#!/usr/bin/env python3
"""Module containing the RemoveMolecules 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 import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from Bio.PDB.PDBParser import PDBParser
from biobb_structure_utils.utils.common import check_input_path, check_output_path, create_residues_list, create_biopython_residue, create_output_file
[docs]class RemoveMolecules(BiobbObject):
"""
| biobb_structure_utils RemoveMolecules
| Class to remove molecules from a 3D structure using Biopython.
Args:
input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/2vgb.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
output_molecules_path (str): Output molcules file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_remove_molecules.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **molecules** (*list*) - (None) List of comma separated res_id (will remove all molecules that match the res_id) or list of dictionaries with the name | res_id | chain | model of the molecules to be removed. Format: [{"name": "HIS", "res_id": "72", "chain": "A", "model": "1"}].
* **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.remove_molecules import remove_molecules
prop = {
'molecules': [
{
'name': 'HIS',
'res_id': '72',
'chain': 'A',
'model': '1'
}
]
}
remove_molecules(input_structure_path='/path/to/myStructure.pdb',
output_molecules_path='/path/to/newMolecules.pdb',
properties=prop)
Info:
* wrapped_software:
* name: In house using Biopython
* version: >=1.79
* license: other
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_structure_path, output_molecules_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_molecules_path": output_molecules_path}
}
# Properties specific for BB
self.molecules = properties.get('molecules', [])
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`RemoveMolecules <utils.remove_molecules.RemoveMolecules>` utils.remove_molecules.RemoveMolecules 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_molecules_path'] = check_output_path(self.io_dict['out']['output_molecules_path'],
self.out_log, self.__class__.__name__)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Business code
# get list of Residues from properties
list_residues = create_residues_list(self.molecules, self.out_log)
# load input into BioPython structure
structure = PDBParser(QUIET=True).get_structure('structure', self.stage_io_dict['in']['input_structure_path'])
remove_structure = []
whole_structure = []
# get desired residues
for residue in structure.get_residues():
r = create_biopython_residue(residue)
whole_structure.append(r)
if list_residues:
for res in list_residues:
match = True
for code in res['code']:
if res[code].strip() != r[code].strip():
match = False
break
if match:
remove_structure.append(r)
else:
remove_structure.append(r)
# if not residues found in structure, raise exit
if not remove_structure:
fu.log(self.__class__.__name__ + ': The residues given by user were not found in input structure', self.out_log)
raise SystemExit(self.__class__.__name__ + ': The residues given by user were not found in input structure')
# substract residues (remove_structure) from whole_structure
new_structure = [x for x in whole_structure if x not in remove_structure]
create_output_file(0, self.stage_io_dict['in']['input_structure_path'], new_structure, self.stage_io_dict['out']['output_molecules_path'], self.out_log)
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 remove_molecules(input_structure_path: str, output_molecules_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`RemoveMolecules <utils.remove_molecules.RemoveMolecules>` class and
execute the :meth:`launch() <utils.remove_molecules.RemoveMolecules.launch>` method."""
return RemoveMolecules(input_structure_path=input_structure_path,
output_molecules_path=output_molecules_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="Removes a list of molecules 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_structure_path', required=True, help="Input structure file path. Accepted formats: pdb.")
required_args.add_argument('-o', '--output_molecules_path', required=True, help="Output molecules file path. Accepted formats: pdb.")
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
remove_molecules(input_structure_path=args.input_structure_path,
output_molecules_path=args.output_molecules_path,
properties=properties)
if __name__ == '__main__':
main()