haddock package

Submodules

haddock.capri_eval module

Module containing the HADDOCK3 CapriEval class and the command line interface.

class haddock.capri_eval.CapriEval(input_haddock_wf_data: str, output_haddock_wf_data: str, output_evaluation_zip_path: str | None = None, reference_pdb_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: HaddockStepBase

biobb_haddock CapriEval

Wrapper class for the HADDOCK3 CapriEval module.

The CapriEval module. HADDOCK3 CapriEval module computes Capri evaluation for a docking.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• 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 (edam:format_1915), zip (edam:format_3987).

• output_evaluation_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• reference_pdb_path (str) (Optional) –

  Path to the input PDB file containing an structure for reference. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: True}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.capri_eval import capri_eval
prop = { 'binary_path': 'haddock' }
capri_eval(input_haddock_wf_data='/path/to/myInputData',
           output_haddock_wf_data='/path/to/myOutputData',
           properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.capri_eval.capri_eval(input_haddock_wf_data: str, output_haddock_wf_data: str, output_evaluation_zip_path: str | None = None, reference_pdb_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_haddock CapriEval

Wrapper class for the HADDOCK3 CapriEval module.

The CapriEval module. HADDOCK3 CapriEval module computes Capri evaluation for a docking.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• 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 (edam:format_1915), zip (edam:format_3987).

• output_evaluation_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• reference_pdb_path (str) (Optional) –

  Path to the input PDB file containing an structure for reference. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: True}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.capri_eval import capri_eval
prop = { 'binary_path': 'haddock' }
capri_eval(input_haddock_wf_data='/path/to/myInputData',
           output_haddock_wf_data='/path/to/myOutputData',
           properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.clust_fcc module

Module containing the HADDOCK3 ClustFCC class and the command line interface.

class haddock.clust_fcc.ClustFCC(input_haddock_wf_data: str, output_haddock_wf_data: str, output_cluster_zip_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: HaddockStepBase

biobb_haddock ClustFCC

Wrapper class for the HADDOCK3 ClustFCC module.

The ClustFCC module. HADDOCK3 ClustFCC module computes clusters of structures using FCC.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• 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 (edam:format_1915), zip (edam:format_3987).

• output_cluster_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.clust_fcc import clust_fcc
prop = { 'binary_path': 'haddock' }
clust_fcc(input_haddock_wf_data='/path/to/myInputData',
          output_haddock_wf_data='/path/to/myOutputData',
          properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.clust_fcc.clust_fcc(input_haddock_wf_data: str, output_haddock_wf_data: str, output_cluster_zip_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_haddock ClustFCC

Wrapper class for the HADDOCK3 ClustFCC module.

The ClustFCC module. HADDOCK3 ClustFCC module computes clusters of structures using FCC.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• 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 (edam:format_1915), zip (edam:format_3987).

• output_cluster_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.clust_fcc import clust_fcc
prop = { 'binary_path': 'haddock' }
clust_fcc(input_haddock_wf_data='/path/to/myInputData',
          output_haddock_wf_data='/path/to/myOutputData',
          properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.contact_map module

Module containing the HADDOCK3 ContactMap class and the command line interface.

class haddock.contact_map.ContactMap(input_haddock_wf_data: str, output_haddock_wf_data: str, output_contactmap_zip_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: HaddockStepBase

biobb_haddock ContactMap

Wrapper class for the HADDOCK3 ContactMap module.

The ContactMap module. HADDOCK3 ContactMap module computes contacts between chains in complexes and generates heatmaps and chordcharts.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• output_contactmap_zip_path (str) (Optional) –

  Path to the output contact map files in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.contact_map import contact_map
prop = { 'binary_path': 'haddock' }
contact_map(input_haddock_wf_data='/path/to/myInputData',
            output_haddock_wf_data='/path/to/myOutputData',
            properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.contact_map.contact_map(input_haddock_wf_data: str, output_haddock_wf_data: str, output_contactmap_zip_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_haddock ContactMap

Wrapper class for the HADDOCK3 ContactMap module.

The ContactMap module. HADDOCK3 ContactMap module computes contacts between chains in complexes and generates heatmaps and chordcharts.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• output_contactmap_zip_path (str) (Optional) –

  Path to the output contact map files in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.contact_map import contact_map
prop = { 'binary_path': 'haddock' }
contact_map(input_haddock_wf_data='/path/to/myInputData',
            output_haddock_wf_data='/path/to/myOutputData',
            properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.em_ref module

Module containing the HADDOCK3 EMRef class and the command line interface.

class haddock.em_ref.EMRef(input_haddock_wf_data: str, output_haddock_wf_data: str, refinement_output_zip_path: str | None = None, ambig_restraints_table_path: str | None = None, unambig_restraints_table_path: str | None = None, hb_restraints_table_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: HaddockStepBase

biobb_haddock EMRef

Wrapper class for the HADDOCK3 EMRef module.

