#!/usr/bin/env python3
"""Module containing the prody_anm class and the command line interface."""
from typing import Optional
import prody # type: ignore
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools.file_utils import launchlogger
[docs]
class ProdyANM(BiobbObject):
"""
| biobb_flexdyn ProdyANM
| Wrapper of the ANM tool from the Prody package.
| Generate an ensemble of structures using the Prody Anisotropic Network Model (ANM), for coarse-grained NMA.
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/prody_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
* **selection** (*str*) - (calpha) Atoms selection (Prody syntax: http://prody.csb.pitt.edu/manual/reference/atomic/select.html)
* **cutoff** (*float*) - (15.0) Cutoff distance (Å) for pairwise interactions, minimum is 4.0 Å
* **gamma** (*float*) - (1.0) Spring constant
* **rmsd** (*float*) - (1.0) Average RMSD that the conformations will have with respect to the initial conformation
* **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_flexdyn.flexdyn.prody_anm import prody_anm
prop = {
'num_structs' : 20,
'rmsd' : 4.0
}
prody_anm( input_pdb_path='/path/to/structure.pdb',
output_pdb_path='/path/to/output.pdb',
properties=prop)
Info:
* wrapped_software:
* name: Prody
* version: >=2.2.0
* license: MIT
* 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.properties = properties
self.num_structs = properties.get('num_structs', 500)
self.selection = properties.get('selection', 'calpha')
self.cutoff = properties.get('cutoff', 15.0)
self.gamma = properties.get('gamma', 1.0)
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 ConcoordDist module."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
prot = prody.parsePDB(self.stage_io_dict["in"]["input_pdb_path"],)
# http://prody.csb.pitt.edu/manual/reference/atomic/select.html
prot_sel = prot.select(self.selection) # type: ignore
enm = prody.ANM('BioBB_flexdyn Prody ANM ensemble generator')
enm.buildHessian(prot_sel, cutoff=self.cutoff, gamma=self.gamma)
enm.calcModes()
bb_enm, bb_atoms = prody.extendModel(enm, prot_sel, prot_sel)
ensemble = prody.sampleModes(bb_enm[:3], bb_atoms, n_confs=self.num_structs, rmsd=self.rmsd)
nmastruct = bb_atoms.copy()
nmastruct.addCoordset(ensemble)
prody.writePDB(self.stage_io_dict["out"]["output_pdb_path"], nmastruct)
# Copy files to host
self.copy_to_host()
# remove temporary folder(s)
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def prody_anm(input_pdb_path: str, output_pdb_path: str,
properties: Optional[dict] = None, **kwargs) -> int:
"""Create :class:`ProdyANM <flexdyn.prody_anm.ProdyANM>`flexdyn.prody_anm.ProdyANM class and
execute :meth:`launch() <flexdyn.prody_anm.ProdyANM.launch>` method"""
return ProdyANM(**dict(locals())).launch()
prody_anm.__doc__ = ProdyANM.__doc__
main = ProdyANM.get_main(prody_anm, "Generate an ensemble of structures using the Prody Anisotropic Network Model (ANM), for coarse-grained NMA.")
if __name__ == '__main__':
main()