global_properties:
  working_dir_path: biobb_wf_structure_checking
  can_write_console_log: False

step0_structure_check_init:
  tool: structure_check
  paths:
    input_structure_path: /data/structure.pdb
    output_summary_path: structure.report.json

step1_extract_model:
  tool: extract_model
  paths:
    input_structure_path: /data/structure.pdb
    output_structure_path: structure.models.pdb
  properties:
    models: [ 1 ]

step2_extract_chain:
  tool: extract_chain
  paths:
    input_structure_path: dependency/step1_extract_model/output_structure_path
    output_structure_path: structure.chains.pdb
  properties:
    chains: [ A ]

step3_fix_altlocs:
  tool: fix_altlocs
  paths:
    input_pdb_path: dependency/step2_extract_chain/output_structure_path
    output_pdb_path: structure.altloc.pdb
  properties:
    altlocs: [ 'A45:A', 'A67:A', 'A85:A' ]

step4_fix_ssbonds:
  tool: fix_ssbonds
  paths:
    input_pdb_path: dependency/step3_fix_altlocs/output_pdb_path
    output_pdb_path: structure.ssbonds.pdb

step5_remove_molecules_ions:
  tool: remove_molecules
  paths:
    input_structure_path: dependency/step4_fix_ssbonds/output_pdb_path
    output_molecules_path: structure.metals.pdb
  properties:
    molecules: [ name: ZN ]

step6_remove_molecules_ligands:
  tool: remove_molecules
  paths:
    input_structure_path: dependency/step5_remove_molecules_ions/output_molecules_path
    output_molecules_path: structure.ligands.pdb
  properties:
    molecules: [ name: SO4, name: AP5 ]

step7_reduce_remove_hydrogens:
  tool: reduce_remove_hydrogens
  paths:
    input_path: dependency/step6_remove_molecules_ligands/output_molecules_path
    output_path: structure.hydrogens.pdb

step8_remove_pdb_water:
  tool: remove_pdb_water
  paths:
    input_pdb_path: dependency/step7_reduce_remove_hydrogens/output_path
    output_pdb_path: structure.water.pdb

step9_fix_amides:
  tool: fix_amides
  paths:
    input_pdb_path: dependency/step8_remove_pdb_water/output_pdb_path
    output_pdb_path: structure.amides.pdb

step10_fix_chirality:
  tool: fix_chirality
  paths:
    input_pdb_path: dependency/step9_fix_amides/output_pdb_path
    output_pdb_path: structure.chiral.pdb

step11_fix_side_chain:
  tool: fix_side_chain
  paths:
    input_pdb_path: dependency/step10_fix_chirality/output_pdb_path
    output_pdb_path: structure.sidechains.pdb

step12_fix_backbone:
  tool: fix_backbone
  paths:
    input_pdb_path: dependency/step11_fix_side_chain/output_pdb_path
    input_fasta_canonical_sequence_path: /data/sequence.fasta
    output_pdb_path: structure.backbone.pdb

step13_leap_gen_top:
  tool: leap_gen_top
  paths:
    input_pdb_path: dependency/step12_fix_backbone/output_pdb_path
    output_pdb_path: structure.amber.pdb
    output_top_path: structure.amber.top
    output_crd_path: structure.amber.crd
  properties:
    forcefield: [ protein.ff14SB ]

step14_sander_mdrun:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step13_leap_gen_top/output_top_path
    input_crd_path: dependency/step13_leap_gen_top/output_crd_path
    output_traj_path: structure.trj.crd
    output_rst_path: structure.trj.rst
    output_log_path: structure.trj.log
  properties:
    simulation_type: minimization
    mdin:
      ntb : 0
      cut : 12
      maxcyc : 500
      ncyc : 50 
      ntwx : 50

step15_amber_to_pdb:
  tool: amber_to_pdb
  paths:
    input_top_path: dependency/step13_leap_gen_top/output_top_path
    input_crd_path: dependency/step14_sander_mdrun/output_rst_path
    output_pdb_path: structure.amber-min.pdb

step16_fix_pdb:
  tool: fix_pdb
  paths:
    input_pdb_path: dependency/step15_amber_to_pdb/output_pdb_path
    output_pdb_path: structure.final.pdb

step17_structure_check:
  tool: structure_check
  paths:
    input_structure_path: dependency/step16_fix_pdb/output_pdb_path
    output_summary_path: structure.report_final.json