# Redesign a SAM-binding pocket: fix the ligand and two motif blocks, graft a fresh
# variable-length helix, and condition sequence / burial / secondary structure.
# Selections mostly use the concise `sel('<chain>/<resname>/<resid>/<atom>')` path syntax
# (trailing fields default to `*`); C_HOT uses the general-purpose query syntax instead.
sam_pocket_redesign:
  input: ../../../../tests/data/sam_binder_generated_minimized.cif   # 150-res binder (chain A) + SAM ligand (chain B)
  contig: "A1-150, /0, B386, /0, EX1:15-30"   # keep binder + SAM, add a de-novo 15-30-residue helix chain
  conditions:
    C_CRD:                             # fix the ligand + two binder motif blocks in space
      true:
        - select: "sel('B')"                     # whole ligand chain (chain field only; rest wildcard)
        - select: "sel('A/*/[1-30, 120-150]')"   # two res_id ranges of chain A in one path
    C_SEQ:                             # lock a few pocket-lining sidechain identities
      true:
        - select: "sel('A/*/[10, 20, 130]')"     # a res_id list
    C_HOT:                             # general-purpose query: hotspot every ligand atom by a computed
      true:                            # annotation rather than a path -- any array annotation is queryable
        - select: "is_ligand"
    C_SEC:                             # secondary-structure conditioning on the expandable segment: force helix
      HELIX:
        - select: "sel('*/EX1')"     # the expandable segment, by the res_name you named it in `contig`
    C_RAS:                             # enum: two binder residues marked buried
      BURIED:
        - select: "sel('A/*/[40, 45]')"
    C_IDX:                             # unindex both motif blocks as one group (free relative placement)
      false:
        - select: "sel('A/*/[1-30]')"
          group: motif
        - select: "sel('A/*/[120-150]')"
          group: motif                 # same label -> the two blocks merge into one unindexed group