#!/usr/bin/env python3
"""Module containing the Pdbtidy 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 Pdbtidy(BiobbObject):
"""
| biobb_pdb_tools Pdbtidy
| Modifies the file to adhere (as much as possible) to the format specifications.
| This tool modifies the file to adhere (as much as possible) to the format specifications. It can be used to fix a PDB file that does not adhere to the format specifications.
Args:
input_file_path (str): Input PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_pdb_tools/blob/master/biobb_pdb_tools/test/data/pdb_tools/1AKI.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_file_path (str): PDB file modified according to the specifications. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_tidy.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dic):
* **strict** (*bool*) - (False) Does not add TER on chain breaks.
* **binary_path** (*str*) - ("pdb_tidy") Path to the pdb_tidy 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_tidy import biobb_pdb_tidy
prop = {
'strict': False
}
biobb_pdb_tidy(input_file_path='/path/to/input.pdb',
output_file_path='/path/to/output.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, input_file_path, output_file_path, properties=None, **kwargs
) -> None:
properties = properties or {}
super().__init__(properties)
self.locals_var_dict = locals().copy()
self.io_dict = {
"in": {"input_file_path": input_file_path},
"out": {"output_file_path": output_file_path},
}
self.binary_path = properties.get("binary_path", "pdb_tidy")
self.strict = properties.get("strict", False)
self.properties = properties
self.check_init(properties)
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Pdbtidy <biobb_pdb_tools.pdb_tools.pdb_tidy>` object."""
if self.check_restart():
return 0
self.stage_files()
instructions = []
if self.strict:
instructions.append("-strict")
fu.log("Appending optional boolean property",
self.out_log, self.global_log)
self.cmd = [
self.binary_path,
" ".join(instructions),
self.io_dict["in"]["input_file_path"],
">",
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_tidy(
input_file_path: str,
output_file_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Pdbtidy <biobb_pdb_tools.pdb_tools.pdb_tidy>` class and
execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_tidy.launch>` method."""
return Pdbtidy(**dict(locals())).launch()
biobb_pdb_tidy.__doc__ = Pdbtidy.__doc__
main = Pdbtidy.get_main(biobb_pdb_tidy, "Modifies the file to adhere (as much as possible) to the format specifications.")
if __name__ == "__main__":
main()