#!/usr/bin/env python3
"""Module containing the FPocketRun class and the command line interface."""
import argparse
import shutil
from pathlib import PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_vs.fpocket.common import check_input_path, check_output_path, process_output_fpocket
[docs]class FPocketRun(BiobbObject):
"""
| biobb_vs FPocketRun
| Wrapper of the fpocket software.
| Finds the binding site of the input_pdb_path file via the `fpocket <https://github.com/Discngine/fpocket>`_ software.
Args:
input_pdb_path (str): Path to the PDB structure where the binding site is to be found. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/fpocket_input.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_pockets_zip (str): Path to all the pockets found by fpocket in the input_pdb_path structure. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_pockets.zip>`_. Accepted formats: zip (edam:format_3987).
output_summary (str): Path to the JSON summary file. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_summary.json>`_. Accepted formats: json (edam:format_3464).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **min_radius** (*float*) - (None) [0.1~1000|0.1] The minimum radius in Ångstroms an alpha sphere might have in a binding pocket.
* **max_radius** (*float*) - (None) [2~1000|0.1] The maximum radius in Ångstroms of alpha spheres in a pocket.
* **num_spheres** (*int*) - (None) [1~1000|1] Indicates how many alpha spheres a pocket must contain at least in order to figure in the results.
* **sort_by** (*str*) - ('druggability_score') From which property the output will be sorted. Values: druggability_score (this score intends to assess the likeliness of the pocket to bind a small drug like molecule), score (fpocket score as defined in the `fpocket paper <https://doi.org/10.1186/1471-2105-10-168>`_), volume (volume of the pocket).
* **binary_path** (*string*) - ('fpocket') path to fpocket in your local computer.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **container_path** (*str*) - (None) Container path definition.
* **container_image** (*str*) - ('fpocket/fpocket:latest') Container image definition.
* **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
* **container_working_dir** (*str*) - (None) Container working directory definition.
* **container_user_id** (*str*) - (None) Container user_id definition.
* **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
Examples:
This is a use example of how to use the building block from Python::
from biobb_vs.fpocket.fpocket_run import fpocket_run
prop = {
'min_radius': 3,
'max_radius': 6,
'num_spheres': 35,
'sort_by': 'druggability_score'
}
fpocket_run(input_pdb_path='/path/to/myStructure.pdb',
output_pockets_zip='/path/to/newPockets.zip',
output_summary='/path/to/newSummary.json',
properties=prop)
Info:
* wrapped_software:
* name: fpocket
* version: >=3.1.4.2
* license: MIT
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_pdb_path, output_pockets_zip, output_summary,
properties=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_pockets_zip": output_pockets_zip, "output_summary": output_summary}
}
# Properties specific for BB
self.binary_path = properties.get('binary_path', 'fpocket')
self.min_radius = properties.get('min_radius', None)
self.max_radius = properties.get('max_radius', None)
self.num_spheres = properties.get('num_spheres', None)
self.sort_by = properties.get('sort_by', 'druggability_score')
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", out_log, self.__class__.__name__)
self.io_dict["out"]["output_pockets_zip"] = check_output_path(self.io_dict["out"]["output_pockets_zip"], "output_pockets_zip", False, out_log, self.__class__.__name__)
self.io_dict["out"]["output_summary"] = check_output_path(self.io_dict["out"]["output_summary"], "output_summary", True, out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`FPocketRun <fpocket.fpocket_run.FPocketRun>` fpocket.fpocket_run.FPocketRun object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
if self.container_path:
tmp_input = str(PurePath(self.container_volume_path).joinpath(PurePath(self.io_dict["in"]["input_pdb_path"]).name))
self.tmp_folder = self.stage_io_dict['unique_dir']
else:
# create tmp_folder
self.tmp_folder = fu.create_unique_dir()
fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
tmp_input = str(PurePath(self.tmp_folder).joinpath('input.pdb'))
# copy input_pdb_path to tmp_folder
shutil.copy(self.io_dict["in"]["input_pdb_path"], tmp_input)
# create cmd
self.cmd = [self.binary_path,
'-f', tmp_input]
# adding extra properties
if self.min_radius:
self.cmd.extend(['-m', str(self.min_radius)])
if self.max_radius:
self.cmd.extend(['-M', str(self.max_radius)])
if self.num_spheres:
self.cmd.extend(['-i', str(self.num_spheres)])
fu.log('Executing fpocket', self.out_log, self.global_log)
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
process_output_fpocket(self.tmp_folder,
self.io_dict["out"]["output_pockets_zip"],
self.io_dict["out"]["output_summary"],
self.sort_by,
self.remove_tmp,
self.container_path,
self.out_log,
self.__class__.__name__)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
self.tmp_folder
])
self.remove_tmp_files()
return self.return_code
[docs]def fpocket_run(input_pdb_path: str, output_pockets_zip: str, output_summary: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`FPocketRun <fpocket.fpocket_run.FPocketRun>` class and
execute the :meth:`launch() <fpocket.fpocket_run.FPocketRun.launch>` method."""
return FPocketRun(input_pdb_path=input_pdb_path,
output_pockets_zip=output_pockets_zip,
output_summary=output_summary,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Finds the binding site of the input_pdb_path file via the fpocket software", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_pdb_path', required=True, help='Path to the PDB structure where the binding site is to be found. Accepted formats: pdb.')
required_args.add_argument('--output_pockets_zip', required=True, help='Path to all the pockets found by fpocket in the input_pdb_path structure. Accepted formats: zip.')
required_args.add_argument('--output_summary', required=True, help='Path to the JSON summary file. Accepted formats: json.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
fpocket_run(input_pdb_path=args.input_pdb_path,
output_pockets_zip=args.output_pockets_zip,
output_summary=args.output_summary,
properties=properties)
if __name__ == '__main__':
main()