global_properties:
  working_dir_path: biobb_wf_flexserv
  can_write_console_log: False

step0_extract_atoms:
  tool: extract_atoms
  paths:
    input_structure_path: /data/structure.pdb
    output_structure_path: structure_ca.pdb
  properties:
    regular_expression_pattern: "^CA"

step1_bd_run:
  tool: bd_run
  paths:
    input_pdb_path: dependency/step0_extract_atoms/output_structure_path
    output_crd_path: bd_ensemble.mdcrd
    output_log_path: bd_ensemble.log
  properties:
    binary_path: bd
    time: 10000
    wfreq: 100

step2_cpptraj_rms:
  tool: cpptraj_rms
  paths:
    input_top_path: dependency/step0_extract_atoms/output_structure_path
    input_traj_path: dependency/step1_bd_run/output_crd_path
    output_cpptraj_path: bd_ensemble_rmsd.dat
    output_traj_path: bd_ensemble.dcd
    input_exp_path: dependency/step0_extract_atoms/output_structure_path
  properties:
    start: 1
    end: -1
    steps: 1
    mask: c-alpha
    reference: experimental

step3_dmd_run:
  tool: dmd_run
  paths:
    input_pdb_path: dependency/step0_extract_atoms/output_structure_path
    output_crd_path: dmd_ensemble.mdcrd
    output_log_path: dmd_ensemble.log

step4_cpptraj_rms:
  tool: cpptraj_rms
  paths:
    input_top_path: dependency/step0_extract_atoms/output_structure_path
    input_traj_path: dependency/step3_dmd_run/output_crd_path
    output_cpptraj_path: dmd_ensemble_rmsd.dat
    output_traj_path: dmd_ensemble.dcd
    input_exp_path: dependency/step0_extract_atoms/output_structure_path
  properties:
    start: 1
    end: -1
    steps: 1
    mask: c-alpha
    reference: experimental

step5_nma_run:
  tool: nma_run
  paths:
    input_pdb_path: dependency/step0_extract_atoms/output_structure_path
    output_crd_path: nma_ensemble.mdcrd
    output_log_path: nma_ensemble.log
  properties:
    frames: 50

step6_cpptraj_rms:
  tool: cpptraj_rms
  paths:
    input_top_path: dependency/step0_extract_atoms/output_structure_path
    input_traj_path: dependency/step5_nma_run/output_crd_path
    output_cpptraj_path: nma_ensemble_rmsd.dat
    output_traj_path: nma_ensemble.dcd
    input_exp_path: dependency/step0_extract_atoms/output_structure_path
  properties:
    start: 1
    end: -1
    steps: 1
    mask: c-alpha
    reference: experimental

step7_pcz_zip:
  tool: pcz_zip
  paths:
    input_pdb_path: dependency/step0_extract_atoms/output_structure_path
    input_crd_path: dependency/step1_bd_run/output_crd_path
    output_pcz_path: bd_ensemble.pcz
  properties:
    variance: 90
    neigenv: 10
    gauss_rmsd: True

step8_pcz_zip:
  tool: pcz_zip
  paths:
    input_pdb_path: dependency/step0_extract_atoms/output_structure_path
    input_crd_path: dependency/step3_dmd_run/output_crd_path
    output_pcz_path: dmd_ensemble.pcz
  properties:
    variance: 90
    neigenv: 10
    gauss_rmsd: True

step9_pcz_zip:
  tool: pcz_zip
  paths:
    input_pdb_path: dependency/step0_extract_atoms/output_structure_path
    input_crd_path: dependency/step5_nma_run/output_crd_path
    output_pcz_path: nma_ensemble.pcz
  properties:
    variance: 90
    neigenv: 10
    gauss_rmsd: True

step10_pcz_unzip:
  tool: pcz_unzip
  paths:
    input_pcz_path: dependency/step7_pcz_zip/output_pcz_path
    output_crd_path: bd_ensemble_uncompressed.crd

step11_pcz_unzip:
  tool: pcz_unzip
  paths:
    input_pcz_path: dependency/step8_pcz_zip/output_pcz_path
    output_crd_path: dmd_ensemble_uncompressed.crd

step12_pcz_unzip:
  tool: pcz_unzip
  paths:
    input_pcz_path: dependency/step9_pcz_zip/output_pcz_path
    output_crd_path: nma_ensemble_uncompressed.crd

step13_cpptraj_rms:
  tool: cpptraj_rms
  paths:
    input_top_path: dependency/step0_extract_atoms/output_structure_path
    input_traj_path: dependency/step10_pcz_unzip/output_crd_path
    output_cpptraj_path: bd_ensemble_uncompressed.rmsd.dat
    output_traj_path: bd_ensemble_uncompressed.dcd
    input_exp_path: dependency/step0_extract_atoms/output_structure_path
  properties:
    start: 1
    end: -1
    steps: 1
    mask: c-alpha
    reference: experimental

