#!/usr/bin/env python3
"""Module containing the Pdbmerge 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
import os
import zipfile
from pathlib import Path
[docs]class Pdbmerge(BiobbObject):
"""
| biobb_pdb_tools Pdbmerge
| Merges several PDB files into one.
Args:
input_file_path (str): ZIP file of selected protein. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_pdb_tools/master/biobb_pdb_tools/test/data/pdb_tools/input_pdb_merge1.pdb>`_. Accepted formats: zip (edam:format_3987).
output_file_path (str): 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_merge.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dic):
* **binary_path** (*str*) - ("pdb_merge") Path to the pdb_merge 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_merge import biobb_pdb_merge
biobb_pdb_merge(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_merge')
self.properties = properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`Pdbmerge <biobb_pdb_tools.pdb_tools.pdb_merge>` 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(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_merge(input_file_path: str, output_file_path: str, properties: dict = None, **kwargs) -> int:
"""Create :class:`Pdbmerge <biobb_pdb_tools.pdb_tools.pdb_merge>` class and
execute the :meth:`launch() <biobb_pdb_tools.pdb_tools.pdb_merge.launch>` method."""
return Pdbmerge(input_file_path=input_file_path,
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='Merges several PDB files into one.', 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('--input_file_path', required=True, help='Description for the first input file path. Accepted formats: pdb.')
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_merge(input_file_path=args.input_file_path, output_file_path=args.output_file_path, properties=properties)
if __name__ == '__main__':
main()