#!/usr/bin/env python3
"""Module containing the FixSideChain 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 import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_model.model.common import modeller_installed
[docs]class FixSideChain(BiobbObject):
"""
| biobb_model FixSideChain
| Class to model the missing atoms in amino acid side chains of a PDB.
| Model the missing atoms in amino acid side chains of a PDB using `biobb_structure_checking <https://anaconda.org/bioconda/biobb_structure_checking>`_ if the use_modeller property is added the `Modeller suite <https://salilab.org/modeller/>`_ will also be used to rebuild the missing atoms.
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/2ki5.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_pdb_path.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **use_modeller** (*bool*) - (False) Use `Modeller suite <https://salilab.org/modeller/>`_ to rebuild the missing side chain atoms.
* **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_side_chain import fix_side_chain
prop = { 'use_modeller': True }
fix_side_chain(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.use_modeller = properties.get('use_modeller', False)
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:`FixSideChain <model.fix_side_chain.FixSideChain>` 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',
'fixside', '--fix', 'ALL']
if self.modeller_key:
self.cmd.insert(1, self.modeller_key)
self.cmd.insert(1, '--modeller_key')
if self.use_modeller:
if modeller_installed(self.out_log, self.global_log):
self.cmd.append('--rebuild')
else:
fu.log("Modeller is not installed --rebuild option can not be used proceeding without using it", self.out_log, self.global_log)
# 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_side_chain(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int:
"""Create :class:`FixSideChain <model.fix_side_chain.FixSideChain>` class and
execute the :meth:`launch() <model.fix_side_chain.FixSideChain.launch>` method."""
return FixSideChain(input_pdb_path=input_pdb_path,
output_pdb_path=output_pdb_path,
properties=properties, **kwargs).launch()
[docs]def main():
parser = argparse.ArgumentParser(description="Model the missing atoms in amino acid side chains of a PDB.",
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_side_chain(input_pdb_path=args.input_pdb_path,
output_pdb_path=args.output_pdb_path,
properties=properties)
if __name__ == '__main__':
main()