#!/usr/bin/env python3
"""Module containing the RemoveLigand class and the command line interface."""
import argparse
from pathlib import Path
from typing import Optional
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.gro_lib.gro import Gro
[docs]
class RemoveLigand(BiobbObject):
"""
| biobb_structure_utils RemoveLigand
| Class to remove the selected ligand atoms from a 3D structure.
| Remove the selected ligand atoms from a 3D structure.
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/WT_aq4_md_1.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
output_structure_path (str): Output structure file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/WT_apo_md_1.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **ligand** (*str*) - ("AQ4") Residue code of the ligand to be removed.
* **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.remove_ligand import remove_ligand
prop = {
'ligand': 'AQ4'
}
remove_ligand(input_structure_path='/path/to/myStructure.pdb',
output_structure_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_structure_path, output_structure_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_structure_path": output_structure_path},
}
# Properties specific for BB
self.ligand = properties.get("ligand", "AQ4")
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`RemoveLigand <utils.remove_ligand.RemoveLigand>` utils.remove_ligand.RemoveLigand object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Business code
extension = Path(
self.stage_io_dict["in"]["input_structure_path"]
).suffix.lower()
if extension.lower() == ".gro":
fu.log(
"GRO format detected, removing all atoms from residues named %s"
% self.ligand,
self.out_log,
)
gro_st = Gro()
gro_st.read_gro_file(self.stage_io_dict["in"]["input_structure_path"])
gro_st.remove_residues([self.ligand])
gro_st.write_gro_file(self.stage_io_dict["out"]["output_structure_path"])
else:
fu.log(
"PDB format detected, removing all atoms from residues named %s"
% self.ligand,
self.out_log,
)
# Direct aproach solution implemented to avoid the issues
# presented in commit message (c92aab9604a6a31d13f4170ff47b231df0a588ef)
# with the Biopython library
with open(
self.stage_io_dict["in"]["input_structure_path"], "r"
) as input_pdb, open(
self.stage_io_dict["out"]["output_structure_path"], "w"
) as output_pdb:
for line in input_pdb:
if len(line) > 19 and self.ligand.lower() in line[17:20].lower():
continue
output_pdb.write(line)
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_ligand(
input_structure_path: str,
output_structure_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Execute the :class:`RemoveLigand <utils.remove_ligand.RemoveLigand>` class and
execute the :meth:`launch() <utils.remove_ligand.RemoveLigand.launch>` method."""
return RemoveLigand(
input_structure_path=input_structure_path,
output_structure_path=output_structure_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="Remove the selected ligand atoms 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 name"
)
required_args.add_argument(
"-o",
"--output_structure_path",
required=True,
help="Output structure 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
remove_ligand(
input_structure_path=args.input_structure_path,
output_structure_path=args.output_structure_path,
properties=properties,
)
if __name__ == "__main__":
main()