Source code for leap.leap_build_linear_structure

#!/usr/bin/env python3

"""Module containing the LeapBuildLinearStructure 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.leap.common import check_output_path

[docs]class LeapBuildLinearStructure(BiobbObject): """ | biobb_amber.leap.leap_build_linear_structure LeapBuildLinearStructure | Wrapper of the `AmberTools (AMBER MD Package) leap tool <>`_ module. | Builds a linear (unfolded) 3D structure from an AA sequence using tLeap tool from the AmberTools MD package. Args: output_pdb_path (str): Linear (unfolded) 3D 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): * **sequence** (*str*) - ("ALA GLY SER PRO ARG ALA PRO GLY") Aminoacid sequence to convert to a linear 3D structure. Aminoacids should be written in 3-letter code, with a blank space between them. * **forcefield** (*list*) - (["protein.ff14SB","DNA.bsc1","gaff"]) Forcefield to be used for the structure generation. Values: protein.ff14SB, protein.ff19SB, DNA.bsc1, DNA.OL15, RNA.OL3, gaff. * **build_library** (*bool*) - (False) Generate AMBER lib file for the structure. * **binary_path** (*str*) - ("tleap") Path to the tleap 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.leap.leap_build_linear_structure import leap_build_linear_structure prop = { 'sequence' : 'ALA PRO SER ARG LYS ASP GLU GLY GLY ALA', 'build_library': False, 'forcefield': ['protein.ff14SB'] } leap_build_linear_structure(output_pdb_path='/path/to/newStructure.pdb', properties=prop) Info: * wrapped_software: * name: AmberTools tLeap * version: >20.9 * license: LGPL 2.1 * ontology: * name: EDAM * schema: """ def __init__(self, output_pdb_path, properties, **kwargs): properties = properties or {} # Call parent class constructor super().__init__(properties) self.locals_var_dict = locals().copy() # Input/Output files self.io_dict = { 'in': {}, 'out': {'output_pdb_path': output_pdb_path} } # Properties specific for BB = properties self.sequence = properties.get('sequence', "ALA GLY SER PRO ARG ALA PRO GLY") self.forcefield = properties.get('forcefield', ["protein.ff14SB", "DNA.bsc1", "gaff"]) self.build_library = properties.get('build_library', False) self.binary_path = properties.get('binary_path', 'tleap') # 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 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): """Launches the execution of the LeapBuildLinearStructure 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() # create .in file # TC5b = sequence { NASN LEU TYR ILE GLN TRP LEU LYS ASP GLY GLY PRO SER SER GLY ARG PRO PRO PRO CSER } # savepdb TC5b TC5b_linear.pdb # quit # Creating temporary folder & Leap configuration (instructions) file 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("")) self.tmp_folder = None 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 # instructions_file = str(PurePath(self.tmp_folder).joinpath("")) with open(instructions_file, 'w') as leapin: # Forcefields loaded from input forcefield property for t in self.forcefield: leapin.write("source leaprc.{}\n".format(t)) leapin.write("struct = sequence {" + self.sequence + " } \n") leapin.write("savepdb struct " + self.stage_io_dict['out']['output_pdb_path'] + "\n") leapin.write("quit \n") # Command line self.cmd = [self.binary_path, '-f', instructions_file_path ] # 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.tmp_folder, "leap.log" ]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs]def leap_build_linear_structure(output_pdb_path: str, properties: dict = None, **kwargs) -> int: """Create :class:`LeapBuildLinearStructure <leap.leap_build_linear_structure.LeapBuildLinearStructure>`leap.leap_build_linear_structure.LeapBuildLinearStructure class and execute :meth:`launch() <leap.leap_build_linear_structure.LeapBuildLinearStructure.launch>` method""" return LeapBuildLinearStructure(output_pdb_path=output_pdb_path, properties=properties).launch()
[docs]def main(): parser = argparse.ArgumentParser(description='Building a linear (unfolded) 3D structure from an AA sequence.', 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('--output_pdb_path', required=True, help='Linear (unfolded) 3D 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 leap_build_linear_structure(output_pdb_path=args.output_pdb_path, properties=properties)
if __name__ == '__main__': main()