haddock_restraints package

Submodules

haddock_restraints.haddock3_accessibility module

Module containing the haddock class and the command line interface.

class haddock_restraints.haddock3_accessibility.Haddock3Accessibility(input_pdb_path: str, output_accessibility_path: str, output_actpass_path: str | None = None, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock Haddock3Accessibility
Wrapper class for the Haddock-Restraints Accessibility module.
Haddock-Restraints Accessibility computes residues accessibility using freesasa included in the Haddock3 package.
Parameters:

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

  • output_accessibility_path (str) –

    Path to the output file with accessibility information. File type: output. Sample file. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), out (edam:format_2330).

  • output_actpass_path (str) (Optional) –

    Path to the output file with active/passive residues to be used as haddock3 restraint information. File type: output. Sample file. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), out (edam:format_2330).

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

    • chain (str) - (“A”) Chain to be used from the input PDB file.

    • cutoff (float) - (0.4) Relative cutoff for sidechain accessibility.

    • probe_radius (float) - (1.4) Probe radius for the accessibility calculation.

    • pass_to_act (bool) - (False) If True, the passive residues become active in the actpass file and vice versa.

    • 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_restraints.haddock3_accessibility import haddock3_accessibility
prop = { 'cutoff': 0.4 }
haddock3_accessibility(input_pdb_path='/path/to/mypdb.pdb',
           output_accessibility_path='/path/to/output_report.txt',
           properties=prop)
Info:
launch() → int[source]

Execute the Haddock3Accessibility object.

haddock_restraints.haddock3_accessibility.haddock3_accessibility(input_pdb_path: str, output_accessibility_path: str, output_actpass_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]
biobb_haddock Haddock3Accessibility
Wrapper class for the Haddock-Restraints Accessibility module.
Haddock-Restraints Accessibility computes residues accessibility using freesasa included in the Haddock3 package.
Parameters:

  • input_pdb_path (str) –

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

  • output_accessibility_path (str) –

    Path to the output file with accessibility information. File type: output. Sample file. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), out (edam:format_2330).

  • output_actpass_path (str) (Optional) –

    Path to the output file with active/passive residues to be used as haddock3 restraint information. File type: output. Sample file. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), out (edam:format_2330).

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

    • chain (str) - (“A”) Chain to be used from the input PDB file.

    • cutoff (float) - (0.4) Relative cutoff for sidechain accessibility.

    • probe_radius (float) - (1.4) Probe radius for the accessibility calculation.

    • pass_to_act (bool) - (False) If True, the passive residues become active in the actpass file and vice versa.

    • 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_restraints.haddock3_accessibility import haddock3_accessibility
prop = { 'cutoff': 0.4 }
haddock3_accessibility(input_pdb_path='/path/to/mypdb.pdb',
           output_accessibility_path='/path/to/output_report.txt',
           properties=prop)
Info:

haddock_restraints.haddock3_actpass_to_ambig module

Module containing the haddock class and the command line interface.

class haddock_restraints.haddock3_actpass_to_ambig.Haddock3ActpassToAmbig(input_actpass1_path: str, input_actpass2_path: str, output_tbl_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock Haddock3ActpassToAmbig
Wrapper class for the Haddock-Restraints active_passive_to_ambig module.
Haddock-Restraints active_passive_to_ambig generates a corresponding ambig.tbl file to be used by HADDOCK from two given files containing active (in the first line) and passive (second line) residues.
Parameters:

  • input_actpass1_path (str) –

    Path to the first input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. Sample file. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), in (edam:format_2330), pass (edam:format_2330).

  • input_actpass2_path (str) –

    Path to the second input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. Sample file. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), in (edam:format_2330), pass (edam:format_2330).

  • output_tbl_path (str) –

    Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. File type: output. Sample file. Accepted formats: tbl (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).

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

    • pass_to_act (bool) - (False) Path to the haddock haddock executable binary.

