#!/usr/bin/env python3
"""Module containing the HADDOCK3 Run class and the command line interface."""
from typing import Optional
import biobb_haddock.haddock.common as common
[docs]
class Haddock3Run(common.HaddockStepBase):
"""
| biobb_haddock Haddock3Run
| Wrapper class for the HADDOCK3 Run module.
| The HADDOCK3 run module launches the HADDOCK3 execution for docking.
Args:
input_haddock_wf_data (dir): Input folder containing all the files defined in the config. File type: input. `Sample folder <https://github.com/bioexcel/biobb_haddock/tree/master/biobb_haddock/test/data/haddock/haddock_wf_data_run.zip>`_. 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 <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.
* **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
"""
def __init__(
self,
input_haddock_wf_data: str,
output_haddock_wf_data: str,
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": {
"input_haddock_wf_data": input_haddock_wf_data,
"haddock_config_path": haddock_config_path,
},
"out": {
"output_haddock_wf_data": output_haddock_wf_data,
},
}
# Properties specific for HADDOCK Step
self.haddock_step_name = "haddock3_run"
# Handle configuration options from properties
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=True))
# Properties specific for BB
self.binary_path = properties.get("binary_path", "haddock3")
# Check the properties
self.check_init(properties)
[docs]
def haddock3_run(
input_haddock_wf_data: str,
output_haddock_wf_data: str,
haddock_config_path: Optional[str] = None,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Haddock3Run <biobb_haddock.haddock.haddock3_run>` class and
execute the :meth:`launch() <biobb_haddock.haddock.haddock3_run.launch>` method."""
# Launch method inherited from HaddockStepBase
return Haddock3Run(**dict(locals())).launch()
haddock3_run.__doc__ = Haddock3Run.__doc__
main = Haddock3Run.get_main(haddock3_run, "Wrapper of the HADDOCK3 Haddock3Run module.")
if __name__ == "__main__":
main()