Source code for utils.structure_check

#!/usr/bin/env python3

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

[docs]class StructureCheck(BiobbObject): """ | biobb_structure_utils StructureCheck | This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file. | Wrapper for the `Structure Checking <>`_ tool to generate summary checking results on a json file from a given structure and a list of features. 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_summary_path (str): Output summary checking results. File type: output. `Sample file <>`_. Accepted formats: json (edam:format_3464). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **features** (*list*) - (None) Features to summarize. If None, all the features will be computed. Values: models (multiple molecules or coordinate sets in a single file), chains (multiple chains in a single file), altloc (atom alternative conformation given an alternate location indicator and occupancy), metals (metals present in the structure), ligands (heteroatoms present in the structure), chiral (to say that a structure is chiral is to say that its mirror image is not the same as it self), getss (detect SS bonds or disulfides), cistransbck (detact cis/trans backbone), backbone (detect backbone breaks), amide (detect too close amides), clashes (detect clashes). * **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.structure_check import structure_check prop = { 'features': ['models', 'chains', 'ligands'] } structure_check(input_structure_path='/path/to/myInputStr.pdb', output_summary_path='/path/to/newSummary.json', 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_summary_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_summary_path": output_summary_path} } # Properties specific for BB self.binary_path = properties.get('binary_path', 'check_structure') self.features = properties.get('features', None) = properties # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`StructureCheck <utils.structure_check.StructureCheck>` utils.structure_check.StructureCheck 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_summary_path'] = check_output_path_json(self.io_dict['out']['output_summary_path'], self.out_log, self.__class__.__name__) # Setup Biobb if self.check_restart(): return 0 self.stage_files() tmp_folder = None if not self.features or self.features is None or self.features == 'None': fu.log('No features provided, all features will be computed: %s' % 'models, chains, altloc, metals, ligands, chiral, getss, cistransbck, backbone, amide, clashes', self.out_log) self.cmd = [self.binary_path, '-i', self.stage_io_dict['in']['input_structure_path'], '--json', self.stage_io_dict['out']['output_summary_path'], '--check_only', '--non_interactive', 'checkall'] else: fu.log('Computing features: %s' % ', '.join(self.features), self.out_log) # create temporary folder tmp_folder = fu.create_unique_dir() fu.log('Creating %s temporary folder' % tmp_folder, self.out_log) command_list = tmp_folder + '/command_list.lst' with open(command_list, 'w') as f: for item in self.features: f.write("%s\n" % item) self.cmd = [self.binary_path, '-i', self.stage_io_dict['in']['input_structure_path'], '--json', self.stage_io_dict['out']['output_summary_path'], '--check_only', '--non_interactive', 'command_list', '--list', command_list] # Run Biobb block self.run_biobb() # 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 structure_check(input_structure_path: str, output_summary_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`StructureCheck <utils.structure_check.StructureCheck>` class and execute the :meth:`launch() <utils.structure_check.StructureCheck.launch>` method.""" return StructureCheck(input_structure_path=input_structure_path, output_summary_path=output_summary_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="This class is a wrapper of the Structure Checking tool to generate summary checking results on a json 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('-i', '--input_structure_path', required=True, help="Input structure file path. Accepted formats: pdb.") required_args.add_argument('-o', '--output_summary_path', required=True, help="Output summary checking results. Accepted formats: json.") 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 structure_check(input_structure_path=args.input_structure_path, output_summary_path=args.output_summary_path, properties=properties)
if __name__ == '__main__': main()