Source code for ambertools.reduce_add_hydrogens

#!/usr/bin/env python3

"""Module containing the ReduceAddHydrogens 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 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. * **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: 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()
[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()