#!/usr/bin/env python3
"""Module containing the HADDOCK3 Topology class and the command line interface."""
from pathlib import Path
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_haddock.haddock.common import create_cfg, move_to_container_path, zip_wf_output
[docs]
class Topology(BiobbObject):
"""
| biobb_haddock Topology
| Wrapper class for the HADDOCK3 Topology module.
| The Topology module. `HADDOCK3 Topology module <https://www.bonvinlab.org/haddock3/modules/topology/haddock.modules.topology.topoaa.html#haddock.modules.topology.topoaa.HaddockModule>`_ creates a topology from a system to be used for docking.
Args:
mol1_input_pdb_path (str): Path to the input PDB file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2aP_1F3G.pdb>`_. 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 <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_mol1_top.zip>`_. Accepted formats: zip (edam:format_3987).
mol2_input_pdb_path (str) (Optional): Path to the input PDB file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/hpr_ensemble.pdb>`_. 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 <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_mol2_top.zip>`_. 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 <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg>`_. 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 <https://www.bonvinlab.org/haddock3-user-manual/global_parameters.html>`_ 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
"""
def __init__(
self,
mol1_input_pdb_path: str,
output_haddock_wf_data: str,
mol1_output_top_zip_path: Optional[str] = None,
mol2_input_pdb_path: Optional[str] = None,
mol2_output_top_zip_path: Optional[str] = None,
haddock_config_path: Optional[str] = None,
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": {
"mol1_input_pdb_path": mol1_input_pdb_path,
"mol2_input_pdb_path": mol2_input_pdb_path,
"haddock_config_path": haddock_config_path,
},
"out": {
"output_haddock_wf_data": output_haddock_wf_data,
"mol1_output_top_zip_path": mol1_output_top_zip_path,
"mol2_output_top_zip_path": mol2_output_top_zip_path,
},
}
# Properties specific for BB
self.haddock_step_name = "topoaa"
# Handle configuration options from propierties
self.cfg = {k: v for k, v in properties.get("cfg", dict()).items()}
# Global HADDOCK configuration options
self.global_cfg = properties.get("global_cfg", dict(postprocess=False))
# Properties specific for BB
self.binary_path = properties.get("binary_path", "haddock3")
# Check the properties
self.check_init(properties)
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Topology <biobb_haddock.haddock.topology>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
self.run_dir = self.stage_io_dict["out"]["output_haddock_wf_data"]
self.run_dir = self.run_dir[:-4] if self.run_dir[-4:] == ".zip" else self.run_dir
workflow_dict = {
"run_dir": self.run_dir,
"molecules": [self.stage_io_dict["in"]["mol1_input_pdb_path"]],
"haddock_step_name": self.haddock_step_name,
}
workflow_dict.update(self.global_cfg)
if mol2_input_pdb_path := self.stage_io_dict["in"].get("mol2_input_pdb_path"):
workflow_dict["molecules"].append(mol2_input_pdb_path)
# Create workflow configuration
self.output_cfg_path = create_cfg(
output_cfg_path=self.create_tmp_file('_haddock.cfg'),
workflow_dict=workflow_dict,
input_cfg_path=self.stage_io_dict["in"].get("haddock_config_path"),
cfg_properties_dict=self.cfg,
)
if self.container_path:
fu.log("Container execution enabled", self.out_log)
move_to_container_path(self)
self.cmd = [self.binary_path, self.output_cfg_path]
# Run Biobb block
self.run_biobb()
# Copy output
haddock_output_path = Path(f'{workflow_dict["run_dir"]}/0_{self.haddock_step_name}')
mol1_name = str(Path(self.io_dict["in"]["mol1_input_pdb_path"]).stem)
mol1_output_file_list = list(
haddock_output_path.glob(mol1_name + r"*_haddock.pdb*")
)
fu.zip_list(
self.io_dict["out"]["mol1_output_top_zip_path"],
mol1_output_file_list,
)
if self.io_dict["out"].get("mol1_output_top_zip_path"):
mol2_name = str(Path(self.io_dict["in"]["mol2_input_pdb_path"]).stem)
mol2_output_file_list = list(
haddock_output_path.glob(mol2_name + r"*_haddock.pdb*")
)
fu.zip_list(
self.io_dict["out"]["mol2_output_top_zip_path"],
mol2_output_file_list,
self.out_log,
)
# Create zip output
if self.stage_io_dict["out"]["output_haddock_wf_data"][-4:] == ".zip":
zip_wf_output(self)
# Copy files to host
self.copy_to_host()
# Remove temporary files
self.remove_tmp_files()
return self.return_code
[docs]
def topology(
mol1_input_pdb_path: str,
output_haddock_wf_data: str,
mol1_output_top_zip_path: Optional[str] = None,
mol2_input_pdb_path: Optional[str] = None,
mol2_output_top_zip_path: Optional[str] = None,
haddock_config_path: Optional[str] = None,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Topology <biobb_haddock.haddock.topology>` class and
execute the :meth:`launch() <biobb_haddock.haddock.topology.launch>` method."""
return Topology(**dict(locals())).launch()
topology.__doc__ = Topology.__doc__
main = Topology.get_main(topology, "Wrapper of the HADDOCK3 Topology module.")
if __name__ == "__main__":
main()