#!/usr/bin/env python3
"""Module containing the Pdbfetch class and the command line interface."""
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
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.
| This tool downloads a structure in PDB format from the RCSB website. It can be used to download 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_init(properties)
[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(" ".join(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.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: Optional[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(**dict(locals())).launch()
main = Pdbfetch.get_main(biobb_pdb_fetch, "Downloads a structure in PDB format from the RCSB website.")
biobb_pdb_fetch.__doc__ = Pdbfetch.__doc__
if __name__ == "__main__":
main()