#!/usr/bin/env python3
"""Module containing the HADDOCK3 FlexRef class and the command line interface."""
from os.path import abspath
from typing import Optional
import biobb_haddock.haddock.common as common
[docs]
class FlexRef(common.HaddockStepBase):
"""
| biobb_haddock FlexRef
| Wrapper class for the HADDOCK3 FlexRef module.
| The FlexRef module.`HADDOCK3 FlexRef module <https://www.bonvinlab.org/haddock3/modules/refinement/haddock.modules.refinement.flexref.html>`_ computes a flexible refinement over selected structures.
Args:
input_haddock_wf_data (dir): Path to the input directory containing all the current Haddock workflow data. File type: input. `Sample file <https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_topology.zip>`_. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).
output_haddock_wf_data (dir): Path to the output directory containing all the current Haddock workflow data. File type: output. Accepted formats: directory (edam:format_1915), zip (edam:format_3987).
refinement_output_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_rigidbody.zip>`_. 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 <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl>`_. 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 <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl>`_. 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 <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl>`_. Accepted formats: tbl (edam:format_2330).
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.flex_ref import flex_ref
prop = { 'binary_path': 'haddock' }
flex_ref(input_haddock_wf_data='/path/to/myInputData',
output_haddock_wf_data='/path/to/myOutputData',
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,
refinement_output_zip_path: Optional[str] = None,
ambig_restraints_table_path: Optional[str] = None,
unambig_restraints_table_path: Optional[str] = None,
hb_restraints_table_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": {
"input_haddock_wf_data": input_haddock_wf_data,
"ambig_restraints_table_path": ambig_restraints_table_path,
"unambig_restraints_table_path": unambig_restraints_table_path,
"hb_restraints_table_path": hb_restraints_table_path,
"haddock_config_path": haddock_config_path,
},
"out": {
"output_haddock_wf_data": output_haddock_wf_data,
"refinement_output_zip_path": refinement_output_zip_path,
},
}
# Properties specific for BB
self.haddock_step_name = "flexref"
# Handle configuration options from propierties
self.cfg = {k: v for k, v in properties.get("cfg", dict()).items()}
# Handle configuration options from arguments
if ambig_restraints_table_path:
self.cfg["ambig_fname"] = ambig_restraints_table_path
if unambig_restraints_table_path:
self.cfg["unambig_fname"] = unambig_restraints_table_path
if hb_restraints_table_path:
self.cfg["hbond_fname"] = hb_restraints_table_path
# 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)
def _handle_config_arguments(self):
"""Handle configuration options from arguments."""
if self.io_dict["in"].get("ambig_restraints_table_path"):
self.cfg["ambig_fname"] = abspath(self.stage_io_dict["in"].get("ambig_restraints_table_path"))
if self.io_dict["in"].get("unambig_restraints_table_path"):
self.cfg["unambig_fname"] = abspath(self.stage_io_dict["in"].get("unambig_restraints_table_path"))
if self.io_dict["in"].get("hb_restraints_table_path"):
self.cfg["hbond_fname"] = abspath(self.stage_io_dict["in"].get("hb_restraints_table_path"))
def _handle_step_output(self):
"""Handle how the output files from the step are copied to host."""
if refinement_output_zip_path := self.io_dict["out"].get("refinement_output_zip_path"):
self.copy_step_output(
lambda path: path.match(self.haddock_step_name + r"*.pdb*"),
refinement_output_zip_path
)
[docs]
def flex_ref(
input_haddock_wf_data: str,
output_haddock_wf_data: str,
refinement_output_zip_path: Optional[str] = None,
ambig_restraints_table_path: Optional[str] = None,
unambig_restraints_table_path: Optional[str] = None,
hb_restraints_table_path: Optional[str] = None,
haddock_config_path: Optional[str] = None,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`FlexRef <biobb_haddock.haddock.flex_ref>` class and
execute the :meth:`launch() <biobb_haddock.haddock.flex_ref.launch>` method."""
# Launch method inherited from HaddockStepBase
return FlexRef(**dict(locals())).launch()
flex_ref.__doc__ = FlexRef.__doc__
main = FlexRef.get_main(flex_ref, "Wrapper of the HADDOCK3 FlexRef module.")
if __name__ == "__main__":
main()