BioBB HADDOCK Command Line Help

Generic usage:

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

Capri_eval

Wrapper class for the HADDOCK3 CapriEval module.

Get help

Command:

capri_eval -h

usage: capri_eval [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--output_evaluation_zip_path OUTPUT_EVALUATION_ZIP_PATH] [--reference_pdb_path REFERENCE_PDB_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the HADDOCK3 CapriEval module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_haddock_wf_data INPUT_HADDOCK_WF_DATA
                        Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip.
  --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip.

optional arguments:
  --output_evaluation_zip_path OUTPUT_EVALUATION_ZIP_PATH
                        Path to the output PDB file collection in zip format. Accepted formats: zip.
  --reference_pdb_path REFERENCE_PDB_PATH
                        Path to the input PDB file containing an structure for reference. Accepted formats: pdb.
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_haddock_wf_data (dir): Path to the input directory containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: DIRECTORY, ZIP
output_haddock_wf_data (dir): Path to the output directory containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: DIRECTORY, 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
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..
global_cfg (object): ({’postprocess’: True}) Global 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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 haddock_wf_data_rigid.zip --output_haddock_wf_data haddock_wf_data_caprieval.zip --output_evaluation_zip_path ref_caprieval.zip --reference_pdb_path e2a-hpr_1GGR.pdb --haddock_config_path run.cfg

JSON

Common config file 

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

Command line

capri_eval --config config_capri_eval.json --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data haddock_wf_data_caprieval.zip --output_evaluation_zip_path ref_caprieval.zip --reference_pdb_path e2a-hpr_1GGR.pdb --haddock_config_path run.cfg

Clust_fcc

Wrapper class for the HADDOCK3 ClustFCC module.

Get help

Command:

clust_fcc -h

usage: clust_fcc [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--output_cluster_zip_path OUTPUT_CLUSTER_ZIP_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the HADDOCK3 ClustFCC module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_haddock_wf_data INPUT_HADDOCK_WF_DATA
                        Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip.
  --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip.

optional arguments:
  --output_cluster_zip_path OUTPUT_CLUSTER_ZIP_PATH
                        Path to the output PDB file collection in zip format. Accepted formats: zip.
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_haddock_wf_data (dir): Path to the input directory containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: DIRECTORY, ZIP
output_haddock_wf_data (dir): Path to the output directory containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: DIRECTORY, ZIP
output_cluster_zip_path (string): Path to the output PDB file collection in zip format. 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..
global_cfg (object): ({’postprocess’: False}) Global 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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 haddock_wf_data_rigid.zip --output_haddock_wf_data haddock_wf_data_clustfcc.zip --output_cluster_zip_path ref_clustfcc.zip --haddock_config_path run.cfg

JSON

Common config file 

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

Command line

clust_fcc --config config_clust_fcc.json --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data haddock_wf_data_clustfcc.zip --output_cluster_zip_path ref_clustfcc.zip --haddock_config_path run.cfg

Contact_map

Wrapper class for the HADDOCK3 ContactMap module.

Get help

Command:

contact_map -h

usage: contact_map [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--output_contactmap_zip_path OUTPUT_CONTACTMAP_ZIP_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the HADDOCK3 ContactMap module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_haddock_wf_data INPUT_HADDOCK_WF_DATA
                        Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip.
  --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip.

optional arguments:
  --output_contactmap_zip_path OUTPUT_CONTACTMAP_ZIP_PATH
                        Path to the output contact map files in zip format. Accepted formats: zip.
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_haddock_wf_data (dir): Path to the input directory containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: DIRECTORY, ZIP
output_haddock_wf_data (dir): Path to the output directory containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: DIRECTORY, ZIP
output_contactmap_zip_path (string): Path to the output contact map files in zip format. 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..
global_cfg (object): ({’postprocess’: False}) Global 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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

contact_map --config config_contact_map.yml --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_contactmap_zip_path ref_contact_map.zip --haddock_config_path run.cfg

JSON

Common config file 

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

Command line

contact_map --config config_contact_map.json --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_contactmap_zip_path ref_contact_map.zip --haddock_config_path run.cfg

Em_ref

Wrapper class for the HADDOCK3 EMRef module.

