haddock package

Submodules

haddock.topology module

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

class haddock.topology.Topology(mol1_input_pdb_path: str, mol1_output_top_zip_path: str, mol2_input_pdb_path: str | None = None, mol2_output_top_zip_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock Topology
Wrapper class for the Haddock Topology module.
The Topology module. The Haddock 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) –

    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_zip (str) (Optional) –

    Path to the output zipball containing all the current Haddock workflow data. 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.

    • 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:
launch() → int[source]

Execute the haddock object.

haddock.topology.main()[source]
haddock.topology.topology(mol1_input_pdb_path: str, mol1_output_top_zip_path: str, mol2_input_pdb_path: str | None = None, mol2_output_top_zip_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs) → int[source]

Create haddock class and execute the launch() method.

haddock.capri_eval module

Module containing the haddock class and the command line interface.

class haddock.capri_eval.CapriEval(input_haddock_wf_data_zip: str, output_evaluation_zip_path: str, reference_pdb_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock CapriEval
Wrapper class for the Haddock CapriEval module.
The CapriEval module. Haddock CapriEval module computes Capri evaluation for a docking.
Parameters:

  • input_haddock_wf_data_zip (str) –

    Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_evaluation_zip_path (str) –

    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).

  • output_haddock_wf_data_zip (str) (Optional) –

    Path to the output zipball containing all the current Haddock workflow data. 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.

    • 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_zip='/path/to/myworkflowdata.zip',
           output_evaluation_zip='/path/to/myevalfiles.zip',
           properties=prop)
Info:
launch() → int[source]

Execute the haddock object.

haddock.capri_eval.capri_eval(input_haddock_wf_data_zip: str, output_evaluation_zip_path: str, reference_pdb_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs) → int[source]

Create haddock class and execute the launch() method.

haddock.capri_eval.main()[source]

haddock.clust_fcc module

Module containing the haddock class and the command line interface.

class haddock.clust_fcc.ClustFCC(input_haddock_wf_data_zip: str, output_cluster_zip_path: str, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock ClustFCC
Wrapper class for the Haddock ClustFCC module.
The ClustFCC module. Haddock ClustFCC module computes clusters of structures using FCC.
Parameters:

  • input_haddock_wf_data_zip (str) –

    Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_cluster_zip_path (str) –

    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_zip (str) (Optional) –

    Path to the output zipball containing all the current Haddock workflow data. 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.

    • 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_zip='/path/to/myworkflowdata.zip',
           output_evaluation_zip='/path/to/myevalfiles.zip',
           properties=prop)
Info:
launch() → int[source]

Execute the haddock object.

haddock.clust_fcc.clust_fcc(input_haddock_wf_data_zip: str, output_cluster_zip_path: str, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs) → int[source]

Create haddock class and execute the launch() method.

haddock.clust_fcc.main()[source]

haddock.em_ref module

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

class haddock.em_ref.EMRef(input_haddock_wf_data_zip: str, refinement_output_zip_path: str, restraints_table_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock EMRef
Wrapper class for the Haddock EMRef module.
The EMRef module. Haddock EMRef module computes an energy minimization refinement over selected structures.
Parameters:

  • input_haddock_wf_data_zip (str) –

    Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • refinement_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).

  • restraints_table_path (str) (Optional) –

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

  • output_haddock_wf_data_zip (str) (Optional) –

    Path to the output zipball containing all the current Haddock workflow data. 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.

    • 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_zip='/path/to/myworkflowdata.zip',
       refinement_output_zip_path='/path/to/mydockingstructures.zip',
       properties=prop)
Info:
launch() → int[source]

Execute the haddock object.

haddock.em_ref.em_ref(input_haddock_wf_data_zip: str, refinement_output_zip_path: str, restraints_table_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs) → int[source]

Create haddock class and execute the launch() method.

haddock.em_ref.main()[source]

haddock.flex_ref module

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

class haddock.flex_ref.FlexRef(input_haddock_wf_data_zip: str, refinement_output_zip_path: str, restraints_table_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock FlexRef
Wrapper class for the Haddock FlexRef module.
The FlexRef module. Haddock FlexRef module computes a flexible refinement over selected structures.
Parameters:

  • input_haddock_wf_data_zip (str) –

    Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • refinement_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).

