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BioBB HADDOCK Command Line Help

Generic usage:

biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>

Em_ref

Wrapper class for the Haddock EMRef module.

Get help

Command:

em_ref -h
/bin/sh: em_ref: command not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_haddock_wf_data_zip (string): Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: ZIP
  • refinement_output_zip_path (string): Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: ZIP
  • restraints_table_path (string): Path to the input TBL file containing a list of restraints for docking. File type: input. Sample file. Accepted formats: TBL
  • output_haddock_wf_data_zip (string): Path to the output zipball containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: ZIP
  • haddock_config_path (string): Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: CFG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • cfg (object): ({}) Haddock configuration options specification..
  • binary_path (string): (haddock) Path to the haddock haddock executable binary..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..
  • container_path (string): (None) Path to the binary executable of your container..
  • container_image (string): (None) Container Image identifier..
  • container_volume_path (string): (/data) Path to an internal directory in the container..
  • container_working_dir (string): (None) Path to the internal CWD in the container..
  • container_user_id (string): (None) User number id to be mapped inside the container..
  • container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file

properties:
  remove_tmp: false

Command line

em_ref --config config_em_ref.yml --input_haddock_wf_data_zip haddock_wf_data_topology.zip --refinement_output_zip_path ref_rigidbody.zip --restraints_table_path e2a-hpr_air.tbl --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

JSON

Common config file

{
  "properties": {
    "remove_tmp": false
  }
}

Command line

em_ref --config config_em_ref.json --input_haddock_wf_data_zip haddock_wf_data_topology.zip --refinement_output_zip_path ref_rigidbody.zip --restraints_table_path e2a-hpr_air.tbl --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

Sele_top

Wrapper class for the Haddock SeleTop module https://www.bonvinlab.org/haddock3/modules/analysis/seletop.html

Get help

Command:

sele_top -h
/bin/sh: sele_top: command not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_haddock_wf_data_zip (string): Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: ZIP
  • output_selection_zip_path (string): Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: ZIP
  • output_haddock_wf_data_zip (string): Path to the output zipball containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: ZIP
  • haddock_config_path (string): Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: CFG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • cfg (object): ({}) Haddock configuration options specification..
  • binary_path (string): (haddock) Path to the haddock haddock executable binary..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..
  • container_path (string): (None) Path to the binary executable of your container..
  • container_image (string): (None) Container Image identifier..
  • container_volume_path (string): (/data) Path to an internal directory in the container..
  • container_working_dir (string): (None) Path to the internal CWD in the container..
  • container_user_id (string): (None) User number id to be mapped inside the container..
  • container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file

properties:
  remove_tmp: false

Command line

sele_top --config config_sele_top.yml --input_haddock_wf_data_zip haddock_wf_data_rigid.zip --output_selection_zip_path ref_seletop.zip --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

JSON

Common config file

{
  "properties": {
    "remove_tmp": false
  }
}

Command line

sele_top --config config_sele_top.json --input_haddock_wf_data_zip haddock_wf_data_rigid.zip --output_selection_zip_path ref_seletop.zip --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

Sele_top_clusts

Wrapper class for the Haddock SeleTopClusts module https://www.bonvinlab.org/haddock3/modules/analysis/seletopclusts.html.

Get help

Command:

sele_top_clusts -h
/bin/sh: sele_top_clusts: command not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_haddock_wf_data_zip (string): Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: ZIP
  • output_selection_zip_path (string): Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: ZIP
  • output_haddock_wf_data_zip (string): Path to the output zipball containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: ZIP
  • haddock_config_path (string): Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: CFG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • cfg (object): ({}) Haddock configuration options specification..
  • binary_path (string): (haddock) Path to the haddock haddock executable binary..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..
  • container_path (string): (None) Path to the binary executable of your container..
  • container_image (string): (None) Container Image identifier..
  • container_volume_path (string): (/data) Path to an internal directory in the container..
  • container_working_dir (string): (None) Path to the internal CWD in the container..
  • container_user_id (string): (None) User number id to be mapped inside the container..
  • container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file

properties:
  remove_tmp: false

Command line

sele_top_clusts --config config_sele_top_clusts.yml --input_haddock_wf_data_zip haddock_wf_data_rigid.zip --output_selection_zip_path ref_seletop.zip --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

JSON

Common config file

{
  "properties": {
    "remove_tmp": false
  }
}

Command line

sele_top_clusts --config config_sele_top_clusts.json --input_haddock_wf_data_zip haddock_wf_data_rigid.zip --output_selection_zip_path ref_seletop.zip --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

Capri_eval

Wrapper class for the Haddock CapriEval module.