Get help

Command:

em_ref -h

usage: em_ref [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH] [--ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH] [--unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH] [--hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the HADDOCK3 EMRef module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_haddock_wf_data INPUT_HADDOCK_WF_DATA
                        Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip.
  --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip.

optional arguments:
  --refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH
                        Path to the output PDB file collection in zip format. Accepted formats: zip.
  --ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH
                        Path to the input TBL file containing a list of ambiguous restraints for docking. Accepted formats: tbl.
  --unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH
                        Path to the input TBL file containing a list of unambiguous restraints for docking. Accepted formats: tbl.
  --hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH
                        Path to the input TBL file containing a list of hydrogen bond restraints for docking. Accepted formats: tbl.
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_haddock_wf_data (dir): Path to the input directory containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: DIRECTORY, ZIP
output_haddock_wf_data (dir): Path to the output directory containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: DIRECTORY, ZIP
refinement_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
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..
global_cfg (object): ({’postprocess’: False}) Global 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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 haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --refinement_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 --haddock_config_path run.cfg

JSON

Common config file 

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

Command line

em_ref --config config_em_ref.json --input_haddock_wf_data haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --refinement_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 --haddock_config_path run.cfg

Flex_ref

Wrapper class for the HADDOCK3 FlexRef module.

Get help

Command:

flex_ref -h

usage: flex_ref [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH] [--ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH] [--unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH] [--hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the HADDOCK3 FlexRef module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_haddock_wf_data INPUT_HADDOCK_WF_DATA
                        Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip.
  --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip.

optional arguments:
  --refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH
                        Path to the output PDB file collection in zip format. Accepted formats: zip.
  --ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH
                        Path to the input TBL file containing a list of ambiguous restraints for docking. Accepted formats: tbl.
  --unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH
                        Path to the input TBL file containing a list of unambiguous restraints for docking. Accepted formats: tbl.
  --hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH
                        Path to the input TBL file containing a list of hydrogen bond restraints for docking. Accepted formats: tbl.
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_haddock_wf_data (dir): Path to the input directory containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: DIRECTORY, ZIP
output_haddock_wf_data (dir): Path to the output directory containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: DIRECTORY, ZIP
refinement_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
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..
global_cfg (object): ({’postprocess’: False}) Global 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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 haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --refinement_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 --haddock_config_path run.cfg

JSON

Common config file 

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

Command line

flex_ref --config config_flex_ref.json --input_haddock_wf_data haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --refinement_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 --haddock_config_path run.cfg

Haddock3_accessibility

Wrapper class for the Haddock-Restraints Accessibility module.

Get help

Command:

haddock3_accessibility -h

usage: haddock3_accessibility [-h] [-c CONFIG] -i INPUT_PDB_PATH --output_accessibility_path OUTPUT_ACCESSIBILITY_PATH [--output_actpass_path OUTPUT_ACTPASS_PATH]

Wrapper of the Haddock-Restraints Accessibility module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  -i INPUT_PDB_PATH, --input_pdb_path INPUT_PDB_PATH
                        Path to the input PDB file. Accepted formats: pdb.
  --output_accessibility_path OUTPUT_ACCESSIBILITY_PATH
                        Path to the output file with accessibility information. Accepted formats: txt, dat, out.

optional arguments:
  --output_actpass_path OUTPUT_ACTPASS_PATH
                        Path to the output file with active/passive residues to be used as haddock3 restraint information. Accepted formats: txt, dat, out.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pdb_path (string): Path to the input PDB file. File type: input. Sample file. Accepted formats: PDB
output_accessibility_path (string): Path to the output file with accessibility information. File type: output. Sample file. Accepted formats: TXT, DAT, OUT
output_actpass_path (string): Path to the output file with active/passive residues to be used as haddock3 restraint information. File type: output. Sample file. Accepted formats: TXT, DAT, OUT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

chain (string): (A) Chain to be used from the input PDB file..
cutoff (number): (0.4) Relative cutoff for sidechain accessibility..
probe_radius (number): (1.4) Probe radius for the accessibility calculation..
pass_to_act (boolean): (False) If True, the passive residues become active in the actpass file and vice versa..
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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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

haddock3_accessibility --config config_haddock3_accessibility.yml --input_pdb_path e2aP_1F3G_noH.pdb --output_accessibility_path mol1_sasa.txt --output_actpass_path mol1_haddock_actpass.txt

JSON

Common config file 

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

Command line

haddock3_accessibility --config config_haddock3_accessibility.json --input_pdb_path e2aP_1F3G_noH.pdb --output_accessibility_path mol1_sasa.txt --output_actpass_path mol1_haddock_actpass.txt

Haddock3_actpass_to_ambig

Wrapper class for the Haddock-Restraints active_passive_to_ambig module.