  • restraints_table_path (str) (Optional) –

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

  • output_haddock_wf_data_zip (str) (Optional) –

    Path to the output zipball containing all the current Haddock workflow data. 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.

    • 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_zip='/path/to/myworkflowdata.zip',
         refinement_output_zip_path='/path/to/mydockingstructures.zip',
         properties=prop)
Info:
launch() → int[source]

Execute the haddock object.

haddock.flex_ref.flex_ref(input_haddock_wf_data_zip: str, refinement_output_zip_path: str, restraints_table_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs) → int[source]

Create haddock class and execute the launch() method.

haddock.flex_ref.main()[source]

haddock.rigid_body module

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

class haddock.rigid_body.RigidBody(input_haddock_wf_data_zip: str, docking_output_zip_path: str, ambig_restraints_table_path: str | None = None, unambig_restraints_table_path: str | None = None, hb_restraints_table_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock RigidBody
Wrapper class for the Haddock RigidBody module.
The RigidBody module. Haddock RigidBody module compute rigid body docking between two molecules.
Parameters:

  • input_haddock_wf_data_zip (str) –

    Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: 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).

  • output_haddock_wf_data_zip (str) (Optional) –

    Path to the output zipball containing all the current Haddock workflow data. 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.

    • 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_zip='/path/to/myworkflowdata.zip',
           docking_output_zip_path='/path/to/mydockingstructures.zip',
           properties=prop)
Info:
launch() → int[source]

Execute the haddock object.

haddock.rigid_body.main()[source]
haddock.rigid_body.rigid_body(input_haddock_wf_data_zip: str, docking_output_zip_path: str, ambig_restraints_table_path: str | None = None, unambig_restraints_table_path: str | None = None, hb_restraints_table_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs) → int[source]

Create haddock class and execute the launch() method.

haddock.sele_top_clusts module

Module containing the haddock class and the command line interface.

class haddock.sele_top_clusts.SeleTopClusts(input_haddock_wf_data_zip: str, output_selection_zip_path: str, reference_pdb_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock SeleTopClusts
Wrapper class for the Haddock SeleTopClusts module https://www.bonvinlab.org/haddock3/modules/analysis/seletopclusts.html.
The SeleTopClusts module. Haddock SeleTopClusts module selects the top clusters of a docking.
Parameters:

  • input_haddock_wf_data_zip (str) –

    Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_selection_zip_path (str) –

    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_zip (str) (Optional) –

    Path to the output zipball containing all the current Haddock workflow data. 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.

    • 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_zip='/path/to/myworkflowdata.zip',
           output_evaluation_zip='/path/to/myevalfiles.zip',
           properties=prop)
Info:
launch() → int[source]

Execute the haddock object.

haddock.sele_top_clusts.main()[source]
haddock.sele_top_clusts.sele_top_clusts(input_haddock_wf_data_zip: str, output_selection_zip_path: str, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs) → int[source]

Create haddock class and execute the launch() method.

haddock.sele_top module

Module containing the haddock class and the command line interface.

class haddock.sele_top.SeleTop(input_haddock_wf_data_zip: str, output_selection_zip_path: str, reference_pdb_path: str | None = None, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock SeleTop
Wrapper class for the Haddock SeleTop module https://www.bonvinlab.org/haddock3/modules/analysis/seletop.html
The SeleTop module. Haddock SeleTop module selects the top models of a docking.
Parameters:

  • input_haddock_wf_data_zip (str) –

    Path to the input zipball containing all the current Haddock workflow data. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_selection_zip_path (str) –

    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_zip (str) (Optional) –

    Path to the output zipball containing all the current Haddock workflow data. 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.

    • 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_zip='/path/to/myworkflowdata.zip',
           output_evaluation_zip='/path/to/myevalfiles.zip',
           properties=prop)
Info:
launch() → int[source]

Execute the haddock object.

haddock.sele_top.main()[source]
haddock.sele_top.sele_top(input_haddock_wf_data_zip: str, output_selection_zip_path: str, output_haddock_wf_data_zip: str | None = None, haddock_config_path: str | None = None, properties: Dict | None = None, **kwargs) → int[source]

Create haddock class and execute the launch() method.