#!/usr/bin/env python3
"""Module containing the Mkensemble class and the command line interface."""
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 Mkensemble(BiobbObject):
"""
| biobb_pdb_tools Mkensemble
| Merges several PDB files into one multi-model (ensemble) file.
| This tool merges several PDB files into one multi-model (ensemble) file. It can be used to merge several PDB files into one multi-model (ensemble) file.
Args:
input_file_path (str): Input ZIP file of selected proteins. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/data/pdb_tools/input_pdb_mkensemble.zip>`_. Accepted formats: zip (edam:format_3987).
output_file_path (str): Multi-model (ensemble) PDB file with input PDBs merged. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/reference/pdb_tools/ref_pdb_mkensemble.pdb>`_. Accepted formats: pdb (edam:format_3987).
properties (dic):
* **binary_path** (*str*) - ("pdb_mkensemble") Path to the pdb_mkensemble 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_mkensemble import biobb_pdb_mkensemble
biobb_pdb_mkensemble(input_file_path='/path/to/input1.zip',
output_file_path='/path/to/output.pdb')
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_mkensemble")
self.properties = properties
self.check_init(properties)
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Mkensemble <biobb_pdb_tools.pdb_tools.pdb_mkensemble>` object."""
if self.check_restart():
return 0
self.stage_files()
input_file_path = self.stage_io_dict["in"]["input_file_path"]
folder_path = os.path.dirname(input_file_path)
if zipfile.is_zipfile(input_file_path):
with zipfile.ZipFile(input_file_path, "r") as zip_ref:
zip_ref.extractall(folder_path)
pdb_files = [
file
for file in os.listdir(folder_path)
if file.lower().endswith(".pdb")
]
input_file_list = [os.path.join(
folder_path, file) for file in pdb_files]
input_file_list = [Path(i) for i in input_file_list]
input_file_list = sorted(
input_file_list, key=lambda i: i.stem.upper())
input_file_list = [str(i) for i in input_file_list]
self.cmd = [
self.binary_path,
*input_file_list,
">",
self.io_dict["out"]["output_file_path"],
]
else:
fu.log(
f"The archive {input_file_path} is not a ZIP!",
self.out_log,
self.global_log,
)
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_mkensemble(
input_file_path: str,
output_file_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Mkensemble <biobb_pdb_tools.pdb_tools.pdb_mkensemble>` class and
execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_mkensemble.launch>` method."""
return Mkensemble(**dict(locals())).launch()
biobb_pdb_mkensemble.__doc__ = Mkensemble.__doc__
main = Mkensemble.get_main(biobb_pdb_mkensemble, "Merges several PDB files into one multi-model (ensemble) file.")
if __name__ == "__main__":
main()