#!/usr/bin/env python3
"""Module containing the haddock class and the command line interface."""
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools.file_utils import launchlogger
[docs]
class Haddock3RestrainBodies(BiobbObject):
"""
| biobb_haddock Haddock3RestrainBodies
| Wrapper class for the Haddock-Restraints restrain_bodies module.
| `Haddock-Restraints restrain_bodies <https://www.bonvinlab.org/haddock3/clients/haddock.clis.restraints.restrain_bodies.html>`_ creates distance restraints to lock several chains together. Useful to avoid unnatural flexibility or movement due to sequence/numbering gaps.
Args:
input_structure_path (str): Path to the input PDB structure to be restrained. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock_restraints/4G6K_clean.pdb>`_. 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 <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/antibody-unambig.tbl>`_. 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:
* wrapped_software:
* name: Haddock3-restraints
* version: 2025.5
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_structure_path: str,
output_tbl_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {
"input_structure_path": input_structure_path
},
"out": {
"output_tbl_path": output_tbl_path,
},
}
# Properties specific for BB
self.binary_path = properties.get("binary_path", "haddock3-restraints")
self.exclude = properties.get("exclude", None)
self.verbose = properties.get("verbose", 0)
# Check the properties
self.check_init(properties)
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Haddock3RestrainBodies <biobb_haddock.haddock_restraints.haddock3_restrain_bodies>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# haddock3-restraints restrain_bodies <structure> [--exclude] [--verbose]
self.cmd = [self.binary_path, "restrain_bodies",
self.stage_io_dict['in']['input_structure_path']]
if self.exclude is not None:
self.cmd.extend(["--exclude", self.exclude])
if self.verbose > 0:
self.cmd.extend(["--verbose", str(self.verbose)])
self.cmd.append(">")
self.cmd.append(self.stage_io_dict['out']['output_tbl_path'])
self.cmd.append("2>&1")
# Run Biobb block
self.run_biobb()
# Remove deprecation warning if present
with open(self.stage_io_dict['out']['output_tbl_path'], 'r') as file:
lines = file.readlines()
if lines and "DEPRECATION NOTICE" in lines[0]:
with open(self.stage_io_dict['out']['output_tbl_path'], 'w') as file:
file.writelines(lines[1:])
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.remove_tmp_files()
return self.return_code
[docs]
def haddock3_restrain_bodies(
input_structure_path: str,
output_tbl_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Haddock3RestrainBodies <biobb_haddock.haddock_restraints.haddock3_restrain_bodies>` class and
execute the :meth:`launch() <biobb_haddock.haddock_restraints.haddock3_restrain_bodies.launch>` method."""
return Haddock3RestrainBodies(**dict(locals())).launch()
haddock3_restrain_bodies.__doc__ = Haddock3RestrainBodies.__doc__
main = Haddock3RestrainBodies.get_main(haddock3_restrain_bodies, "Wrapper of the HADDOCK3 restrain_bodies module.")
if __name__ == "__main__":
main()