Currently, ESM and SLAE cannot provide embeddings for ligands or other non-amino acid atoms. Will need a strategy to encode them as a separate node type with specific features.
Most simple strategy on ProteinGVPEncoder would be to initialize all non-water het atoms as another node type and modify the encoder to update embeddings based on heteroconvs.
Currently, ESM and SLAE cannot provide embeddings for ligands or other non-amino acid atoms. Will need a strategy to encode them as a separate node type with specific features.
Most simple strategy on ProteinGVPEncoder would be to initialize all non-water het atoms as another node type and modify the encoder to update embeddings based on heteroconvs.