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workflow.yml
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workflow.yml
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working_dir_path: biobb_wf_flexserv
can_write_console_log: False
step0_extract_atoms:
tool: extract_atoms
paths:
input_structure_path: /path/to/inputs/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: /path/to/inputs/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: /path/to/inputs/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: /path/to/inputs/Files/1a32.MoDEL.pcz
output_json_path: simIndex_bd_report_nma_vs_md.json