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

usage: em_ref [-h] [-c CONFIG] --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP --refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH [--restraints_table_path RESTRAINTS_TABLE_PATH] [--output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the haddock EMRef module.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --restraints_table_path RESTRAINTS_TABLE_PATH
  --output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP
  --haddock_config_path HADDOCK_CONFIG_PATH

required arguments:
  --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP
  --refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH

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

usage: sele_top [-h] [-c CONFIG] --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP --output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH [--output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the haddock SeleTop module.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP
  --haddock_config_path HADDOCK_CONFIG_PATH

required arguments:
  --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP
  --output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH

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

usage: sele_top_clusts [-h] [-c CONFIG] --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP --output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH [--output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the haddock SeleTopClusts module.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP
  --haddock_config_path HADDOCK_CONFIG_PATH

required arguments:
  --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP
  --output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH

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

usage: capri_eval [-h] [-c CONFIG] --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP --output_evaluation_zip_path OUTPUT_EVALUATION_ZIP_PATH [--reference_pdb_path REFERENCE_PDB_PATH] [--output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the haddock CapriEval module.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --reference_pdb_path REFERENCE_PDB_PATH
  --output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP
  --haddock_config_path HADDOCK_CONFIG_PATH

required arguments:
  --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP
  --output_evaluation_zip_path OUTPUT_EVALUATION_ZIP_PATH

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

usage: flex_ref [-h] [-c CONFIG] --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP --refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH [--restraints_table_path RESTRAINTS_TABLE_PATH] [--output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the haddock FlexRef module.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --restraints_table_path RESTRAINTS_TABLE_PATH
  --output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP
  --haddock_config_path HADDOCK_CONFIG_PATH

required arguments:
  --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP
  --refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH

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

usage: rigid_body [-h] [-c CONFIG] --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP --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] [--output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the haddock RigidBody module.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH
  --unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH
  --hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH
  --output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP
  --haddock_config_path HADDOCK_CONFIG_PATH

required arguments:
  --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP
  --docking_output_zip_path DOCKING_OUTPUT_ZIP_PATH

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

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] [--output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP] [--mol2_output_top_zip_path MOL2_OUTPUT_TOP_ZIP_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the haddock haddock module.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --mol2_input_pdb_path MOL2_INPUT_PDB_PATH
  --output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP
  --mol2_output_top_zip_path MOL2_OUTPUT_TOP_ZIP_PATH
  --haddock_config_path HADDOCK_CONFIG_PATH

required arguments:
  --mol1_input_pdb_path MOL1_INPUT_PDB_PATH
  --mol1_output_top_zip_path MOL1_OUTPUT_TOP_ZIP_PATH

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

usage: clust_fcc [-h] [-c CONFIG] --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP --output_cluster_zip_path OUTPUT_CLUSTER_ZIP_PATH [--output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP] [--haddock_config_path HADDOCK_CONFIG_PATH]

Wrapper of the haddock ClustFCC module.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --output_haddock_wf_data_zip OUTPUT_HADDOCK_WF_DATA_ZIP
  --haddock_config_path HADDOCK_CONFIG_PATH

required arguments:
  --input_haddock_wf_data_zip INPUT_HADDOCK_WF_DATA_ZIP
  --output_cluster_zip_path OUTPUT_CLUSTER_ZIP_PATH

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