#!/usr/bin/env python3
"""Module containing the ReduceRemoveHydrogens 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.file_utils import launchlogger
from biobb_chemistry.ambertools.common import get_binary_path, check_input_path, check_output_path
[docs]class ReduceRemoveHydrogens(BiobbObject):
"""
| biobb_chemistry ReduceRemoveHydrogens
| This class is a wrapper of the `Ambertools <http://ambermd.org/doc12/AmberTools12.pdf>`_ reduce module for removing hydrogens from a given structure.
| Reduce is a program for `adding or removing hydrogens to a Protein DataBank (PDB) molecular structure file <http://ambermd.org/doc12/AmberTools12.pdf>`_.
Args:
input_path (str): Path to the input file. File type: input. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/ambertools/reduce.H.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_path (str): Path to the output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/ambertools/ref_reduce.remove.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **binary_path** (*str*) - ("reduce") Path to the reduce executable binary.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **container_path** (*str*) - (None) Container path definition.
* **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
* **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
* **container_working_dir** (*str*) - (None) Container working directory definition.
* **container_user_id** (*str*) - (None) Container user_id definition.
* **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
Examples:
This is a use example of how to use the building block from Python::
from biobb_chemistry.ambertools.reduce_remove_hydrogens import reduce_remove_hydrogens
prop = { }
reduce_remove_hydrogens(input_path='/path/to/myStructure.pdb',
output_path='/path/to/newStructure.pdb',
properties=prop)
Info:
* wrapped_software:
* name: AmberTools Reduce
* version: >=20.0
* license: GNU
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_path, output_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_path": input_path},
"out": {"output_path": output_path}
}
# Properties specific for BB
self.binary_path = get_binary_path(properties, 'binary_path')
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.io_dict["in"]["input_path"] = check_input_path(self.io_dict["in"]["input_path"], out_log, self.__class__.__name__)
self.io_dict["out"]["output_path"] = check_output_path(self.io_dict["out"]["output_path"], out_log, self.__class__.__name__)
[docs] def create_cmd(self, container_io_dict, out_log, err_log):
"""Creates the command line instruction using the properties file settings"""
instructions_list = []
# executable path
instructions_list.append(self.binary_path)
instructions_list.append('-Trim')
instructions_list.append(container_io_dict["in"]["input_path"])
instructions_list.append('>')
instructions_list.append(container_io_dict["out"]["output_path"])
return instructions_list
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`ReduceRemoveHydrogens <ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens>` ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# create command line instruction
self.cmd = self.create_cmd(self.stage_io_dict, self.out_log, self.err_log)
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# remove temporary folder(s)
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 reduce_remove_hydrogens(input_path: str, output_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`ReduceRemoveHydrogens <ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens>` class and
execute the :meth:`launch() <ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens.launch>` method."""
return ReduceRemoveHydrogens(input_path=input_path,
output_path=output_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 hydrogen atoms to small molecules.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_path', required=True, help='Path to the input file. Accepted formats: pdb.')
required_args.add_argument('--output_path', required=True, help='Path to the output file. Accepted formats: pdb.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
reduce_remove_hydrogens(input_path=args.input_path,
output_path=args.output_path,
properties=properties)
if __name__ == '__main__':
main()