entities:
  - protein:
      id: G
      sequence: 15..20AAAAAAVTTTT18PPP # range between 15 and 20 inclusive on both sides
      residue_constraints:
        - position: 1
          allowed: A # Only Alanine at position 1
        - position: 3..5
          disallowed: CM # No Cysteine or Methionine at positions 3-5
        - position: 8
          allowed: AGS # Only Ala, Gly, or Ser at position 8
  - protein: 
      id: R
      sequence: 3..5C6C3 # Random number of design residues between 3 and 5, then a Cystein, then 6 design residues, then ...
  - ligand:
      id: Q
      ccd: WHL
  - protein:
      id: H
      sequence: 17
      secondary_structure: # No secondary structure specified, defaults 
  - file:
      path: 7rpz.cif
       
      include: 
        - chain:
            id: A
        - chain:
            id: B

      include_proximity:
        - chain: 
            id: A
            res_index: 10..16
            radius: 35

      binding_types:
        - chain:
            id: A
            binding: 5..7,13
        - chain:
            id: B
            not_binding: "all" 
          


      structure_groups:
        - group:
            visibility: 1
            id: A
            res_index: 10..16
        - group:
            visibility: 2
            id: B
        - group:
            visibility: 0
            id: A
            res_index: 13

      design:
        - chain:
            id: A
            res_index: ..4,20..27

      secondary_structure:
        - chain:
            id: A
            loop: 1
            helix: 2..3
            sheet: 4
        
      design_insertions:
        - insertion:
            id: A
            res_index: 20 # The 20th residue will be a designed one (starting to count from 1)
            num_residues: 2..9
            secondary_structure: HELIX # One of UNSPECIFIED (default), LOOP, HELIX, SHEET. 

  - protein: 
      id: A
      sequence: AAAAAAAAAAAAAAAAAAAAAAAA
      binding_types: uuuuBBBuNNNuBuu # the missing specifications will be 'u' by default
  - file:
      path: 7rpz.cif
      fuse: A
      include: 
        - chain:
            id: A
            res_index: ..5
            
  - protein:
      id: B
      sequence: AAAAAAAAAAAAAAAAAAAAAAAA
      binding_types:
        binding: 5..7,13
        not_binding: 9..11
  - ligand:
      id: [C, D]
      ccd: SAH
  - ligand:
      id: [E, F]
      smiles: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O'
      binding_types: B


  - file:
      path: 7rpz.cif
      include: "all"
      exclude: 
        - chain:
            id: A
            res_index: ..5

      structure_groups:
        - group:
            visibility: 1
            id: "all"

        - group:
            visibility: 0
            id: A
            res_index: 10..16
  - file:
      path: 8r3a.cif
       
      include: 
        - chain:
            id: A
        - chain:
            id: B

      binding_types:
        - chain:
            id: A
            binding: 5..7,13
        - chain:
            id: B
            not_binding: "all" 
          


      structure_groups:
        - group:
            visibility: 1
            id: A
            res_index: 10..13
        - group:
            visibility: 2
            id: B
        - group:
            visibility: 0
            id: A
            res_index: 13

      design:
        - chain:
            id: A
            res_index: 14..19

      secondary_structure:
        - chain:
            id: A
            loop: 14
            helix: 15..17
            sheet: 19
  - protein:
      id: S
      sequence: 10C6C3
  - protein:
      id: T
      sequence: C10C6C3C
      cyclic: true

constraints:
    # specify connections as if the minimum possible number of residues was sampled
  - bond:
      atom1: [R, 4, SG] # connection for a helical peptides with WHL staple 
      atom2: [Q, 1, CK]
  - bond:
      atom1: [R, 11, SG]
      atom2: [Q, 1, CH]
  - bond:
      atom1: [S, 11, SG] # connection for a disulfide bond
      atom2: [S, 18, SG]
  - bond:
      atom1: [T, 12, SG]
      atom2: [T, 19, SG]

  - total_len:
      min: 10
      max: 20