#!/usr/bin/env python3
"""Module containing the haddock class and the command line interface."""
import glob
import os
import shutil
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools.file_utils import launchlogger
[docs]
class Haddock3Accessibility(BiobbObject):
"""
| biobb_haddock Haddock3Accessibility
| Wrapper class for the Haddock-Restraints Accessibility module.
| `Haddock-Restraints Accessibility <https://www.bonvinlab.org/haddock3/clients/haddock.clis.restraints.calc_accessibility.html>`_ computes residues accessibility using freesasa included in the Haddock3 package.
Args:
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_noH.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_accessibility_path (str): Path to the output file with accessibility information. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/mol1_sasa.txt>`_. 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 <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/mol1_haddock_actpass.txt>`_. 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:
* 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_pdb_path: str,
output_accessibility_path: str,
output_actpass_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_pdb_path": input_pdb_path,
},
"out": {
"output_accessibility_path": output_accessibility_path,
"output_actpass_path": output_actpass_path,
},
}
# Properties specific for BB
self.chain = properties.get("chain", "A")
self.cutoff = properties.get("cutoff", 0.4)
self.probe_radius = properties.get("probe_radius", 1.4)
self.pass_to_act = properties.get("pass_to_act", False)
# Properties specific for BB
self.binary_path = properties.get("binary_path", "haddock3-restraints")
# Check the properties
self.check_init(properties)
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Haddock3Accessibility <biobb_haddock.haddock_restraints.haddock3_accessibility>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# haddock3-restraints calc_accessibility 1UBQ.pdb --export_to_actpass
self.cmd = [self.binary_path, "calc_accessibility", self.stage_io_dict['in']['input_pdb_path']]
if self.io_dict["out"]["output_actpass_path"] is not None:
self.cmd.append("--export_to_actpass")
self.cmd.append(f"-c {self.cutoff}")
self.cmd.append(">")
self.cmd.append(self.stage_io_dict['out']['output_accessibility_path'])
self.cmd.append("2>&1")
# Run Biobb block
self.run_biobb()
# Check chain
target_string = f"Chain {self.chain}"
found = False
with open(self.stage_io_dict['out']['output_accessibility_path'], 'r') as file:
for line in file:
if target_string in line:
found = True
if found:
# Rename/Copy output file to the given output file name
file_name = os.path.basename(self.io_dict['in']['input_pdb_path'])
shutil.copyfile(f"{file_name[:-4]}_passive_{self.chain}.actpass", self.io_dict["out"]["output_actpass_path"])
if self.pass_to_act:
with open(self.io_dict["out"]["output_actpass_path"], 'r') as file:
lines = file.readlines()
with open(self.io_dict["out"]["output_actpass_path"], 'w') as file:
file.write(lines[1])
file.write('\n\n')
else:
print(f"\nWARNING: Chain {self.chain} not found in input PDB file. Please check and modify the chain property accordingly.\n")
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.tmp_files.extend(glob.glob('*.actpass'))
self.remove_tmp_files()
return self.return_code
[docs]
def haddock3_accessibility(
input_pdb_path: str,
output_accessibility_path: str,
output_actpass_path: Optional[str] = None,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Haddock3Accessibility <biobb_haddock.haddock_restraints.haddock3_accessibility>` class and
execute the :meth:`launch() <biobb_haddock.haddock_restraints.haddock3_accessibility.launch>` method."""
return Haddock3Accessibility(**dict(locals())).launch()
haddock3_accessibility.__doc__ = Haddock3Accessibility.__doc__
main = Haddock3Accessibility.get_main(haddock3_accessibility, "Wrapper of the Haddock-Restraints Accessibility module.")
if __name__ == "__main__":
main()