The EMRef module. HADDOCK3 EMRef module computes an energy minimization refinement over selected structures.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• refinement_output_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• ambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of ambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• unambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of unambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• hb_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of hydrogen bond restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.em_ref import em_ref
prop = { 'binary_path': 'haddock' }
em_ref(input_haddock_wf_data='/path/to/myInputData',
       output_haddock_wf_data='/path/to/myOutputData',
       properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.em_ref.em_ref(input_haddock_wf_data: str, output_haddock_wf_data: str, refinement_output_zip_path: str | None = None, ambig_restraints_table_path: str | None = None, unambig_restraints_table_path: str | None = None, hb_restraints_table_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_haddock EMRef

Wrapper class for the HADDOCK3 EMRef module.

The EMRef module. HADDOCK3 EMRef module computes an energy minimization refinement over selected structures.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• refinement_output_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• ambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of ambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• unambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of unambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• hb_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of hydrogen bond restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.em_ref import em_ref
prop = { 'binary_path': 'haddock' }
em_ref(input_haddock_wf_data='/path/to/myInputData',
       output_haddock_wf_data='/path/to/myOutputData',
       properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.flex_ref module

Module containing the HADDOCK3 FlexRef class and the command line interface.

class haddock.flex_ref.FlexRef(input_haddock_wf_data: str, output_haddock_wf_data: str, refinement_output_zip_path: str | None = None, ambig_restraints_table_path: str | None = None, unambig_restraints_table_path: str | None = None, hb_restraints_table_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: HaddockStepBase

biobb_haddock FlexRef

Wrapper class for the HADDOCK3 FlexRef module.

The FlexRef module.`HADDOCK3 FlexRef module <https://www.bonvinlab.org/haddock3/modules/refinement/haddock.modules.refinement.flexref.html>`_ computes a flexible refinement over selected structures.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• refinement_output_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• ambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of ambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• unambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of unambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• hb_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of hydrogen bond restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.flex_ref import flex_ref
prop = { 'binary_path': 'haddock' }
flex_ref(input_haddock_wf_data='/path/to/myInputData',
         output_haddock_wf_data='/path/to/myOutputData',
         properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.flex_ref.flex_ref(input_haddock_wf_data: str, output_haddock_wf_data: str, refinement_output_zip_path: str | None = None, ambig_restraints_table_path: str | None = None, unambig_restraints_table_path: str | None = None, hb_restraints_table_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_haddock FlexRef

Wrapper class for the HADDOCK3 FlexRef module.

The FlexRef module.`HADDOCK3 FlexRef module <https://www.bonvinlab.org/haddock3/modules/refinement/haddock.modules.refinement.flexref.html>`_ computes a flexible refinement over selected structures.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• refinement_output_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• ambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of ambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• unambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of unambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• hb_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of hydrogen bond restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.flex_ref import flex_ref
prop = { 'binary_path': 'haddock' }
flex_ref(input_haddock_wf_data='/path/to/myInputData',
         output_haddock_wf_data='/path/to/myOutputData',
         properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.haddock3_extend module

Module containing the haddock3 run class and the command line interface.

class haddock.haddock3_extend.Haddock3Extend(input_haddock_wf_data: str, haddock_config_path: str, output_haddock_wf_data: str, properties: dict | None = None, **kwargs)

Bases: HaddockStepBase

biobb_haddock Haddock3Extend

Wrapper class for the HADDOCK3 extend module.

The HADDOCK3 extend. module continues the HADDOCK3 execution for docking of an already started run.

Parameters:

• 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 (edam:format_3987).

• haddock_config_path (str) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• 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 (edam:format_3987).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: True}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.haddock3_extend import haddock3_extend
haddock3_extend(input_haddock_wf_data='/path/to/myworkflowdata.zip',
                haddock_config_path='/path/to/myHaddockConfig.cfg',
                output_haddock_wf_data='/path/to/haddock_output.zip',
                properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.haddock3_extend.haddock3_extend(input_haddock_wf_data: str, haddock_config_path: str, output_haddock_wf_data: str, properties: dict | None = None, **kwargs) → int

biobb_haddock Haddock3Extend

Wrapper class for the HADDOCK3 extend module.

