Source code for cpptraj.cpptraj_randomize_ions

#!/usr/bin/env python3

"""Module containing the CpptrajRandomizeIons class and the command line interface."""
import argparse
from pathlib import PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from import file_utils as fu
from import launchlogger
from biobb_amber.cpptraj.common import check_input_path, check_output_path

[docs]class CpptrajRandomizeIons(BiobbObject): """ | biobb_amber.cpptraj.cpptraj_randomize_ions CpptrajRandomizeIons | Wrapper of the `AmberTools (AMBER MD Package) cpptraj tool <>`_ module. | Swap specified ions with randomly selected solvent molecules using cpptraj tool from the AmberTools MD package. Args: input_top_path (str): Input topology file (AMBER ParmTop). File type: input. `Sample file <>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881). input_crd_path (str): Input coordinates file (AMBER crd). File type: input. `Sample file <>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878). output_pdb_path (str): Structure PDB file with randomized ions. File type: output. `Sample file <>`_. Accepted formats: pdb (edam:format_1476). output_crd_path (str): Structure CRD file with coordinates including randomized ions. File type: output. `Sample file <>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **ion_mask** (*str*) - (":K+,Cl-,Na+") Ions to be randomized. Cpptraj mask syntax can be found at the official `Cpptraj manual <>`_. * **solute_mask** (*str*) - (":DA,DC,DG,DT,D?3,D?5") Solute (or set of atoms) around which the ions can get no closer than the distance specified. Cpptraj mask syntax can be found at the official `Cpptraj manual <>`_. * **distance** (*float*) - (5.0) Minimum distance cutoff for the ions around the defined solute. * **overlap** (*float*) - (3.5) Minimum distance between ions. * **binary_path** (*str*) - ("cpptraj") Path to the cpptraj 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_amber.cpptraj.cpptraj_randomize_ions import cpptraj_randomize_ions prop = { 'remove_tmp': True } cpptraj_randomize_ions(input_top_path='/path/to/', input_crd_path='/path/to/coordinates.crd', output_pdb_path='/path/to/newStructure.pdb', output_crd_path='/path/to/newCoordinates.crd', properties=prop) Info: * wrapped_software: * name: AmberTools cpptraj * version: >20.9 * license: LGPL 2.1 * ontology: * name: EDAM * schema: """ def __init__(self, input_top_path: str, input_crd_path: str, output_pdb_path: str, output_crd_path: str, properties, **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_top_path': input_top_path, 'input_crd_path': input_crd_path }, 'out': { 'output_pdb_path': output_pdb_path, 'output_crd_path': output_crd_path } } # Properties specific for BB = properties self.ion_mask = properties.get('ion_mask', ":K+,Cl-,Na+") self.solute_mask = properties.get('solute_mask', ":DA,DC,DG,DT,D?3,D?5") self.distance = properties.get('distance', 5.0) self.overlap = properties.get('overlap', 3.5) self.binary_path = properties.get('binary_path', 'cpptraj') # Check the properties self.check_properties(properties) self.check_arguments()
[docs] def check_data_params(self, out_log, err_log): """ Checks input/output paths correctness """ # Check input(s) self.io_dict["in"]["input_top_path"] = check_input_path(self.io_dict["in"]["input_top_path"], "input_top_path", False, out_log, self.__class__.__name__) self.io_dict["in"]["input_crd_path"] = check_input_path(self.io_dict["in"]["input_crd_path"], "input_crd_path", False, out_log, self.__class__.__name__) # Check output(s) self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, out_log, self.__class__.__name__) self.io_dict["out"]["output_crd_path"] = check_output_path(self.io_dict["out"]["output_crd_path"], "output_crd_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger def launch(self): """Launches the execution of the CpptrajRandomizeIons module.""" # 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() if self.container_path: instructions_file = str(PurePath(self.stage_io_dict['unique_dir']).joinpath("")) instructions_file_path = str(PurePath(self.container_volume_path).joinpath("")) else: self.tmp_folder = fu.create_unique_dir() instructions_file = str(PurePath(self.tmp_folder).joinpath("")) fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log) instructions_file_path = instructions_file # create file # trajin randomizeIons.crd # randomizeions :K+,Cl-,Na+ around :DA,DC,DG,DT,D?3,D?5 by 5.0 overlap 3.5 # trajout solv_randion.crd restart # trajout solv_randion.pdb pdb # go with open(instructions_file, 'w') as cpptrajin: cpptrajin.write("trajin " + self.stage_io_dict['in']['input_crd_path'] + " \n") cpptrajin.write("randomizeions " + self.ion_mask + " around " + self.solute_mask + " by " + str(self.distance) + " overlap " + str(self.overlap) + " \n") cpptrajin.write("trajout " + self.stage_io_dict['out']['output_crd_path'] + " restart \n") cpptrajin.write("trajout " + self.stage_io_dict['out']['output_pdb_path'] + " pdb \n") cpptrajin.write("go\n") # Command line self.cmd = [self.binary_path, self.stage_io_dict['in']['input_top_path'], '-i', instructions_file_path ] # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() # Remove temporary file(s) self.tmp_files.extend([ self.stage_io_dict.get("unique_dir"), self.tmp_folder, "cpptraj.log" ]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs]def cpptraj_randomize_ions(input_top_path: str, input_crd_path: str, output_pdb_path: str, output_crd_path: str, properties: dict = None, **kwargs) -> int: """Create :class:`CpptrajRandomizeIons <cpptraj.cpptraj_randomize_ions.CpptrajRandomizeIons>`cpptraj.cpptraj_randomize_ions.CpptrajRandomizeIons class and execute :meth:`launch() <cpptraj.cpptraj_randomize_ions.CpptrajRandomizeIons.launch>` method""" return CpptrajRandomizeIons(input_top_path=input_top_path, input_crd_path=input_crd_path, output_pdb_path=output_pdb_path, output_crd_path=output_crd_path, properties=properties).launch()
[docs]def main(): parser = argparse.ArgumentParser(description='Swap specified ions with randomly selected solvent molecules using cpptraj tool from the AmberTools MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_top_path', required=True, help='Input topology file (AMBER ParmTop). Accepted formats: top, parmtop, prmtop.') required_args.add_argument('--input_crd_path', required=True, help='Input coordinates file (AMBER crd). Accepted formats: crd, mdcrd, inpcrd.') required_args.add_argument('--output_pdb_path', required=True, help='Structure PDB file with randomized ions. Accepted formats: pdb.') required_args.add_argument('--output_crd_path', required=True, help='Structure CRD file with coordinates including randomized ions. Accepted formats: crd, mdcrd, inpcrd.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call cpptraj_randomize_ions(input_top_path=args.input_top_path, input_crd_path=args.input_crd_path, output_pdb_path=args.output_pdb_path, output_crd_path=args.output_crd_path, properties=properties)
if __name__ == '__main__': main()