Source code for utils.extract_heteroatoms
#!/usr/bin/env python3
"""Module containing the ExtractHeteroAtoms class and the command line interface."""
import argparse
from typing import Optional
from Bio.PDB.PDBParser import PDBParser
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 biobb_structure_utils.utils.common import (
_from_string_to_list,
check_format_heteroatoms,
check_input_path,
check_output_path,
create_biopython_residue,
create_output_file,
)
[docs]
class ExtractHeteroAtoms(BiobbObject):
"""
| biobb_structure_utils ExtractHeteroAtoms
| Class to extract hetero-atoms from a 3D structure using Biopython.
| Extracts a list of heteroatoms 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/extract_heteroatom.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
output_heteroatom_path (str): Output heteroatom file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_heteroatom.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **heteroatoms** (*list*) - (None) List of dictionaries with the name | res_id | chain | model of the heteroatoms to be extracted. Format: [{"name": "ZZ7", "res_id": "302", "chain": "B", "model": "1"}]. If empty, all the heteroatoms of the structure will be returned.
* **water** (*bool*) - (False) Add or not waters.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
Examples:
This is a use example of how to use the building block from Python::
from biobb_structure_utils.utils.extract_heteroatoms import extract_heteroatoms
prop = {
'heteroatoms': [
{
'name': 'ZZ7',
'res_id': '302',
'chain': 'B',
'model': '1'
}
]
}
extract_heteroatoms(input_structure_path='/path/to/myStructure.pdb',
output_heteroatom_path='/path/to/newHeteroatom.pdb',
properties=prop)
Info:
* wrapped_software:
* name: In house using Biopython
* version: >=1.76
* license: other
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self, input_structure_path, output_heteroatom_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_heteroatom_path": output_heteroatom_path},
}
# Properties specific for BB
self.heteroatoms = _from_string_to_list(properties.get("heteroatoms", []))
self.water = properties.get("water", False)
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`ExtractHeteroAtoms <utils.extract_heteroatoms.ExtractHeteroAtoms>` utils.extract_heteroatoms.ExtractHeteroAtoms 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_heteroatom_path"] = check_output_path(
self.io_dict["out"]["output_heteroatom_path"],
self.out_log,
self.__class__.__name__,
)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Business code
# get list of heteroatoms from properties
list_heteroatoms = check_format_heteroatoms(self.heteroatoms, self.out_log)
# load input into BioPython structure
structure = PDBParser(QUIET=True).get_structure(
"structure", self.stage_io_dict["in"]["input_structure_path"]
)
new_structure = []
# get desired heteroatoms
for residue in structure.get_residues():
r = create_biopython_residue(residue)
if list_heteroatoms:
for het in list_heteroatoms:
match = True
for code in het["code"]:
if het[code].strip() != r[code].strip():
match = False
break
if match:
if not self.water and (
r["name"] == "HOH"
or r["name"] == "SOL"
or r["name"] == "WAT"
):
pass
else:
new_structure.append(r)
else:
if not self.water and (
r["name"] == "HOH" or r["name"] == "SOL" or r["name"] == "WAT"
):
pass
else:
new_structure.append(r)
# if not heteroatoms found in structure, raise exit
if not new_structure:
fu.log(
self.__class__.__name__
+ ": The heteroatoms given by user were not found in input structure",
self.out_log,
)
raise SystemExit(
self.__class__.__name__
+ ": The heteroatoms given by user were not found in input structure"
)
create_output_file(
1,
self.stage_io_dict["in"]["input_structure_path"],
new_structure,
self.stage_io_dict["out"]["output_heteroatom_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 extract_heteroatoms(
input_structure_path: str,
output_heteroatom_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Execute the :class:`ExtractHeteroAtoms <utils.extract_heteroatoms.ExtractHeteroAtoms>` class and
execute the :meth:`launch() <utils.extract_heteroatoms.ExtractHeteroAtoms.launch>` method."""
return ExtractHeteroAtoms(
input_structure_path=input_structure_path,
output_heteroatom_path=output_heteroatom_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="Extract a list of heteroatoms 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_heteroatom_path",
required=True,
help="Output heteroatom 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
extract_heteroatoms(
input_structure_path=args.input_structure_path,
output_heteroatom_path=args.output_heteroatom_path,
properties=properties,
)
if __name__ == "__main__":
main()