#!/usr/bin/env python3
"""Module containing the Pdbfetch class and the command line interface."""
import argparse
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
[docs]class Pdbfetch(BiobbObject):
"""
| biobb_pdb_tools Pdbfetch
| Downloads a structure in PDB format from the RCSB website.
Args:
output_file_path (str): PDB file of the protein selected. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_fetch.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dic):
* **pdbid** (*string*) - ('1aki') ID of the protein.
* **biounit** (*string*) - (False) Allows downloading the (first) biological structure if selected.
* **binary_path** (*str*) - ("pdb_fetch") Path to the pdb_fetch executable binary.
* **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_pdb_tools.pdb_tools.biobb_pdb_fetch import biobb_pdb_fetch
prop = {
'biounit': False,
'pdbid': '1aki'
}
biobb_pdb_fetch(output_file_path='/path/to/file.pdb',
properties=prop)
Info:
* wrapped_software:
* name: pdb_tools
* version: >=2.5.0
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, output_file_path, properties=None, **kwargs) -> None:
properties = properties or {}
super().__init__(properties)
self.locals_var_dict = locals().copy()
self.io_dict = {
'out': {'output_file_path': output_file_path}
}
self.pdbid = properties.get('pdbid', '1aki')
self.binary_path = properties.get('binary_path', 'pdb_fetch')
self.biounit = properties.get('biounit', False)
self.properties = properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`Pdbfetch <biobb_pdb_tools.pdb_tools.pdb_fetch>` object."""
if self.check_restart():
return 0
instructions = []
if self.biounit:
instructions.append('-biounit')
fu.log('Appending optional boolean property', self.out_log, self.global_log)
self.cmd = [self.binary_path, ' '.join(instructions), self.pdbid, '>', self.io_dict['out']['output_file_path']]
fu.log(self.cmd, self.out_log, self.global_log)
fu.log('Creating command line with instructions and required arguments', self.out_log, self.global_log)
self.run_biobb()
self.copy_to_host()
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir")
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def biobb_pdb_fetch(output_file_path: str, properties: dict = None, **kwargs) -> int:
"""Create :class:`Pdbfetch <biobb_pdb_tools.pdb_tools.pdb_fetch>` class and
execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_fetch.launch>` method."""
return Pdbfetch(output_file_path=output_file_path,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description='Downloads a structure in PDB format from the RCSB website.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=True, help='Configuration file')
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--output_file_path', required=True, help='Description for the output file path. Accepted formats: zip.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
biobb_pdb_fetch(output_file_path=args.output_file_path, properties=properties)
if __name__ == '__main__':
main()