Get help

Command:

capri_eval -h
/bin/sh: capri_eval: command not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_haddock_wf_data_zip (string): Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: ZIP
  • output_evaluation_zip_path (string): Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: ZIP
  • reference_pdb_path (string): Path to the input PDB file containing an structure for reference. File type: input. Sample file. Accepted formats: PDB
  • output_haddock_wf_data_zip (string): Path to the output zipball containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: ZIP
  • haddock_config_path (string): Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: CFG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • cfg (object): ({}) Haddock configuration options specification..
  • binary_path (string): (haddock) Path to the haddock haddock executable binary..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..
  • container_path (string): (None) Path to the binary executable of your container..
  • container_image (string): (None) Container Image identifier..
  • container_volume_path (string): (/data) Path to an internal directory in the container..
  • container_working_dir (string): (None) Path to the internal CWD in the container..
  • container_user_id (string): (None) User number id to be mapped inside the container..
  • container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file

properties:
  remove_tmp: false

Command line

capri_eval --config config_capri_eval.yml --input_haddock_wf_data_zip haddock_wf_data_rigid.zip --output_evaluation_zip_path ref_caprieval.zip --reference_pdb_path e2a-hpr_1GGR.pdb --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

JSON

Common config file

{
  "properties": {
    "remove_tmp": false
  }
}

Command line

capri_eval --config config_capri_eval.json --input_haddock_wf_data_zip haddock_wf_data_rigid.zip --output_evaluation_zip_path ref_caprieval.zip --reference_pdb_path e2a-hpr_1GGR.pdb --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

Flex_ref

Wrapper class for the Haddock FlexRef module.

Get help

Command:

flex_ref -h
/bin/sh: flex_ref: command not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_haddock_wf_data_zip (string): Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: ZIP
  • refinement_output_zip_path (string): Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: ZIP
  • restraints_table_path (string): Path to the input TBL file containing a list of restraints for docking. File type: input. Sample file. Accepted formats: TBL
  • output_haddock_wf_data_zip (string): Path to the output zipball containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: ZIP
  • haddock_config_path (string): Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: CFG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • cfg (object): ({}) Haddock configuration options specification..
  • binary_path (string): (haddock) Path to the haddock haddock executable binary..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..
  • container_path (string): (None) Path to the binary executable of your container..
  • container_image (string): (None) Container Image identifier..
  • container_volume_path (string): (/data) Path to an internal directory in the container..
  • container_working_dir (string): (None) Path to the internal CWD in the container..
  • container_user_id (string): (None) User number id to be mapped inside the container..
  • container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file

properties:
  remove_tmp: false

Command line

flex_ref --config config_flex_ref.yml --input_haddock_wf_data_zip haddock_wf_data_topology.zip --refinement_output_zip_path ref_rigidbody.zip --restraints_table_path e2a-hpr_air.tbl --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

JSON

Common config file

{
  "properties": {
    "remove_tmp": false
  }
}

Command line

flex_ref --config config_flex_ref.json --input_haddock_wf_data_zip haddock_wf_data_topology.zip --refinement_output_zip_path ref_rigidbody.zip --restraints_table_path e2a-hpr_air.tbl --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

Rigid_body

Wrapper class for the Haddock RigidBody module.

Get help

Command:

rigid_body -h
/bin/sh: rigid_body: command not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_haddock_wf_data_zip (string): Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: ZIP
  • docking_output_zip_path (string): Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: ZIP
  • ambig_restraints_table_path (string): Path to the input TBL file containing a list of ambiguous restraints for docking. File type: input. Sample file. Accepted formats: TBL
  • unambig_restraints_table_path (string): Path to the input TBL file containing a list of unambiguous restraints for docking. File type: input. Sample file. Accepted formats: TBL
  • hb_restraints_table_path (string): Path to the input TBL file containing a list of hydrogen bond restraints for docking. File type: input. Sample file. Accepted formats: TBL
  • output_haddock_wf_data_zip (string): Path to the output zipball containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: ZIP
  • haddock_config_path (string): Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: CFG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • cfg (object): ({}) Haddock configuration options specification..
  • binary_path (string): (haddock) Path to the haddock haddock executable binary..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..
  • container_path (string): (None) Path to the binary executable of your container..
  • container_image (string): (None) Container Image identifier..
  • container_volume_path (string): (/data) Path to an internal directory in the container..
  • container_working_dir (string): (None) Path to the internal CWD in the container..
  • container_user_id (string): (None) User number id to be mapped inside the container..
  • container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file

