Source code for utils.str_check_add_hydrogens

#!/usr/bin/env python3

"""Module containing the StrCheckAddHydrogens 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 biobb_structure_utils.utils.common import check_input_path, check_output_path_pdbqt, check_output_end

[docs]class StrCheckAddHydrogens(BiobbObject): """ | biobb_structure_utils StrCheckAddHydrogens | This class is a wrapper of the Structure Checking tool to add hydrogens to a 3D structure. | Wrapper for the `Structure Checking <>`_ tool to add hydrogens to a 3D structure. Args: input_structure_path (str): Input structure file path. File type: input. `Sample file <>`_. Accepted formats: pdb (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): * **charges** (*bool*) - (False) Whether or not to add charges to the output file. If True the output is in PDBQT format. * **mode** (*string*) - (auto) Selection mode. Values: auto, list, ph * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH. Only in case mode ph selected. * **list** (*string*) - ("") List of residues to modify separated by commas (i.e HISA234HID,HISB33HIE). Only in case mode list selected. * **keep_canonical_resnames** (*bool*) - (False) Whether or not keep canonical residue names * **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.str_check_add_hydrogens import str_check_add_hydrogens prop = { 'charges': False, 'mode': 'auto' } str_check_add_hydrogens(input_structure_path='/path/to/myInputStr.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.charges = properties.get('charges', False) self.mode = properties.get('mode', 'auto') = properties.get('ph', 7.4) self.list = properties.get('list', '') self.keep_canonical_resnames = properties.get('keep_canonical_resnames', False) = properties # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`StrCheckAddHydrogens <utils.str_check_add_hydrogens.StrCheckAddHydrogens>` utils.str_check_add_hydrogens.StrCheckAddHydrogens 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_pdbqt(self.io_dict['out']['output_structure_path'], self.out_log, self.__class__.__name__) # Setup Biobb if self.check_restart(): return 0 self.stage_files() self.cmd = [self.binary_path, '-i', self.stage_io_dict['in']['input_structure_path'], '-o', self.stage_io_dict['out']['output_structure_path'], '--non_interactive', '--force_save'] if self.keep_canonical_resnames: self.cmd.append('--keep_canonical_resnames') self.cmd.extend(['command_list', '--list', "'add_hydrogen"]) if self.charges: self.cmd.append('--add_charges') self.cmd.append('ADT') if self.mode: self.cmd.extend(['--add_mode', self.mode]) if self.mode == 'ph': self.cmd.extend(['--pH',]) if self.mode == 'list': self.cmd.extend(['--list', self.list]) else: self.cmd.extend(['--add_mode', 'None']) self.cmd.append("'") # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() check_output_end(self.io_dict["out"]["output_structure_path"], self.out_log) # 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 str_check_add_hydrogens(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`StrCheckAddHydrogens <utils.str_check_add_hydrogens.StrCheckAddHydrogens>` class and execute the :meth:`launch() <utils.str_check_add_hydrogens.StrCheckAddHydrogens.launch>` method.""" return StrCheckAddHydrogens(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="Class to add hydrogens to 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, pdbqt.") 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 str_check_add_hydrogens(input_structure_path=args.input_structure_path, output_structure_path=args.output_structure_path, properties=properties)
if __name__ == '__main__': main()