#!/usr/bin/env python3
"""Module containing the FixChirality class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
[docs]class FixChirality(BiobbObject):
"""
| biobb_model FixChirality
| Fix chirality errors of residues.
| Fix stereochemical errors in residue side-chains changing It's chirality.
Args:
input_pdb_path (str): Input PDB file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/data/model/5s2z.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_pdb_path (str): Output PDB file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/reference/model/output_amide_pdb_path.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **modeller_key** (*str*) - (None) Modeller license key.
* **binary_path** (*str*) - ("check_structure") Path to the check_structure executable binary.
* **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_model.model.fix_chirality import fix_chirality
prop = { 'restart': False }
fix_chirality(input_pdb_path='/path/to/myStructure.pdb',
output_pdb_path='/path/to/newStructure.pdb',
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_pdb_path: str, output_pdb_path: str, properties: dict = 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_pdb_path": input_pdb_path},
"out": {"output_pdb_path": output_pdb_path}
}
# Properties specific for BB
self.binary_path = properties.get('binary_path', 'check_structure')
self.modeller_key = properties.get('modeller_key')
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`FixChirality <model.fix_amides.FixChirality>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Create command line
self.cmd = [self.binary_path,
'-i', self.stage_io_dict["in"]["input_pdb_path"],
'-o', self.stage_io_dict["out"]["output_pdb_path"],
'--force_save', 'chiral',
'--fix', 'All']
if self.modeller_key:
self.cmd.insert(1, self.modeller_key)
self.cmd.insert(1, '--modeller_key')
# 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")])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def fix_chirality(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int:
"""Create :class:`FixChirality <model.fix_amides.FixChirality>` class and
execute the :meth:`launch() <model.fix_amides.FixChirality.launch>` method."""
return FixChirality(input_pdb_path=input_pdb_path,
output_pdb_path=output_pdb_path,
properties=properties, **kwargs).launch()
[docs]def main():
parser = argparse.ArgumentParser(description="Fix stereochemical errors in residues changing It's chirality.",
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_pdb_path', required=True, help="Input PDB file name")
required_args.add_argument('-o', '--output_pdb_path', required=True, help="Output PDB 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
fix_chirality(input_pdb_path=args.input_pdb_path,
output_pdb_path=args.output_pdb_path,
properties=properties)
if __name__ == '__main__':
main()