#!/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 biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils 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 <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"]) 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: 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}
}
# Properties specific for BB
self.properties = 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("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 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()