#!/usr/bin/env python3
"""Module containing the FPocketSelect 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
[docs]class FPocketSelect(BiobbObject):
"""
| biobb_vs FPocketSelect
| Selects a single pocket in the outputs of the fpocket building block.
| Selects a single pocket in the outputs of the fpocket building block from a given parameter.
Args:
input_pockets_zip (str): Path to the pockets found by fpocket. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/input_pockets.zip>`_. Accepted formats: zip (edam:format_3987).
output_pocket_pdb (str): Path to the PDB file with the cavity found by fpocket. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_pocket.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_pocket_pqr (str): Path to the PQR file with the pocket found by fpocket. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_pocket.pqr>`_. Accepted formats: pqr (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **pocket** (*int*) - (1) [1~1000|1] Pocket id from the summary json given by the fpocket building block.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the building block from Python::
from biobb_vs.fpocket.fpocket_select import fpocket_select
prop = {
'pocket': 2
}
fpocket_select(input_pockets_zip='/path/to/myPockets.zip',
output_pocket_pdb='/path/to/myCavity.pdb',
output_pocket_pqr='/path/to/myPocket.pqr',
properties=prop)
Info:
* wrapped_software:
* name: In house
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_pockets_zip, output_pocket_pdb, output_pocket_pqr,
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_pockets_zip": input_pockets_zip},
"out": {"output_pocket_pdb": output_pocket_pdb, "output_pocket_pqr": output_pocket_pqr}
}
# Properties specific for BB
self.pocket = properties.get('pocket', None)
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_pockets_zip"] = check_input_path(self.io_dict["in"]["input_pockets_zip"], "input_pockets_zip", out_log, self.__class__.__name__)
self.io_dict["out"]["output_pocket_pdb"] = check_output_path(self.io_dict["out"]["output_pocket_pdb"], "output_pocket_pdb", False, out_log, self.__class__.__name__)
self.io_dict["out"]["output_pocket_pqr"] = check_output_path(self.io_dict["out"]["output_pocket_pqr"], "output_pocket_pqr", True, out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`FPocketSelect <fpocket.fpocket_select.FPocketSelect>` fpocket.fpocket_select.FPocketSelect 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()
# create tmp_folder
self.tmp_folder = fu.create_unique_dir()
fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
# decompress the input_pockets_zip file to tmp_folder
all_pockets = fu.unzip_list(zip_file=self.io_dict["in"]["input_pockets_zip"], dest_dir=self.tmp_folder, out_log=self.out_log)
pockets_list = [i for i in all_pockets if ('pocket' + str(self.pocket)) in i]
for p in pockets_list:
if PurePath(p).suffix == '.pdb':
fu.log('Saving %s file' % self.io_dict["out"]["output_pocket_pdb"], self.out_log)
shutil.copy(p, self.io_dict["out"]["output_pocket_pdb"])
else:
fu.log('Saving %s file' % self.io_dict["out"]["output_pocket_pqr"], self.out_log)
shutil.copy(p, self.io_dict["out"]["output_pocket_pqr"])
# Copy files to host
self.copy_to_host()
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
self.tmp_folder
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def fpocket_select(input_pockets_zip: str, output_pocket_pdb: str, output_pocket_pqr: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`FPocketSelect <fpocket.fpocket_select.FPocketSelect>` class and
execute the :meth:`launch() <fpocket.fpocket_select.FPocketSelect.launch>` method."""
return FPocketSelect(input_pockets_zip=input_pockets_zip,
output_pocket_pdb=output_pocket_pdb,
output_pocket_pqr=output_pocket_pqr,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Selects a single pocket in the outputs of the fpocket building block from a given parameter.", 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_pockets_zip', required=True, help='Path to all the pockets found by fpocket. Accepted formats: zip.')
required_args.add_argument('--output_pocket_pdb', required=True, help='Path to the PDB file with the cavity found by fpocket. Accepted formats: pdb.')
required_args.add_argument('--output_pocket_pqr', required=True, help='Path to the PQR file with the pocket found by fpocket. Accepted formats: pqr.')
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_select(input_pockets_zip=args.input_pockets_zip,
output_pocket_pdb=args.output_pocket_pdb,
output_pocket_pqr=args.output_pocket_pqr,
properties=properties)
if __name__ == '__main__':
main()