global_properties:
  working_dir_path: biobb_wf_godmd
  can_write_console_log: False

step0_extract_chain:
  tool: extract_chain
  paths:
    input_structure_path: /data/origin.pdb
    output_structure_path: origin.chains.pdb
  properties:
    chains: ['A']

step1_extract_chain:
  tool: extract_chain
  paths:
    input_structure_path: /data/target.pdb
    output_structure_path: target.chains.pdb
  properties:
    chains: ['A']

step2_remove_molecules:
  tool: remove_molecules
  paths:
    input_structure_path: dependency/step0_extract_chain/output_structure_path
    output_molecules_path: origin.chains.nolig.pdb
  properties:
    molecules: [
      { name: AP5 }
    ]

step3_remove_molecules:
  tool: remove_molecules
  paths:
    input_structure_path: dependency/step1_extract_chain/output_structure_path
    output_molecules_path: target.chains.nolig.pdb
  properties:
    molecules: []

step4_godmd_prep:
  tool: godmd_prep
  paths:
    input_pdb_orig_path: dependency/step2_remove_molecules/output_molecules_path
    input_pdb_target_path: dependency/step3_remove_molecules/output_molecules_path
    output_aln_orig_path: origin.aln
    output_aln_target_path: target.aln
  properties:
    gapopen: '12.0'
    gapextend: '2'

step5_godmd_run:
  tool: godmd_run
  paths:
    input_pdb_orig_path: dependency/step2_remove_molecules/output_molecules_path
    input_pdb_target_path: dependency/step3_remove_molecules/output_molecules_path
    input_aln_orig_path: dependency/step4_godmd_prep/output_aln_orig_path
    input_aln_target_path: dependency/step4_godmd_prep/output_aln_target_path
    output_log_path: origin-target.godmd.log
    output_ene_path: origin-target.godmd.ene.out
    output_trj_path: origin-target.godmd.mdcrd
    output_pdb_path: origin-target.godmd.pdb
  properties:
    godmdin:
      temp: 400

step6_cpptraj_convert:
  tool: cpptraj_convert
  paths:
    input_top_path: dependency/step5_godmd_run/output_pdb_path
    input_traj_path: dependency/step5_godmd_run/output_pdb_path
    output_cpptraj_path: origin-target.godmd.dcd
  properties:
    format: dcd