    • segid_one (str) - (None) Segid of the first model.

    • segid_two (str) - (None) Segid of the second model.

    • 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_restraints.haddock3_actpass_to_ambig import haddock3_actpass_to_ambig
haddock3_actpass_to_ambig(
    input_actpass1_path='/path/to/haddock_actpass1.txt',
    input_actpass2_path='/path/to/haddock_actpass2.txt',
    output_tbl_path='/path/to/output_AIR.tbl'
)
Info:
launch() → int[source]

Execute the Haddock3ActpassToAmbig object.

haddock_restraints.haddock3_actpass_to_ambig.haddock3_actpass_to_ambig(input_actpass1_path: str, input_actpass2_path: str, output_tbl_path: str, properties: dict | None = None, **kwargs) → int[source]
biobb_haddock Haddock3ActpassToAmbig
Wrapper class for the Haddock-Restraints active_passive_to_ambig module.
Haddock-Restraints active_passive_to_ambig generates a corresponding ambig.tbl file to be used by HADDOCK from two given files containing active (in the first line) and passive (second line) residues.
Parameters:

  • input_actpass1_path (str) –

    Path to the first input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. Sample file. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), in (edam:format_2330), pass (edam:format_2330).

  • input_actpass2_path (str) –

    Path to the second input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. Sample file. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), in (edam:format_2330), pass (edam:format_2330).

  • output_tbl_path (str) –

    Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. File type: output. Sample file. Accepted formats: tbl (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).

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

    • pass_to_act (bool) - (False) Path to the haddock haddock executable binary.

    • segid_one (str) - (None) Segid of the first model.

    • segid_two (str) - (None) Segid of the second model.

    • 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_restraints.haddock3_actpass_to_ambig import haddock3_actpass_to_ambig
haddock3_actpass_to_ambig(
    input_actpass1_path='/path/to/haddock_actpass1.txt',
    input_actpass2_path='/path/to/haddock_actpass2.txt',
    output_tbl_path='/path/to/output_AIR.tbl'
)
Info:

haddock_restraints.haddock3_passive_from_active module

Module containing the Haddock3PassiveFromActive class and the command line interface.

class haddock_restraints.haddock3_passive_from_active.Haddock3PassiveFromActive(input_pdb_path: str, output_actpass_path: str, input_active_list_path: str | None = None, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock Haddock3PassiveFromActive
Wrapper class for the Haddock3-Restraints passive_from_active module.
Haddock3-Restraints passive_from_active given a list of active_residues and a PDB structure, it will return a list of surface exposed passive residues within a radius (6.5Å by default) from the active residues.
Parameters:

  • input_pdb_path (str) –

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

  • output_actpass_path (str) –

    Path to the output file with list of passive residues. File type: output. Sample file. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), list (edam:format_2330), out (edam:format_2330).

  • input_active_list_path (str) (Optional) – Path to the input file with list of active residues. File type: input. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), list (edam:format_2330).

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

    • active_list (str) - (‘’) List of active residues as a comma-separated string. Required if input_active_list_path is not provided.

    • chain_id (str) - (None) Chain ID to consider when calculating passive residues.

    • surface_list_path (str) - (“”) Path to file with list of surface residues to filter.

    • radius (float) - (6.5) Radius in Angstroms to look for surface residues around active ones.

    • binary_path (str) - (“haddock3-restraints”) Path to the haddock3-restraints 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_restraints.haddock3_passive_from_active import haddock3_passive_from_active
haddock3_passive_from_active(
    input_pdb_path='/path/to/structure.pdb',
    input_active_list_path='/path/to/active_residues.txt',
    output_actpass_path='/path/to/actpass.tbl.txt',
    properties={
        'chain_id': 'A',
        'radius': 6.5
    }
)
Info:
launch() → int[source]

Execute the Haddock3PassiveFromActive object.

