#!/usr/bin/env python3
"""Module containing the nolb class and the command line interface."""
import argparse
import shutil
from pathlib import Path
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
[docs]class Nolb_nma(BiobbObject):
"""
| biobb_flexdyn Nolb_nma
| Wrapper of the NOLB tool
| Generate an ensemble of structures using the NOLB (NOn-Linear rigid Block) NMA tool.
Args:
input_pdb_path (str): Input PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/structure.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_pdb_path (str): Output multi-model PDB file with the generated ensemble. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/nolb_output.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **num_structs** (*int*) - (500) Number of structures to be generated
* **cutoff** (*float*) - (5.0) This options specifies the interaction cutoff distance for the elastic network models (in angstroms), 5 by default. The Hessian matrix is constructed according to this interaction distance. Some artifacts should be expected for too short distances (< 5 Å).
* **rmsd** (*float*) - (1.0) Maximum RMSd for decoy generation.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the building block from Python::
from biobb_flexdyn.flexdyn.nolb_nma import nolb_nma
prop = {
'num_structs' : 20
}
nolb_nma( input_pdb_path='/path/to/structure.pdb',
output_pdb_path='/path/to/output.pdb',
properties=prop)
Info:
* wrapped_software:
* name: NOLB
* version: >=1.9
* license: other
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_pdb_path: str, output_pdb_path: str,
properties: 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.properties = properties
self.binary_path = properties.get('binary_path', 'NOLB')
self.num_structs = properties.get('num_structs', 500)
# self.num_modes = properties.get('num_modes', 10)
self.cutoff = properties.get('cutoff', 5.0)
self.rmsd = properties.get('rmsd', 1.0)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self):
"""Launches the execution of the FlexDyn NOLB module."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Output temporary file
out_file_prefix = Path(self.stage_io_dict.get("unique_dir")).joinpath("nolb_ensemble")
out_file = Path(self.stage_io_dict.get("unique_dir")).joinpath("nolb_ensemble_nlb_decoys.pdb")
# Command line
# ./NOLB 1ake_monomer.pdb -s 100 --rmsd 5 -m -o patata # Output: patata_nlb_decoys.pdb
self.cmd = [self.binary_path,
str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path.cwd())),
"-o", str(out_file_prefix),
"-m" # Minimizing the generated structures by default
]
# Properties
if self.num_structs:
self.cmd.append('-s')
self.cmd.append(str(self.num_structs))
# Num modes is deactivated for the decoys generation. CHECK!
# * **num_modes** (*int*) - (10) Number of non-trivial modes to compute, 10 by default. If this number exceeds the size of the Hessian matrix, it will be adapted accordingly.
# if self.num_modes:
# self.cmd.append('-n')
# self.cmd.append(str(self.num_modes))
if self.cutoff:
self.cmd.append('-c')
self.cmd.append(str(self.cutoff))
if self.rmsd:
self.cmd.append('--rmsd')
self.cmd.append(str(self.rmsd))
# --dist 1 -m --nSteps 5000 --tol 0.001
self.cmd.append("--dist 1 --nSteps 5000 --tol 0.001")
# Run Biobb block
self.run_biobb()
# Copying generated output file to the final (user-given) file name
shutil.copy2(out_file, self.stage_io_dict["out"]["output_pdb_path"])
# Copy files to host
self.copy_to_host()
# remove temporary folder(s)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir")
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def nolb_nma(input_pdb_path: str, output_pdb_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`Nolb_nma <flexdyn.nolb_nma.Nolb_nma>`flexdyn.nolb_nma.Nolb_nma class and
execute :meth:`launch() <flexdyn.nolb_nma.Nolb_nma.launch>` method"""
return Nolb_nma(input_pdb_path=input_pdb_path,
output_pdb_path=output_pdb_path,
properties=properties).launch()
[docs]def main():
parser = argparse.ArgumentParser(description='Generate an ensemble of structures using the NOLB (NOn-Linear rigid Block) NMA tool.', 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('--input_pdb_path', required=True, help='Input structure file. Accepted formats: pdb')
required_args.add_argument('--output_pdb_path', required=True, help='Output pdb file. Accepted formats: pdb.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call
nolb_nma(input_pdb_path=args.input_pdb_path,
output_pdb_path=args.output_pdb_path,
properties=properties)
if __name__ == '__main__':
main()