#!/usr/bin/env python3
"""Module containing the ReduceAddHydrogens class and the command line interface."""
import argparse
from typing import Optional
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 ReduceAddHydrogens(BiobbObject):
"""
| biobb_chemistry ReduceAddHydrogens
| This class is a wrapper of the `Ambertools <http://ambermd.org/doc12/AmberTools12.pdf>`_ reduce module for adding hydrogens to 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.no.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.add.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **flip** (*bool*) - (False) add H and rotate and flip NQH groups
* **noflip** (*bool*) - (False) add H and rotate groups with no NQH flips
* **nuclear** (*bool*) - (False) use nuclear X-H distances rather than default electron cloud distances
* **nooh** (*bool*) - (False) remove hydrogens on OH and SH groups
* **oh** (*bool*) - (True) add hydrogens on OH and SH groups (default)
* **his** (*bool*) - (False) create NH hydrogens on HIS rings (usually used with -HIS)
* **noheth** (*bool*) - (False) do not attempt to add NH proton on Het groups
* **rotnh3** (*bool*) - (True) allow lysine NH3 to rotate (default)
* **norotnh3** (*bool*) - (False) do not allow lysine NH3 to rotate
* **rotexist** (*bool*) - (False) allow existing rotatable groups (OH, SH, Met-CH3) to rotate
* **rotexoh** (*bool*) - (False) allow existing OH & SH groups to rotate
* **allalt** (*bool*) - (True) process adjustments for all conformations (default)
* **onlya** (*bool*) - (False) only adjust 'A' conformations
* **charges** (*bool*) - (False) output charge state for appropriate hydrogen records
* **dorotmet** (*bool*) - (False) allow methionine methyl groups to rotate (not recommended)
* **noadjust** (*bool*) - (False) do not process any rot or flip adjustments
* **metal_bump** (*float*) - (None) [0~5|0.005] H 'bumps' metals at radius plus this
* **non_metal_bump** (*float*) - (None) [0~5|0.005] 'bumps' nonmetal at radius plus this
* **build** (*bool*) - (False) add H, including His sc NH, then rotate and flip groups (except for pre-existing methionine methyl hydrogens)
* **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.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
* **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_add_hydrogens import reduce_add_hydrogens
prop = {
'flip': False,
'charges': True,
'build': False
}
reduce_add_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.flip = properties.get('flip', False)
self.noflip = properties.get('noflip', False)
self.nuclear = properties.get('nuclear', False)
self.nooh = properties.get('nooh', False)
self.oh = properties.get('oh', True)
self.his = properties.get('his', False)
self.noheth = properties.get('noheth', False)
self.rotnh3 = properties.get('rotnh3', True)
self.norotnh3 = properties.get('norotnh3', False)
self.rotexist = properties.get('rotexist', False)
self.rotexoh = properties.get('rotexoh', False)
self.allalt = properties.get('allalt', True)
self.onlya = properties.get('onlya', False)
self.charges = properties.get('charges', False)
self.dorotmet = properties.get('dorotmet', False)
self.noadjust = properties.get('noadjust', False)
self.build = properties.get('build', False)
self.metal_bump = properties.get('metal_bump', None)
self.non_metal_bump = properties.get('non_metal_bump', None)
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)
if self.flip:
instructions_list.append('-FLIP')
if self.noflip:
instructions_list.append('-NOFLIP')
if self.nuclear:
instructions_list.append('-NUClear')
if self.nooh:
instructions_list.append('-NOOH')
if self.oh:
instructions_list.append('-OH')
if self.his:
instructions_list.append('-HIS')
if self.noheth:
instructions_list.append('-NOHETh')
if self.rotnh3:
instructions_list.append('-ROTNH3')
if self.norotnh3:
instructions_list.append('-NOROTNH3')
if self.rotexist:
instructions_list.append('-ROTEXist')
if self.rotexoh:
instructions_list.append('-ROTEXOH')
if self.allalt:
instructions_list.append('-ALLALT')
if self.onlya:
instructions_list.append('-ONLYA')
if self.charges:
instructions_list.append('-CHARGEs')
if self.dorotmet:
instructions_list.append('-DOROTMET')
if self.noadjust:
instructions_list.append('-NOADJust')
if self.build:
instructions_list.append('-BUILD')
if self.metal_bump:
instructions_list.append('-METALBump ' + str(self.metal_bump))
if self.non_metal_bump:
instructions_list.append('-NONMETALBump ' + str(self.non_metal_bump))
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:`ReduceAddHydrogens <ambertools.reduce_add_hydrogens.ReduceAddHydrogens>` ambertools.reduce_add_hydrogens.ReduceAddHydrogens 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_add_hydrogens(input_path: str, output_path: str, properties: Optional[dict] = None, **kwargs) -> int:
"""Execute the :class:`ReduceAddHydrogens <ambertools.reduce_add_hydrogens.ReduceAddHydrogens>` class and
execute the :meth:`launch() <ambertools.reduce_add_hydrogens.ReduceAddHydrogens.launch>` method."""
return ReduceAddHydrogens(input_path=input_path,
output_path=output_path,
properties=properties, **kwargs).launch()
reduce_add_hydrogens.__doc__ = ReduceAddHydrogens.__doc__
[docs]
def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Adds 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_add_hydrogens(input_path=args.input_path,
output_path=args.output_path,
properties=properties)
if __name__ == '__main__':
main()