haddock_restraints.haddock3_passive_from_active.haddock3_passive_from_active(input_pdb_path: str, output_actpass_path: str, input_active_list_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]
biobb_haddock Haddock3PassiveFromActive
Wrapper class for the Haddock3-Restraints passive_from_active module.
Haddock3-Restraints passive_from_active given a list of active_residues and a PDB structure, it will return a list of surface exposed passive residues within a radius (6.5Å by default) from the active residues.
Parameters:

  • input_pdb_path (str) –

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

  • output_actpass_path (str) –

    Path to the output file with list of passive residues. File type: output. Sample file. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), list (edam:format_2330), out (edam:format_2330).

  • input_active_list_path (str) (Optional) – Path to the input file with list of active residues. File type: input. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), list (edam:format_2330).

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

    • active_list (str) - (‘’) List of active residues as a comma-separated string. Required if input_active_list_path is not provided.

    • chain_id (str) - (None) Chain ID to consider when calculating passive residues.

    • surface_list_path (str) - (“”) Path to file with list of surface residues to filter.

    • radius (float) - (6.5) Radius in Angstroms to look for surface residues around active ones.

    • binary_path (str) - (“haddock3-restraints”) Path to the haddock3-restraints 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_restraints.haddock3_passive_from_active import haddock3_passive_from_active
haddock3_passive_from_active(
    input_pdb_path='/path/to/structure.pdb',
    input_active_list_path='/path/to/active_residues.txt',
    output_actpass_path='/path/to/actpass.tbl.txt',
    properties={
        'chain_id': 'A',
        'radius': 6.5
    }
)
Info:

haddock_restraints.haddock3_actpass_to_ambig haddock3_restrain_bodies

Module containing the haddock class and the command line interface.

class haddock_restraints.haddock3_restrain_bodies.Haddock3RestrainBodies(input_structure_path: str, output_tbl_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock Haddock3RestrainBodies
Wrapper class for the Haddock-Restraints restrain_bodies module.
Haddock-Restraints restrain_bodies creates distance restraints to lock several chains together. Useful to avoid unnatural flexibility or movement due to sequence/numbering gaps.
Parameters:

  • input_structure_path (str) –

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

  • output_tbl_path (str) –

    Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. File type: output. Sample file. Accepted formats: tbl (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).

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

    • exclude (str) - (None) Chains to exclude from the calculation.

    • verbose (int) - (0) Tune verbosity of the output.

    • binary_path (str) - (“haddock3-restraints”) Path to the HADDOCK3 restraints 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_restraints.haddock3_restrain_bodies import haddock3_restrain_bodies
haddock3_restrain_bodies(
    input_structure_path='/path/to/structure.pdb',
    output_tbl_path='/path/to/body_restraints.tbl'
)
Info:
launch() → int[source]

Execute the Haddock3RestrainBodies object.

haddock_restraints.haddock3_restrain_bodies.haddock3_restrain_bodies(input_structure_path: str, output_tbl_path: str, properties: dict | None = None, **kwargs) → int[source]
biobb_haddock Haddock3RestrainBodies
Wrapper class for the Haddock-Restraints restrain_bodies module.
Haddock-Restraints restrain_bodies creates distance restraints to lock several chains together. Useful to avoid unnatural flexibility or movement due to sequence/numbering gaps.
Parameters:

  • input_structure_path (str) –

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

  • output_tbl_path (str) –

    Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. File type: output. Sample file. Accepted formats: tbl (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).

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

    • exclude (str) - (None) Chains to exclude from the calculation.

    • verbose (int) - (0) Tune verbosity of the output.

    • binary_path (str) - (“haddock3-restraints”) Path to the HADDOCK3 restraints 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_restraints.haddock3_restrain_bodies import haddock3_restrain_bodies
haddock3_restrain_bodies(
    input_structure_path='/path/to/structure.pdb',
    output_tbl_path='/path/to/body_restraints.tbl'
)
Info: