#!/usr/bin/env python3
"""Module containing the FixBackbone 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
[docs]
class FixBackbone(BiobbObject):
"""
| biobb_model FixBackbone
| Class to model the missing atoms in the backbone of a PDB structure.
| Model the missing atoms in the backbone of a PDB structure using `biobb_structure_checking <https://anaconda.org/bioconda/biobb_structure_checking>`_ and the `Modeller suite <https://salilab.org/modeller/>`_.
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).
input_fasta_canonical_sequence_path (str): Input FASTA file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/data/model/2ki5.fasta>`_. Accepted formats: fasta (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_pdb_path.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **add_caps** (*bool*) - (False) Add caps to terminal residues.
* **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.fix_backbone import fix_backbone
prop = { 'restart': False }
fix_backbone(input_pdb_path='/path/to/myStructure.pdb',
input_fasta_canonical_sequence_path='/path/to/myCanonicalSequence.fasta',
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,
input_fasta_canonical_sequence_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,
"input_fasta_canonical_sequence_path": input_fasta_canonical_sequence_path,
},
"out": {"output_pdb_path": output_pdb_path},
}
# Properties specific for BB
self.binary_path = properties.get("binary_path", "check_structure")
self.add_caps = properties.get("add_caps", 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:`FixBackbone <model.fix_backbone.FixBackbone>` object."""
self.io_dict["in"]["stdin_file_path"] = fu.create_stdin_file(f'{self.io_dict["in"]["input_fasta_canonical_sequence_path"]}')
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Create command line
self.cmd = [
self.binary_path,
"-i",
self.io_dict["in"]["input_pdb_path"],
"-o",
self.io_dict["out"]["output_pdb_path"],
"--force_save",
"backbone",
"--fix_atoms",
"All",
"--fix_chain",
"All",
"--add_caps",
]
if self.modeller_key:
self.cmd.insert(5, self.modeller_key)
self.cmd.insert(5, "--modeller_key")
if self.add_caps:
self.cmd.append("All")
else:
self.cmd.append("None")
# Add stdin input file
self.cmd.append("<")
self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
# if not modeller_installed(self.out_log, self.global_log):
# fu.log(f"Modeller is not installed, the execution of this block will be interrupted", self.out_log, self.global_log)
# return 1
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.tmp_files.append(self.io_dict["in"].get("stdin_file_path", ""))
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def fix_backbone(
input_pdb_path: str,
input_fasta_canonical_sequence_path: str,
output_pdb_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`FixBackbone <model.fix_backbone.FixBackbone>` class and
execute the :meth:`launch() <model.fix_backbone.FixBackbone.launch>` method."""
return FixBackbone(**dict(locals())).launch()
fix_backbone.__doc__ = FixBackbone.__doc__
main = FixBackbone.get_main(fix_backbone, "Model the missing atoms in the backbone of a PDB structure.")
if __name__ == "__main__":
main()