step14_cpptraj_rms:
  tool: cpptraj_rms
  paths:
    input_top_path: dependency/step0_extract_atoms/output_structure_path
    input_traj_path: dependency/step11_pcz_unzip/output_crd_path
    output_cpptraj_path: dmd_ensemble_uncompressed.rmsd.dat
    output_traj_path: dmd_ensemble_uncompressed.dcd
    input_exp_path: dependency/step0_extract_atoms/output_structure_path
  properties:
    start: 1
    end: -1
    steps: 1
    mask: c-alpha
    reference: experimental

step15_cpptraj_rms:
  tool: cpptraj_rms
  paths:
    input_top_path: dependency/step0_extract_atoms/output_structure_path
    input_traj_path: dependency/step12_pcz_unzip/output_crd_path
    output_cpptraj_path: nma_ensemble_uncompressed.rmsd.dat
    output_traj_path: nma_ensemble_uncompressed.dcd
    input_exp_path: dependency/step0_extract_atoms/output_structure_path
  properties:
    start: 1
    end: -1
    steps: 1
    mask: c-alpha
    reference: experimental

step16_pcz_info:
  tool: pcz_info
  paths:
    input_pcz_path: dependency/step9_pcz_zip/output_pcz_path
    output_json_path: pcz_report.json

step17_pcz_evecs:
  tool: pcz_evecs
  paths:
    input_pcz_path: dependency/step9_pcz_zip/output_pcz_path
    output_json_path: pcz_evecs.json
  properties:
    eigenvector: 1

step18_pcz_animate:
  tool: pcz_animate
  paths:
    input_pcz_path: dependency/step9_pcz_zip/output_pcz_path
    output_crd_path: pcz_proj1.crd
  properties:
    eigenvector: 1

step19_cpptraj_convert:
  tool: cpptraj_convert
  paths:
    input_top_path: dependency/step0_extract_atoms/output_structure_path
    input_traj_path: dependency/step18_pcz_animate/output_crd_path
    output_cpptraj_path: pcz_proj1.dcd
  properties:
    start: 1
    end: -1
    steps: 1
    mask: c-alpha
    format: dcd

step20_pcz_bfactor:
  tool: pcz_bfactor
  paths:
    input_pcz_path: dependency/step9_pcz_zip/output_pcz_path
    output_dat_path: bfactor_all.dat
    output_pdb_path: bfactor_all.pdb
  properties:
    eigenvector: 0
    pdb: True

step21_pcz_hinges:
  tool: pcz_hinges
  paths:
    input_pcz_path: dependency/step7_pcz_zip/output_pcz_path
    output_json_path: hinges_bfactor_report.json
  properties:
    eigenvector: 0
    method: Bfactor_slope

step22_pcz_hinges:
  tool: pcz_hinges
  paths:
    input_pcz_path: dependency/step7_pcz_zip/output_pcz_path
    output_json_path: hinges_dyndom_report.json
  properties:
    eigenvector: 0
    method: Dynamic_domain

step23_pcz_hinges:
  tool: pcz_hinges
  paths:
    input_pcz_path: dependency/step7_pcz_zip/output_pcz_path
    output_json_path: hinges_fcte_report.json
  properties:
    eigenvector: 0
    method: Force_constant

step24_pcz_stiffness:
  tool: pcz_stiffness
  paths:
    input_pcz_path: dependency/step9_pcz_zip/output_pcz_path
    output_json_path: pcz_stiffness.json
  properties:
    eigenvector: 0

step25_pcz_collectivity:
  tool: pcz_collectivity
  paths:
    input_pcz_path: dependency/step9_pcz_zip/output_pcz_path
    output_json_path: pcz_collectivity.json
  properties:
    eigenvector: 0

step26_pcz_similarity:
  tool: pcz_similarity
  paths:
    input_pcz_path1: dependency/step7_pcz_zip/output_pcz_path
    input_pcz_path2: /data/Files/1a32.MoDEL.pcz
    output_json_path: simIndex_bd_report_bd_vs_md.json

step27_pcz_similarity:
  tool: pcz_similarity
  paths:
    input_pcz_path1: dependency/step8_pcz_zip/output_pcz_path
    input_pcz_path2: /data/Files/1a32.MoDEL.pcz
    output_json_path: simIndex_bd_report_dmd_vs_md.json

step28_pcz_similarity:
  tool: pcz_similarity
  paths:
    input_pcz_path1: dependency/step9_pcz_zip/output_pcz_path
    input_pcz_path2: /data/Files/1a32.MoDEL.pcz
    output_json_path: simIndex_bd_report_nma_vs_md.json