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arneschneuing / DiffSBDD

A Euclidean diffusion model for structure-based drug design.
MIT License
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The initial ligand part #6

Closed 1121091694 closed 1 year ago

1121091694 commented 2 years ago

Nice Paper，could you tell me how to add the atom and atomic coordinate of the initial ligand in the sample of protein pocket? Just like smiles seq2seq, we give the prompt of sequence like CCCC. In this work, can we give the initial ligand like atom and xyz Could we generate the whole ligand with certain part which we can give

arneschneuing commented 1 year ago

Thank you! The inpainting function generally supports this. You can fix arbitrary parts of the pocket or ligand using the binary masks lig_fixed and pocket_fixed. Unfortunately, we have not implemented an interface for SDF/PDB files yet but it should look similar to the generate_ligands function.