Get help

Command:

haddock3_actpass_to_ambig -h

usage: haddock3_actpass_to_ambig [-h] [-c CONFIG] --input_actpass1_path INPUT_ACTPASS1_PATH --input_actpass2_path INPUT_ACTPASS2_PATH -o OUTPUT_TBL_PATH

Wrapper of the Haddock-Restraints active_passive_to_ambig module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_actpass1_path INPUT_ACTPASS1_PATH
                        Path to the first input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. Accepted formats: txt, dat, in, pass.
  --input_actpass2_path INPUT_ACTPASS2_PATH
                        Path to the second input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. Accepted formats: txt, dat, in, pass.
  -o OUTPUT_TBL_PATH, --output_tbl_path OUTPUT_TBL_PATH
                        Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. Accepted formats: tbl, txt, out.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_actpass1_path (string): Path to the first input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. Sample file. Accepted formats: TXT, DAT, IN, PASS
input_actpass2_path (string): Path to the second input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. Sample file. Accepted formats: TXT, DAT, IN, PASS
output_tbl_path (string): Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. File type: output. Sample file. Accepted formats: TBL, TXT, OUT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

pass_to_act (boolean): (False) Path to the haddock haddock executable binary..
segid_one (string): (None) Segid of the first model..
segid_two (string): (None) Segid of the second model..
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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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

haddock3_actpass_to_ambig --config config_haddock3_actpass_to_ambig.yml --input_actpass1_path haddock_actpass1.pass --input_actpass2_path haddock_actpass2.pass --output_tbl_path haddock_actpass.tbl

JSON

Common config file 

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

Command line

haddock3_actpass_to_ambig --config config_haddock3_actpass_to_ambig.json --input_actpass1_path haddock_actpass1.pass --input_actpass2_path haddock_actpass2.pass --output_tbl_path haddock_actpass.tbl

Haddock3_extend

Wrapper class for the HADDOCK3 extend module.

Get help

Command:

haddock3_extend -h

usage: haddock3_extend [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --haddock_config_path HADDOCK_CONFIG_PATH -o OUTPUT_HADDOCK_WF_DATA

Wrapper of the HADDOCK3 Haddock3Extend module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_haddock_wf_data INPUT_HADDOCK_WF_DATA
                        Path to the input zipball containing all the current Haddock workflow data. Accepted formats: zip.
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.
  -o OUTPUT_HADDOCK_WF_DATA, --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output zipball containing all the current Haddock workflow data. Accepted formats: zip.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_haddock_wf_data (dir): Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: ZIP
haddock_config_path (string): Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: CFG
output_haddock_wf_data (dir): Path to the output zipball containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: ZIP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

cfg (object): ({}) Haddock configuration options specification..
global_cfg (object): ({’postprocess’: True}) Global 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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

haddock3_extend --config config_haddock3_extend.yml --input_haddock_wf_data haddock_wf_data_caprieval.zip --haddock_config_path run.cfg --output_haddock_wf_data ref_haddock3_extend.zip

JSON

Common config file 

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

Command line

haddock3_extend --config config_haddock3_extend.json --input_haddock_wf_data haddock_wf_data_caprieval.zip --haddock_config_path run.cfg --output_haddock_wf_data ref_haddock3_extend.zip

Haddock3_passive_from_active

Wrapper class for the Haddock3-Restraints passive_from_active module.

Get help

Command:

haddock3_passive_from_active -h

usage: haddock3_passive_from_active [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH -o OUTPUT_ACTPASS_PATH [--input_active_list_path INPUT_ACTIVE_LIST_PATH]

Wrapper of the Haddock3-Restraints passive_from_active module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Path to the input PDB structure file. Accepted formats: pdb.
  -o OUTPUT_ACTPASS_PATH, --output_actpass_path OUTPUT_ACTPASS_PATH
                        Path to the output file with list of passive residues. Accepted formats: txt, dat, list, out.

optional arguments:
  --input_active_list_path INPUT_ACTIVE_LIST_PATH
                        Path to the input file with list of active residues. Accepted formats: txt, dat, list.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pdb_path (string): Path to the input PDB structure file. File type: input. Sample file. Accepted formats: PDB
output_actpass_path (string): Path to the output file with list of passive residues. File type: output. Sample file. Accepted formats: TXT, DAT, LIST, OUT
input_active_list_path (string): Path to the input file with list of active residues. File type: input. Sample file. Accepted formats: TXT, DAT, LIST

