#!/usr/bin/env python3
"""Module containing the Mutate class and the command line interface."""
from typing import Optional
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_model.model.common import modeller_installed
[docs]
class Mutate(BiobbObject):
"""
| biobb_model Mutate
| Class to mutate one amino acid by another in a 3d structure.
| Mutate side chain with minimal atom replacement. if the use_modeller property is added the `Modeller suite <https://salilab.org/modeller/>`_ will be used to optimize the side chains.
Args:
input_pdb_path (str): Input PDB file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/data/model/2ki5.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_pdb_path (str): Output PDB file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/reference/model/output_mutated_pdb_path.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **mutation_list** (*str*) - (None) Mutation list in the format "Chain:WT_AA_ThreeLeterCode Resnum MUT_AA_ThreeLeterCode" (no spaces between the elements) separated by commas. If no chain is provided as chain code all the chains in the pdb file will be mutated. ie: "A:ALA15CYS"
* **use_modeller** (*bool*) - (False) Use `Modeller suite <https://salilab.org/modeller/>`_ to optimize the side chains.
* **modeller_key** (*str*) - (None) Modeller license key.
* **binary_path** (*str*) - ("check_structure") Path to the check_structure 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.
Examples:
This is a use example of how to use the building block from Python::
from biobb_model.model.mutate import mutate
prop = { 'mutation_list': 'A:Val2Ala',
'use_modeller': True }
mutate(input_pdb_path='/path/to/myStructure.pdb',
output_pdb_path='/path/to/newStructure.pdb',
properties=prop)
Info:
* wrapped_software:
* name: In house
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_pdb_path: str,
output_pdb_path: str,
properties: Optional[dict] = None,
**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_pdb_path": input_pdb_path},
"out": {"output_pdb_path": output_pdb_path},
}
# Properties specific for BB
self.binary_path = properties.get("binary_path", "check_structure")
self.mutation_list = properties.get("mutation_list", "").replace(" ", "")
self.use_modeller = properties.get("use_modeller", False)
self.modeller_key = properties.get("modeller_key")
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Mutate <model.mutate.Mutate>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Create command line
self.cmd = [
self.binary_path,
"-i",
self.stage_io_dict["in"]["input_pdb_path"],
"-o",
self.stage_io_dict["out"]["output_pdb_path"],
"--force_save",
"--non_interactive",
"mutateside",
]
if self.mutation_list:
self.cmd.append("--mut")
self.cmd.append(self.mutation_list)
if self.modeller_key:
self.cmd.insert(1, self.modeller_key)
self.cmd.insert(1, "--modeller_key")
if self.use_modeller:
if modeller_installed(self.out_log, self.global_log):
self.cmd.append("--rebuild")
else:
fu.log(
"Modeller is not installed --rebuild option can not be used proceeding without using it",
self.out_log,
self.global_log,
)
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def mutate(
input_pdb_path: str,
output_pdb_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Mutate <model.mutate.Mutate>` class and
execute the :meth:`launch() <model.mutate.Mutate.launch>` method."""
return Mutate(**dict(locals())).launch()
mutate.__doc__ = Mutate.__doc__
main = Mutate.get_main(mutate, "Model the missing atoms in aminoacid side chains of a PDB.")
if __name__ == "__main__":
main()