name: pl_decomp
version: linker
raw_path: ./raw_data/crossdocked_v1.1_rmsd1.0_pocket10
split_path: ./data/split_by_name_10m.pt
transform:
  - type: choose_ctx_gen
  - type: featurize_protein_fa
  - type: featurize_ligand_gen_ctx_ar
    mode: basic

  - type: count_bond_neighbors
    graph_name: ligand

  - type: mixed_mask
    mask_target: ligand
  
  - type: count_bond_neighbors
    graph_name: ligand_context
  
  - type: build_focal_for_ligand
  - type: sample_edge_for_ligand
    k: 8
  - type: contrastive_sample

  - type: add_pos_noise
    noise_std: 0.1

  - type: hetero_merge
    keys: 
      - protein
      - ligand_masked
      - ligand_context
      - ligand_masked_contrast
      - protein_cross_ligand_masked
      - ligand_context_cross_ligand_masked
      - ligand_context_cross_ligand_masked_contrast
      - edge_graph

    ignore_attrs:
      - num_neighbors
      - num_neighbors_per_bond
      - context_idx
      - masked_idx
      - atom_valence
      - gen_bond_index
      - gen_bond_type
      - ctx_bond_index
      - ctx_bond_type
      - cross_bond_index
      - cross_bond_type


