Source code for leap.leap_build_linear_structure

#!/usr/bin/env python3

"""Module containing the LeapBuildLinearStructure class and the command line interface."""

import os
import argparse
from pathlib import PurePath
from typing import List, Optional

from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger

from biobb_amber.leap.common import _from_string_to_list, check_output_path


[docs] class LeapBuildLinearStructure(BiobbObject): """ | biobb_amber.leap.leap_build_linear_structure LeapBuildLinearStructure | Wrapper of the `AmberTools (AMBER MD Package) leap tool <https://ambermd.org/AmberTools.php>`_ 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 <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.pdb>`_. 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"]) Forcefields to be used for the structure generation. Each item should be either a path to a leaprc file or a string with the leaprc file name if the force field is included with Amber (e.g. "/path/to/leaprc.protein.ff14SB" or "protein.ff14SB"). Default values: ["protein.ff14SB","DNA.bsc1","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. * **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_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: http://edamontology.org/EDAM.owl """ 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}} # Set default forcefields amber_home_path = os.getenv("AMBERHOME") protein_ff14SB_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.protein.ff14SB') dna_bsc1_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.DNA.bsc1') gaff_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.gaff') # Properties specific for BB self.properties = properties self.sequence = properties.get("sequence", "ALA GLY SER PRO ARG ALA PRO GLY") self.forcefield = _from_string_to_list( properties.get("forcefield", [protein_ff14SB_path, dna_bsc1_path, gaff_path]) ) # Find the paths of the leaprc files if only the force field names are provided self.forcefield = self.find_leaprc_paths(self.forcefield) 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] def find_leaprc_paths(self, forcefields: List[str]) -> List[str]: """ Find the leaprc paths for the force fields provided. For each item in the forcefields list, the function checks if the str is a path to an existing file. If not, it tries to find the file in the $AMBERHOME/dat/leap/cmd/ directory or the $AMBERHOME/dat/leap/cmd/oldff/ directory with and without the leaprc prefix. Args: forcefields (List[str]): List of force fields to find the leaprc files for. Returns: List[str]: List of leaprc file paths. """ leaprc_paths = [] for forcefield in forcefields: num_paths = len(leaprc_paths) # Check if the forcefield is a path to an existing file if os.path.exists(forcefield): leaprc_paths.append(forcefield) continue # Check if the forcefield is in the leaprc directory leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', f"leaprc.{forcefield}") if os.path.exists(leaprc_path): leaprc_paths.append(leaprc_path) continue # Check if the forcefield is in the oldff directory leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', 'oldff', f"leaprc.{forcefield}") if os.path.exists(leaprc_path): leaprc_paths.append(leaprc_path) continue # Check if the forcefield is in the leaprc directory without the leaprc prefix leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', f"{forcefield}") if os.path.exists(leaprc_path): leaprc_paths.append(leaprc_path) continue # Check if the forcefield is in the oldff directory without the leaprc prefix leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', 'oldff', f"{forcefield}") if os.path.exists(leaprc_path): leaprc_paths.append(leaprc_path) continue new_num_paths = len(leaprc_paths) if new_num_paths == num_paths: raise ValueError(f"Force field {forcefield} not found. Check the $AMBERHOME/dat/leap/cmd/ directory for available force fields or provide the path to an existing leaprc file.") return leaprc_paths
[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("leap.in") ) instructions_file_path = str( PurePath(self.container_volume_path).joinpath("leap.in") ) self.tmp_folder = None else: self.tmp_folder = fu.create_unique_dir() instructions_file = str(PurePath(self.tmp_folder).joinpath("leap.in")) 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("leap.in")) with open(instructions_file, "w") as leapin: # Forcefields loaded from input forcefield property for t in self.forcefield: leapin.write("source {}\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", ""), str(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: Optional[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() leap_build_linear_structure.__doc__ = LeapBuildLinearStructure.__doc__
[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()