#!/usr/bin/env python3
"""Module containing the Pdbsplitmodel class and the command line interface."""
import glob
import os
import zipfile
from pathlib import Path
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 Pdbsplitmodel(BiobbObject):
"""
| biobb_pdb_tools Pdbsplitmodel
| Splits a PDB file into several, each containing one MODEL.
| This tool splits a PDB file into several, each containing one MODEL. It can be used to split a PDB file into several, each containing one MODEL.
Args:
input_file_path (str): Input PDB file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/data/pdb_tools/input_pdb_splitmodel.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_file_path (str): ZIP file containing all PDB files splited by protein model. File type: output. `Sample file <https://github.com/bioexcel/biobb_pdb_tools/blob/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_splitmodel.zip>`_. Accepted formats: zip (edam:format_3987).
properties (dic):
* **binary_path** (*str*) - ("pdb_splitmodel") Path to the pdb_splitmodel 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_splitmodel import biobb_pdb_splitmodel
biobb_pdb_splitmodel(input_file_path='/path/to/input.pdb',
output_file_path='/path/to/output.zip)
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_splitmodel")
self.properties = properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Pdbsplitmodel <biobb_pdb_tools.pdb_tools.pdb_splitmodel>` object."""
if self.check_restart():
return 0
self.stage_files()
self.cmd = [
"cd",
self.stage_io_dict.get("unique_dir", ""),
";",
self.binary_path,
self.stage_io_dict["in"]["input_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()
stem = Path(self.stage_io_dict["in"]["input_file_path"]).stem
pdb_files = glob.glob(
os.path.join(self.stage_io_dict.get(
"unique_dir", ""), stem + "_*.pdb")
)
if len(pdb_files) > 1:
output_zip_path = os.path.join(
self.stage_io_dict.get("unique_dir", ""),
self.stage_io_dict["out"]["output_file_path"],
)
fu.log(
"Saving %d pdb model files in a zip" % len(pdb_files),
self.out_log,
self.global_log,
)
with zipfile.ZipFile(output_zip_path, "w") as zipf:
for pdb_file in pdb_files:
zipf.write(pdb_file, os.path.basename(pdb_file))
else:
fu.log("The given input file has no models.",
self.out_log, self.global_log)
output_zip_path = os.path.join(
self.stage_io_dict.get("unique_dir", ""),
self.stage_io_dict["out"]["output_file_path"],
)
with zipfile.ZipFile(output_zip_path, "w") as zipf:
zipf.write(
self.stage_io_dict["in"]["input_file_path"],
os.path.basename(
self.stage_io_dict["in"]["input_file_path"]),
)
pass
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_splitmodel(
input_file_path: str,
output_file_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Pdbsplitmodel <biobb_pdb_tools.pdb_tools.pdb_splitmodel>` class and
execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_splitmodel.launch>` method."""
return Pdbsplitmodel(**dict(locals())).launch()
biobb_pdb_splitmodel.__doc__ = Pdbsplitmodel.__doc__
main = Pdbsplitmodel.get_main(biobb_pdb_splitmodel, "Splits a PDB file into several, each containing one MODEL.")
if __name__ == "__main__":
main()