The HADDOCK3 extend. module continues the HADDOCK3 execution for docking of an already started run.

Parameters:

• 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 (edam:format_3987).

• haddock_config_path (str) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• 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 (edam:format_3987).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: True}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.haddock3_extend import haddock3_extend
haddock3_extend(input_haddock_wf_data='/path/to/myworkflowdata.zip',
                haddock_config_path='/path/to/myHaddockConfig.cfg',
                output_haddock_wf_data='/path/to/haddock_output.zip',
                properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.haddock3_run module

Module containing the HADDOCK3 Run class and the command line interface.

class haddock.haddock3_run.Haddock3Run(input_haddock_wf_data: str, output_haddock_wf_data: str, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: HaddockStepBase

biobb_haddock Haddock3Run

Wrapper class for the HADDOCK3 Run module.

The HADDOCK3 run module launches the HADDOCK3 execution for docking.

Parameters:

• input_haddock_wf_data (dir) – Input folder containing all the files defined in the config. File type: input. Sample folder. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output zipball containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.haddock3_run import haddock3_run
haddock3_run(input_haddock_wf_data='/path/to/myInputData',
             output_haddock_wf_data='/path/to/myOutputData',
             haddock_config_path='/path/to/myHaddockConfig.cfg',
             properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.haddock3_run.haddock3_run(input_haddock_wf_data: str, output_haddock_wf_data: str, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_haddock Haddock3Run

Wrapper class for the HADDOCK3 Run module.

The HADDOCK3 run module launches the HADDOCK3 execution for docking.

Parameters:

• input_haddock_wf_data (dir) –

  Input folder containing all the files defined in the config. File type: input. Sample folder. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output zipball containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.haddock3_run import haddock3_run
haddock3_run(input_haddock_wf_data='/path/to/myInputData',
             output_haddock_wf_data='/path/to/myOutputData',
             haddock_config_path='/path/to/myHaddockConfig.cfg',
             properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.rigid_body module

Module containing the HADDOCK3 RigidBody class and the command line interface.

class haddock.rigid_body.RigidBody(input_haddock_wf_data: str, output_haddock_wf_data: str, docking_output_zip_path: str | None = None, ambig_restraints_table_path: str | None = None, unambig_restraints_table_path: str | None = None, hb_restraints_table_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: HaddockStepBase

biobb_haddock RigidBody

Wrapper class for the HADDOCK3 RigidBody module.

The RigidBody module. HADDOCK3 RigidBody module compute rigid body docking between two molecules.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• docking_output_zip_path (str) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• ambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of ambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• unambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of unambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• hb_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of hydrogen bond restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.rigid_body import rigid_body
prop = { 'binary_path': 'haddock' }
rigid_body(input_haddock_wf_data='/path/to/myInputData',
           output_haddock_wf_data='/path/to/myOutputData',
           properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.rigid_body.rigid_body(input_haddock_wf_data: str, output_haddock_wf_data: str, docking_output_zip_path: str | None = None, ambig_restraints_table_path: str | None = None, unambig_restraints_table_path: str | None = None, hb_restraints_table_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_haddock RigidBody

Wrapper class for the HADDOCK3 RigidBody module.

The RigidBody module. HADDOCK3 RigidBody module compute rigid body docking between two molecules.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• docking_output_zip_path (str) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• ambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of ambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• unambig_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of unambiguous restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• hb_restraints_table_path (str) (Optional) –

  Path to the input TBL file containing a list of hydrogen bond restraints for docking. File type: input. Sample file. Accepted formats: tbl (edam:format_2330).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.rigid_body import rigid_body
prop = { 'binary_path': 'haddock' }
rigid_body(input_haddock_wf_data='/path/to/myInputData',
           output_haddock_wf_data='/path/to/myOutputData',
           properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.sele_top_clusts module

Module containing the HADDOCK3 SeleTopClusts class and the command line interface.

class haddock.sele_top_clusts.SeleTopClusts(input_haddock_wf_data: str, output_haddock_wf_data: str, output_selection_zip_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: HaddockStepBase

biobb_haddock SeleTopClusts

Wrapper class for the HADDOCK3 SeleTopClusts module.

The SeleTopClusts module. HADDOCK3 SeleTopClusts module selects the top clusters of a docking.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• output_selection_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.sele_top_clusts import sele_top_clusts
prop = { 'binary_path': 'haddock' }
sele_top_clusts(input_haddock_wf_data='/path/to/myInputData',
               output_haddock_wf_data='/path/to/myOutputData',
               properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.sele_top_clusts.sele_top_clusts(input_haddock_wf_data: str, output_haddock_wf_data: str, output_selection_zip_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_haddock SeleTopClusts

Wrapper class for the HADDOCK3 SeleTopClusts module.

