model:
  type: pocket2mol
  checkpoint: ./logs/denovo/pocket2mol/pocket2mol_2024_04_15__16_23_49/checkpoints/410000.pt
data:
  batch_size: 1
  test: 
    name: pl_fa
    raw_path: ./data/case_study
    split_path: ./data/case_study/split_by_name.pt
    processed_dir: ./data/case_study/processed/
    transform:
      - type: featurize_protein_fa   
      - type: remove_ligand

      - type: init_empty_mol
        mode: basic

      - type: prefixed_mask

      - type: count_bond_neighbors
        graph_name: ligand
      - type: hetero_merge
        keys: 
          - protein
          - ligand_masked
          - ligand_context

        ignore_attrs:
          - num_neighbors
          - num_neighbors_per_bond
          - context_idx
          - masked_idx
          - atom_valence
    

sampling:
  seed: 2022
  num_samples: 500
  translate: false
  hetero_to_graph: true

reconstruct:
  basic_mode: true