properties:
  remove_tmp: false

Command line

rigid_body --config config_rigid_body.yml --input_haddock_wf_data_zip haddock_wf_data_topology.zip --docking_output_zip_path ref_rigidbody.zip --ambig_restraints_table_path e2a-hpr_air.tbl --unambig_restraints_table_path e2a-hpr_air.tbl --hb_restraints_table_path e2a-hpr_air.tbl --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

JSON

Common config file

{
  "properties": {
    "remove_tmp": false
  }
}

Command line

rigid_body --config config_rigid_body.json --input_haddock_wf_data_zip haddock_wf_data_topology.zip --docking_output_zip_path ref_rigidbody.zip --ambig_restraints_table_path e2a-hpr_air.tbl --unambig_restraints_table_path e2a-hpr_air.tbl --hb_restraints_table_path e2a-hpr_air.tbl --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

Topology

Wrapper class for the Haddock Topology module.

Get help

Command:

topology -h
/bin/sh: topology: command not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • mol1_input_pdb_path (string): Path to the input PDB file. File type: input. Sample file. Accepted formats: PDB
  • mol1_output_top_zip_path (string): Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: ZIP
  • mol2_input_pdb_path (string): Path to the input PDB file. File type: input. Sample file. Accepted formats: PDB
  • mol2_output_top_zip_path (string): Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: ZIP
  • output_haddock_wf_data_zip (string): Path to the output zipball containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: ZIP
  • haddock_config_path (string): Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: CFG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • cfg (object): ({}) Haddock configuration options specification..
  • binary_path (string): (haddock) Path to the haddock haddock executable binary..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..
  • container_path (string): (None) Path to the binary executable of your container..
  • container_image (string): (None) Container Image identifier..
  • container_volume_path (string): (/data) Path to an internal directory in the container..
  • container_working_dir (string): (None) Path to the internal CWD in the container..
  • container_user_id (string): (None) User number id to be mapped inside the container..
  • container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file

properties:
  remove_tmp: false

Command line

topology --config config_topology.yml --mol1_input_pdb_path e2aP_1F3G.pdb --mol1_output_top_zip_path ref_mol1_top.zip --mol2_input_pdb_path hpr_ensemble.pdb --mol2_output_top_zip_path ref_mol2_top.zip --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

JSON

Common config file

{
  "properties": {
    "remove_tmp": false
  }
}

Command line

topology --config config_topology.json --mol1_input_pdb_path e2aP_1F3G.pdb --mol1_output_top_zip_path ref_mol1_top.zip --mol2_input_pdb_path hpr_ensemble.pdb --mol2_output_top_zip_path ref_mol2_top.zip --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

Clust_fcc

Wrapper class for the Haddock ClustFCC module.

Get help

Command:

clust_fcc -h
/bin/sh: clust_fcc: command not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_haddock_wf_data_zip (string): Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: ZIP
  • output_cluster_zip_path (string): Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: ZIP
  • output_haddock_wf_data_zip (string): Path to the output zipball containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: ZIP
  • haddock_config_path (string): Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: CFG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • cfg (object): ({}) Haddock configuration options specification..
  • binary_path (string): (haddock) Path to the haddock haddock executable binary..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..
  • container_path (string): (None) Path to the binary executable of your container..
  • container_image (string): (None) Container Image identifier..
  • container_volume_path (string): (/data) Path to an internal directory in the container..
  • container_working_dir (string): (None) Path to the internal CWD in the container..
  • container_user_id (string): (None) User number id to be mapped inside the container..
  • container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file

properties:
  remove_tmp: false

Command line

clust_fcc --config config_clust_fcc.yml --input_haddock_wf_data_zip haddock_wf_data_rigid.zip --output_cluster_zip_path ref_clustfcc.zip --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg

JSON

Common config file

{
  "properties": {
    "remove_tmp": false
  }
}

Command line

clust_fcc --config config_clust_fcc.json --input_haddock_wf_data_zip haddock_wf_data_rigid.zip --output_cluster_zip_path ref_clustfcc.zip --output_haddock_wf_data_zip ref_topology.zip --haddock_config_path configuration.cfg