analysis_realtime_ligand.wic

# NOTE: The biobb gmx_rms CWL adapter does not support the -b flag
# (See https://manual.gromacs.org/documentation/current/onlinehelp/gmx-rms.html)
# This causes the rmsd w.r.t. the last equil timestep to start at exactly zero,
# which distorts the comparison between the xray and equil cases.
# NOTE: Most paths can be inferred, but explicitly specify them anyway because
# for cwl_subinterpreter and so we can re-order steps in analysis.
steps:
    gmxselect: # NOTE: make_ndx does NOT work! (It erroneously selects all of the atoms.)
      in:
        input_structure_path: !* min.tpr
        config: !ii {"selection": "resname MOL"}
      out:
      - output_ndx_path: !& MOL.ndx
    gmx_rms:
      in:
        input_structure_path: !* prod.tpr
        input_traj_path: !* prod.trr
        config: !ii
          selection: resname_MOL
        input_index_path: !* MOL.ndx
        output_xvg_path: !ii rmsd_equil_ligand_fit.xvg

wic:
  graphviz:
    #label: Real-time Analysis
    style: invis # Make this subgraph invisible (but NOT the parent graph).
    ranksame:
    - (1, gmxselect)
    - (2, gmx_rms)
  steps:
    (1, gmxselect):
      wic:
        graphviz:
          label: Select Ligand\nResidue Indices
    (2, gmx_rms):
      wic:
        graphviz:
          label: Ligand RMSD (fit)\nw.r.t. Equil Coords