The SeleTopClusts module. HADDOCK3 SeleTopClusts module selects the top clusters of a docking.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• output_selection_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.sele_top_clusts import sele_top_clusts
prop = { 'binary_path': 'haddock' }
sele_top_clusts(input_haddock_wf_data='/path/to/myInputData',
               output_haddock_wf_data='/path/to/myOutputData',
               properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.sele_top module

Module containing the HADDOCK3 SeleTop class and the command line interface.

class haddock.sele_top.SeleTop(input_haddock_wf_data: str, output_haddock_wf_data: str, output_selection_zip_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: HaddockStepBase

biobb_haddock SeleTop

Wrapper class for the HADDOCK3 SeleTop module.

The SeleTop module. HADDOCK3 SeleTop module selects the top models of a docking.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• output_selection_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.sele_top import sele_top
prop = { 'binary_path': 'haddock' }
sele_top(input_haddock_wf_data='/path/to/myInputData',
         output_haddock_wf_data='/path/to/myOutputData',
         properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.sele_top.sele_top(input_haddock_wf_data: str, output_haddock_wf_data: str, output_selection_zip_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_haddock SeleTop

Wrapper class for the HADDOCK3 SeleTop module.

The SeleTop module. HADDOCK3 SeleTop module selects the top models of a docking.

Parameters:

• 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 (edam:format_1915), zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).

• output_selection_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.sele_top import sele_top
prop = { 'binary_path': 'haddock' }
sele_top(input_haddock_wf_data='/path/to/myInputData',
         output_haddock_wf_data='/path/to/myOutputData',
         properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

haddock.topology module

Module containing the HADDOCK3 Topology class and the command line interface.

class haddock.topology.Topology(mol1_input_pdb_path: str, output_haddock_wf_data: str, mol1_output_top_zip_path: str | None = None, mol2_input_pdb_path: str | None = None, mol2_output_top_zip_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: BiobbObject

biobb_haddock Topology

Wrapper class for the HADDOCK3 Topology module.

The Topology module. HADDOCK3 Topology module creates a topology from a system to be used for docking.

Parameters:

• mol1_input_pdb_path (str) –

  Path to the input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• mol1_output_top_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• mol2_input_pdb_path (str) (Optional) –

  Path to the input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• mol2_output_top_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output zipball containing all the current Haddock workflow data. File type: output. Accepted formats: zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.topology import topology
prop = { 'binary_path': 'haddock' }
topology(mol1_input_pdb_path='/path/to/myStructure.pdb',
         mol1_output_top_zip_path='/path/to/topology.zip',
         properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

launch() → int

Execute the Topology object.

haddock.topology.topology(mol1_input_pdb_path: str, output_haddock_wf_data: str, mol1_output_top_zip_path: str | None = None, mol2_input_pdb_path: str | None = None, mol2_output_top_zip_path: str | None = None, haddock_config_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_haddock Topology

Wrapper class for the HADDOCK3 Topology module.

The Topology module. HADDOCK3 Topology module creates a topology from a system to be used for docking.

Parameters:

• mol1_input_pdb_path (str) –

  Path to the input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• mol1_output_top_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• mol2_input_pdb_path (str) (Optional) –

  Path to the input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• mol2_output_top_zip_path (str) (Optional) –

  Path to the output PDB file collection in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• output_haddock_wf_data (dir) – Path to the output zipball containing all the current Haddock workflow data. File type: output. Accepted formats: zip (edam:format_3987).

• haddock_config_path (str) (Optional) –

  Haddock configuration CFG file path. File type: input. Sample file. Accepted formats: cfg (edam:format_1476).

• properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

  • cfg (dict) - ({}) Haddock configuration options specification.

  • global_cfg (dict) - ({“postprocess”: False}) Global configuration options specification.

  • binary_path (str) - (“haddock”) Path to the haddock haddock executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • container_path (str) - (None) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.haddock.topology import topology
prop = { 'binary_path': 'haddock' }
topology(mol1_input_pdb_path='/path/to/myStructure.pdb',
         mol1_output_top_zip_path='/path/to/topology.zip',
         properties=prop)

Info:

• wrapped_software:

  • name: HADDOCK3

  • version: 2025.5

  • license: Apache-2.0

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl