Source code for ambpdb.amber_to_pdb

#!/usr/bin/env python3

"""Module containing the AmberToPDB class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from import launchlogger
from biobb_amber.ambpdb.common import check_input_path, check_output_path

[docs]class AmberToPDB(BiobbObject): """ | biobb_amber AmberToPDB | Wrapper of the `AmberTools (AMBER MD Package) ambpdb tool <>`_ module. | Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb tool from the AmberTools MD package. Args: input_top_path (str): AMBER topology file. File type: input. `Sample file <>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881). input_crd_path (str): AMBER coordinates file. File type: input. `Sample file <>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878), rst (edam:format_3886). output_pdb_path (str): Structure PDB file. File type: output. `Sample file <>`_. Accepted formats: pdb (edam:format_1476). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **binary_path** (*str*) - ("ambpdb") Path to the ambpdb 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.ambpdb.amber_to_pdb import amber_to_pdb prop = { 'remove_tmp': True } amber_to_pdb(input_top_path='/path/to/', input_crd_path='/path/to/coordinates.crd', output_pdb_path='/path/to/newStructure.pdb', properties=prop) Info: * wrapped_software: * name: AmberTools ambpdb * version: >20.9 * license: LGPL 2.1 * ontology: * name: EDAM * schema: """ def __init__(self, input_top_path, input_crd_path, output_pdb_path, properties: dict = None, **kwargs): 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} } # Properties specific for BB = properties self.binary_path = properties.get('binary_path', 'ambpdb') # 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__)
[docs] @launchlogger def launch(self): # 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() # Command line self.cmd = [self.binary_path, '-p', self.stage_io_dict['in']['input_top_path'], '-c', self.stage_io_dict['in']['input_crd_path'], '> ', self.stage_io_dict['out']['output_pdb_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.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs]def amber_to_pdb(input_top_path: str, input_crd_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int: """Create :class:`AmberToPDB <amber.amber_to_pdb.AmberToPDB>`amber.amber_to_pdb.AmberToPDB class and execute :meth:`launch() <amber.amber_to_pdb.AmberToPDB.launch>` method""" return AmberToPDB(input_top_path=input_top_path, input_crd_path=input_crd_path, output_pdb_path=output_pdb_path, properties=properties).launch()
[docs]def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser(description='Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb 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='AMBER topology file. Accepted formats: top, parmtop, prmtop.') required_args.add_argument('--input_crd_path', required=True, help='AMBER coordinates file. Accepted formats: crd, mdcrd, inpcrd.') required_args.add_argument('--output_pdb_path', required=True, help='Structure PDB file. Accepted formats: pdb.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call amber_to_pdb(input_top_path=args.input_top_path, input_crd_path=args.input_crd_path, output_pdb_path=args.output_pdb_path, properties=properties)
if __name__ == '__main__': main()