Source code for utils.extract_chain

#!/usr/bin/env python3

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

[docs]class ExtractChain(BiobbObject): """ | biobb_structure_utils ExtractAtoms | This class is a wrapper of the Structure Checking tool to extract a chain from a 3D structure. | Wrapper for the `Structure Checking <>`_ tool to extract a chain from a 3D structure. Args: input_structure_path (str): Input structure file path. File type: input. `Sample file <>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476). output_structure_path (str): Output structure file path. File type: output. `Sample file <>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **chains** (*list*) - (None) List of chains to be extracted from the input_structure_path file. If empty, all the chains of the structure will be returned. * **permissive** (*bool*) - (False) Use non standard PDB files. * **binary_path** (*string*) - ("check_structure") path to the check_structure application * **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.extract_chain import extract_chain prop = { 'chains': [ 'A', 'B' ] } extract_chain(input_structure_path='/path/to/myStructure.pdb', output_structure_path='/path/to/newStructure.pdb', properties=prop) Info: * wrapped_software: * name: Structure Checking from MDWeb * version: >=3.0.3 * license: Apache-2.0 * ontology: * name: EDAM * schema: """ def __init__(self, input_structure_path, 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_structure_path": input_structure_path}, "out": {"output_structure_path": output_structure_path} } # Properties specific for BB self.binary_path = properties.get('binary_path', 'check_structure') self.chains = properties.get('chains', []) self.permissive = properties.get('permissive', False) = properties # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`ExtractChain <utils.extract_chain.ExtractChain>` utils.extract_chain.ExtractChain object.""" self.io_dict['in']['input_structure_path'] = check_input_path(self.io_dict['in']['input_structure_path'], 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() # check if user has passed chains properly chains = check_format_chains(self.chains, self.out_log) fu.log(f"Selected Chains: {chains}", self.out_log, self.global_log) if self.permissive: fu.log('Warning: Use permissive=True is a risky option use it under your own responsability', self.out_log, self.global_log) if chains.upper() == 'ALL': shutil.copyfile(self.io_dict['in']['input_structure_path'], self.io_dict['out']['output_structure_path']) else: chain_list = chains.upper().replace(" ", "").split(",") with open(self.io_dict['in']['input_structure_path']) as structure_in, open(self.io_dict['out']['output_structure_path'], 'w') as structure_out: for line in structure_in: if line.strip().upper().startswith(('ATOM', 'HETATM')) and line.strip().upper()[21] in chain_list: structure_out.write(line) else: # run command line self.cmd = [self.binary_path, '-i', self.io_dict['in']['input_structure_path'], '-o', self.io_dict['out']['output_structure_path'], '--force_save', 'chains', '--select', chains] # Run Biobb block self.run_biobb() # 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 check_format_chains(chains, out_log): """ Check format of chains list """ if not chains: fu.log('Empty chains parameter, all chains will be returned.', out_log) return 'All' if not isinstance(chains, list): fu.log('Incorrect format of chains parameter, all chains will be returned.', out_log) return 'All' return ','.join(chains)
[docs]def extract_chain(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`ExtractChain <utils.extract_chain.ExtractChain>` class and execute the :meth:`launch() <utils.extract_chain.ExtractChain.launch>` method.""" return ExtractChain(input_structure_path=input_structure_path, 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="Extract a chain from a 3D structure.", 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('-i', '--input_structure_path', required=True, help="Input structure 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 extract_chain(input_structure_path=args.input_structure_path, output_structure_path=args.output_structure_path, properties=properties)
if __name__ == '__main__': main()