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

active_list (string): () List of active residues as a comma-separated string. Required if input_active_list_path is not provided..
chain_id (string): (None) Chain ID to consider when calculating passive residues..
surface_list_path (string): () Path to file with list of surface residues to filter..
radius (number): (6.5) Radius in Angstroms to look for surface residues around active ones..
binary_path (string): (haddock3-restraints) Path to the haddock3-restraints executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
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:
  active_list: 27,73,83,87
  remove_tmp: false

Command line

haddock3_passive_from_active --config config_haddock3_passive_from_active.yml --input_pdb_path 1A2P_ch.pdb --output_actpass_path 1A2P_manual_actpass.txt --input_active_list_path input.txt

JSON

Common config file 

{
  "properties": {
    "remove_tmp": false,
    "active_list": "27,73,83,87"
  }
}

Command line

haddock3_passive_from_active --config config_haddock3_passive_from_active.json --input_pdb_path 1A2P_ch.pdb --output_actpass_path 1A2P_manual_actpass.txt --input_active_list_path input.txt

Haddock3_restrain_bodies

Wrapper class for the Haddock-Restraints restrain_bodies module.

Get help

Command:

haddock3_restrain_bodies -h

usage: haddock3_restrain_bodies [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_TBL_PATH

Wrapper of the HADDOCK3 restrain_bodies module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Path to the input PDB structure to be restrained. Accepted formats: pdb.
  -o OUTPUT_TBL_PATH, --output_tbl_path OUTPUT_TBL_PATH
                        Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. Accepted formats: tbl, txt, out.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Path to the input PDB structure to be restrained. File type: input. Sample file. Accepted formats: PDB
output_tbl_path (string): Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. File type: output. Sample file. Accepted formats: TBL, TXT, OUT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

exclude (string): (None) Chains to exclude from the calculation..
verbose (integer): (0) Tune verbosity of the output..
binary_path (string): (haddock3-restraints) Path to the HADDOCK3 restraints executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
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

haddock3_restrain_bodies --config config_haddock3_restrain_bodies.yml --input_structure_path 4G6K_clean.pdb --output_tbl_path antibody-unambig.tbl

JSON

Common config file 

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

Command line

haddock3_restrain_bodies --config config_haddock3_restrain_bodies.json --input_structure_path 4G6K_clean.pdb --output_tbl_path antibody-unambig.tbl

Haddock3_run

Wrapper class for the HADDOCK3 Run module.

Get help

Command:

haddock3_run -h

usage: haddock3_run [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA -o OUTPUT_HADDOCK_WF_DATA [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the HADDOCK3 Haddock3Run module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_haddock_wf_data INPUT_HADDOCK_WF_DATA
                        Input folder containing all the files defined in the config. Accepted formats: directory, zip.
  -o OUTPUT_HADDOCK_WF_DATA, --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output zipball containing all the current Haddock workflow data. Accepted formats: directory, zip.

optional arguments:
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_haddock_wf_data (dir): Input folder containing all the files defined in the config. File type: input. Sample file. Accepted formats: DIRECTORY, ZIP
output_haddock_wf_data (dir): Path to the output zipball containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: DIRECTORY, 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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

haddock3_run --config config_haddock3_run.yml --input_haddock_wf_data haddock_wf_data_run.zip --output_haddock_wf_data output.directory --haddock_config_path run.cfg

JSON

Common config file 

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

Command line

haddock3_run --config config_haddock3_run.json --input_haddock_wf_data haddock_wf_data_run.zip --output_haddock_wf_data output.directory --haddock_config_path run.cfg

Rigid_body

Wrapper class for the HADDOCK3 RigidBody module.

