Source code for utils.cat_pdb

#!/usr/bin/env python3

"""Module containing the CatPDB class and the command line interface."""
import argparse
from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools.file_utils import launchlogger
from biobb_structure_utils.utils.common import check_input_path, check_output_path


[docs]class CatPDB(BiobbObject): """ | biobb_structure_utils CatPDB | Class to concat two PDB structures in a single PDB file. Args: input_structure1 (str): Input structure 1 file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/cat_protein.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476). input_structure2 (str): Input structure 2 file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/cat_ligand.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476). output_structure_path (str): Output protein file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_cat_pdb.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **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_structure_utils.utils.cat_pdb import cat_pdb prop = { } cat_pdb(input_structure1='/path/to/myInputStr1.pdb', input_structure2='/path/to/myInputStr2.pdb', output_structure_path='/path/to/newStructure.pdb', properties=prop) Info: * wrapped_software: * name: In house * license: Apache-2.0 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_structure1, input_structure2, output_structure_path, properties=None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) self.locals_var_dict = locals().copy() # Input/Output files self.io_dict = { "in": {"input_structure1": input_structure1, "input_structure2": input_structure2}, "out": {"output_structure_path": output_structure_path} } # Properties specific for BB self.properties = properties # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`CatPDB <utils.cat_pdb.CatPDB>` utils.cat_pdb.CatPDB object.""" self.io_dict['in']['input_structure1'] = check_input_path(self.io_dict['in']['input_structure1'], self.out_log, self.__class__.__name__) self.io_dict['in']['input_structure2'] = check_input_path(self.io_dict['in']['input_structure2'], self.out_log, self.__class__.__name__) self.io_dict['out']['output_structure_path'] = check_output_path(self.io_dict['out']['output_structure_path'], self.out_log, self.__class__.__name__) # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Business code filenames = [self.io_dict['in']['input_structure1'], self.io_dict['in']['input_structure2']] # check if self.input_structure1 and self.input_structure2 end with newline newline = [False, False] for idx, fname in enumerate(filenames): with open(fname, 'rb') as fh: fh.seek(-2, 2) last = fh.readlines()[-1].decode() newline[idx] = "\n" in last # concat both input files and save them into output file with open(self.io_dict['out']['output_structure_path'], 'w') as outfile: for idx, fname in enumerate(filenames): with open(fname) as infile: for line in infile: if not line.startswith("END"): outfile.write(line) # if not ends in newline, add it if not newline[idx]: outfile.write("\n") self.return_code = 0 # Copy files to host self.copy_to_host() # Remove temporal files self.tmp_files.append(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 cat_pdb(input_structure1: str, input_structure2: str, output_structure_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`CatPDB <utils.cat_pdb.CatPDB>` class and execute the :meth:`launch() <utils.cat_pdb.CatPDB.launch>` method.""" return CatPDB(input_structure1=input_structure1, input_structure2=input_structure2, output_structure_path=output_structure_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="Concat two PDB structures in a single PDB file.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('-i1', '--input_structure1', required=True, help="Input structure 1 file path. Accepted formats: pdb.") required_args.add_argument('-i2', '--input_structure2', required=True, help="Input structure 2 file path. Accepted formats: pdb.") required_args.add_argument('-o', '--output_structure_path', required=True, help="Output structure file path. Accepted formats: pdb.") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block cat_pdb(input_structure1=args.input_structure1, input_structure2=args.input_structure2, output_structure_path=args.output_structure_path, properties=properties)
if __name__ == '__main__': main()