Source code for utils.extract_model

#!/usr/bin/env python3

"""Module containing the ExtractModel 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 check_input_path, check_output_path


[docs] class ExtractModel(BiobbObject): """ | biobb_structure_utils ExtractModel | This class is a wrapper of the Structure Checking tool to extract a model from a 3D structure. | Wrapper for the `Structure Checking <https://github.com/bioexcel/biobb_structure_checking>`_ tool to extract a model 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_model.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_model.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **models** (*list*) - (None) List of models to be extracted from the input_structure_path file. If empty, all the models of the structure will be returned. * **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_model import extract_model prop = { 'models': [ 1, 2, 3 ] } extract_model(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.models = properties.get("models", []) self.properties = properties # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`ExtractModel <utils.extract_model.ExtractModel>` utils.extract_model.ExtractModel 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 models properly models = check_format_models(self.models, self.out_log) if models == "All": shutil.copyfile( self.io_dict["in"]["input_structure_path"], self.io_dict["out"]["output_structure_path"], ) return 0 else: # create temporary folder tmp_folder = fu.create_unique_dir() fu.log("Creating %s temporary folder" % tmp_folder, self.out_log) filenames = [] for model in models: tmp_file = tmp_folder + "/model" + str(model) + ".pdb" self.cmd = [ self.binary_path, "-i", self.stage_io_dict["in"]["input_structure_path"], "-o", tmp_file, "--force_save", "models", "--select", str(model), ] # Run Biobb block self.run_biobb() filenames.append(tmp_file) # concat tmp_file and save them into output file with open(self.io_dict["out"]["output_structure_path"], "w") as outfile: for i, fname in enumerate(filenames): with open(fname) as infile: outfile.write("MODEL " + "{:>4}".format(str(i + 1)) + "\n") for line in infile: if not line.startswith("END"): outfile.write(line) else: outfile.write("ENDMDL\n") # Copy files to host self.copy_to_host() # Remove temporal files self.tmp_files.extend( [self.stage_io_dict.get("unique_dir", ""), tmp_folder] ) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs] def check_format_models(models, out_log): """Check format of models list""" if not models: fu.log("Empty models parameter, all models will be returned.", out_log) return "All" if not isinstance(models, list): fu.log( "Incorrect format of models parameter, all models will be returned.", out_log, ) return "All" return models
[docs] def extract_model( input_structure_path: str, output_structure_path: str, properties: Optional[dict] = None, **kwargs, ) -> int: """Execute the :class:`ExtractModel <utils.extract_model.ExtractModel>` class and execute the :meth:`launch() <utils.extract_model.ExtractModel.launch>` method.""" return ExtractModel( 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 model 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_model( input_structure_path=args.input_structure_path, output_structure_path=args.output_structure_path, properties=properties, )
if __name__ == "__main__": main()