtke
• OpenMM (https://openmm.org/)
• Open Force Field foundation packages (https://openforcefield.org/)
• mols2grid (https://mols2grid.readthedocs.io/)
• Prody (http://prody.csb.pitt.edu/)
• TeachOpenCADD (https://projects.volkamerlab.org/teachopencadd/)
• OpenChemistry (https://www.openchemistry.org/, molecules as R-groups)
• Py3Dmol (https://github.com/3dmol/3Dmol.js)
• PDBFixer (https://github.com/openmm/pdbfixer)
• PyTorch (https://pytorch.org/)
• openmmforcefields (https://github.com/openmm/openmmforcefields)
• openmm-torch (https://github.com/openmm/openmm-torch)
• parmed (https://www.parmed.com/)
• OpenBabel (https://openbabel.org/)
• torchani (https://aiqm.github.io/torchani/)

Please cite the packages accordingly.