Acknowledgments

We are grateful to many open source softwares available, including but not limited to:

• RDKit (https://rdkit.org/):

  • Constrained Embedding - Joshua Meyers’ Notebook, Tim Dudgeon example

  • Grafting, Peter Schmidtke

• 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.