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 typing import Optional

from biobb_common.configuration import settings
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

from biobb_structure_utils.utils.common import (
    _from_string_to_list,
    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 <https://github.com/bioexcel/biobb_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 <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_chain.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476). output_structure_path (str): Output structure file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_chain.pdb>`_. 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. * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. 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: http://edamontology.org/EDAM.owl """ 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 = _from_string_to_list(properties.get("chains", [])) self.permissive = properties.get("permissive", False) self.properties = 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: Optional[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()