#!/usr/bin/env python3
"""Module containing the SortGroResidues class and the command line interface."""
import argparse
from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools.file_utils import launchlogger
from biobb_structure_utils.gro_lib.gro import Gro
[docs]class SortGroResidues(BiobbObject):
"""
| biobb_structure_utils SortGroResidues
| Class to sort the selected residues from a GRO 3D structure.
Args:
input_gro_path (str): Input GRO file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro>`_. Accepted formats: gro (edam:format_2033).
output_gro_path (str): Output sorted GRO file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/WT_aq4_md_sorted.gro>`_. Accepted formats: gro (edam:format_2033).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **residue_name_list** (*list*) - (["NA", "CL", "SOL"]) Ordered residue name list.
* **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.sort_gro_residues import sort_gro_residues
prop = {
'residue_name_list': ['NA', 'CL', 'SOL']
}
sort_gro_residues(input_gro_path='/path/to/myInputStr.gro',
output_gro_path='/path/to/newStructure.gro',
properties=prop)
Info:
* wrapped_software:
* name: In house
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_gro_path, output_gro_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_gro_path": input_gro_path},
"out": {"output_gro_path": output_gro_path}
}
# Properties specific for BB
self.residue_name_list = properties.get('residue_name_list', ["NA", "CL", "SOL"])
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`SortGroResidues <utils.sort_gro_residues.SortGroResidues>` utils.sort_gro_residues.SortGroResidues object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Business code
in_gro = Gro()
in_gro.read_gro_file(self.stage_io_dict['in']['input_gro_path'])
in_gro.sort_residues2(self.residue_name_list)
in_gro.write_gro_file(self.stage_io_dict['out']['output_gro_path'])
self.return_code = 0
##########
# 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 sort_gro_residues(input_gro_path: str, output_gro_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`SortGroResidues <utils.sort_gro_residues.SortGroResidues>` class and
execute the :meth:`launch() <utils.sort_gro_residues.SortGroResidues.launch>` method."""
return SortGroResidues(input_gro_path=input_gro_path,
output_gro_path=output_gro_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="Renumber atoms and residues 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_gro_path', required=True, help="Input GRO file name")
required_args.add_argument('-o', '--output_gro_path', required=True, help="Output sorted GRO file name")
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
sort_gro_residues(input_gro_path=args.input_gro_path,
output_gro_path=args.output_gro_path,
properties=properties)
if __name__ == '__main__':
main()