Get help

Command:

rigid_body -h

usage: rigid_body [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA --docking_output_zip_path DOCKING_OUTPUT_ZIP_PATH [--ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH] [--unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH] [--hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the HADDOCK3 RigidBody module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_haddock_wf_data INPUT_HADDOCK_WF_DATA
                        Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip.
  --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip.
  --docking_output_zip_path DOCKING_OUTPUT_ZIP_PATH
                        Path to the output PDB file collection in zip format. Accepted formats: zip.

optional arguments:
  --ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH
                        Path to the input TBL file containing a list of ambiguous restraints for docking. Accepted formats: tbl.
  --unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH
                        Path to the input TBL file containing a list of unambiguous restraints for docking. Accepted formats: tbl.
  --hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH
                        Path to the input TBL file containing a list of hydrogen bond restraints for docking. Accepted formats: tbl.
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_haddock_wf_data (dir): Path to the input directory containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: DIRECTORY, ZIP
output_haddock_wf_data (dir): Path to the output directory containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: DIRECTORY, 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
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..
global_cfg (object): ({’postprocess’: False}) Global 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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 haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --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 --haddock_config_path run.cfg

JSON

Common config file 

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

Command line

rigid_body --config config_rigid_body.json --input_haddock_wf_data haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --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 --haddock_config_path run.cfg

Sele_top

Wrapper class for the HADDOCK3 SeleTop module.

Get help

Command:

sele_top -h

usage: sele_top [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the HADDOCK3 SeleTop module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_haddock_wf_data INPUT_HADDOCK_WF_DATA
                        Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip.
  --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip.

optional arguments:
  --output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH
                        Path to the output PDB file collection in zip format. Accepted formats: zip.
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_haddock_wf_data (dir): Path to the input directory containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: DIRECTORY, ZIP
output_haddock_wf_data (dir): Path to the output directory containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: DIRECTORY, ZIP
output_selection_zip_path (string): Path to the output PDB file collection in zip format. 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..
global_cfg (object): ({’postprocess’: False}) Global 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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 haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_selection_zip_path ref_seletop.zip --haddock_config_path run.cfg

JSON

Common config file 

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

Command line

sele_top --config config_sele_top.json --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_selection_zip_path ref_seletop.zip --haddock_config_path run.cfg

Sele_top_clusts

Wrapper class for the HADDOCK3 SeleTopClusts module.

Get help

Command:

sele_top_clusts -h

usage: sele_top_clusts [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the HADDOCK3 SeleTopClusts module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_haddock_wf_data INPUT_HADDOCK_WF_DATA
                        Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip.
  --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip.

optional arguments:
  --output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH
                        Path to the output PDB file collection in zip format. Accepted formats: zip.
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_haddock_wf_data (dir): Path to the input directory containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: DIRECTORY, ZIP
output_haddock_wf_data (dir): Path to the output directory containing all the current Haddock workflow data. File type: output. Sample file. Accepted formats: DIRECTORY, ZIP
output_selection_zip_path (string): Path to the output PDB file collection in zip format. 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..
global_cfg (object): ({’postprocess’: False}) Global 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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 haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_selection_zip_path ref_seletop.zip --haddock_config_path run.cfg

JSON

Common config file 

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

Command line

sele_top_clusts --config config_sele_top_clusts.json --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_selection_zip_path ref_seletop.zip --haddock_config_path run.cfg

Topology

Wrapper class for the HADDOCK3 Topology module.

Get help

Command:

topology -h

usage: topology [-h] [-c CONFIG] --mol1_input_pdb_path MOL1_INPUT_PDB_PATH [--mol1_output_top_zip_path MOL1_OUTPUT_TOP_ZIP_PATH] [--mol2_input_pdb_path MOL2_INPUT_PDB_PATH] [--mol2_output_top_zip_path MOL2_OUTPUT_TOP_ZIP_PATH] --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the HADDOCK3 Topology module.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --mol1_input_pdb_path MOL1_INPUT_PDB_PATH
                        Path to the input PDB file. Accepted formats: pdb.
  --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA
                        Path to the output zipball containing all the current Haddock workflow data. Accepted formats: zip.

optional arguments:
  --mol1_output_top_zip_path MOL1_OUTPUT_TOP_ZIP_PATH
                        Path to the output PDB file collection in zip format. Accepted formats: zip.
  --mol2_input_pdb_path MOL2_INPUT_PDB_PATH
                        Path to the input PDB file. Accepted formats: pdb.
  --mol2_output_top_zip_path MOL2_OUTPUT_TOP_ZIP_PATH
                        Path to the output PDB file collection in zip format. Accepted formats: zip.
  --haddock_config_path HADDOCK_CONFIG_PATH
                        Haddock configuration CFG file path. Accepted formats: cfg.

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 (dir): 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..
global_cfg (object): ({’postprocess’: False}) Global 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..
sandbox_path (string): (./) Parent path to the sandbox directory..
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 output.zip --haddock_config_path run.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 output.zip --haddock_config_path run.cfg