#!/usr/bin/env python3
"""Module containing the RemovePdbWater class and the command line interface."""
import argparse
from typing import Optional
from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools.file_utils import launchlogger
[docs]
class RemovePdbWater(BiobbObject):
"""
| biobb_structure_utils RemovePdbWater
| This class is a wrapper of the Structure Checking tool to remove water molecules from PDB 3D structures.
| Wrapper for the `Structure Checking <https://github.com/bioexcel/biobb_structure_checking>`_ tool to remove water molecules from PDB 3D structures.
Args:
input_pdb_path (str): Input PDB 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_WAT.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_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/WT_apo_no_wat.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **binary_path** (*string*) - ("check_structure") path to the check_structure application
* **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_pdb_water import remove_pdb_water
prop = { }
remove_pdb_water(input_pdb_path='/path/to/myStructure.pdb',
output_pdb_path='/path/to/newStructure.pdb',
properties=prop)
Info:
* wrapped_software:
* name: Structure Checking from MDWeb
* version: >=3.0.3
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self, input_pdb_path, output_pdb_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_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")
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`RemovePdbWater <utils.remove_pdb_water.RemovePdbWater>` utils.remove_pdb_water.RemovePdbWater object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
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",
"water",
"--remove",
"yes",
]
# Run Biobb block
self.run_biobb()
# 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_pdb_water(
input_pdb_path: str,
output_pdb_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Execute the :class:`RemovePdbWater <utils.remove_pdb_water.RemovePdbWater>` class and
execute the :meth:`launch() <utils.remove_pdb_water.RemovePdbWater.launch>` method."""
return RemovePdbWater(
input_pdb_path=input_pdb_path,
output_pdb_path=output_pdb_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 water molecules from a PDB 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_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
remove_pdb_water(
input_pdb_path=args.input_pdb_path,
output_pdb_path=args.output_pdb_path,
properties=properties,
)
if __name__ == "__main__":
main()