#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
Protrein Block assignation --- :mod:`pbxplore.assignment`
=========================================================
.. autofunction:: assign
"""
from __future__ import print_function, absolute_import
# Third-party module
import numpy
# Local module
from . import PB
[docs]def assign(dihedrals, pb_ref=PB.REFERENCES):
"""
Assign Protein Blocks.
Dihedral angles are provided as a dictionnary with one item per residue.
The key is the residue number, and the value is a dictionnary with phi and
psi as keys, and the dihedral angles as values.
The protein block definitions are provided as a dictionnary. Each key is a
block name, the values are lists of dihedral angles.
Parameters
----------
dihedrals : dict
Phi and psi dihedral angles for each residue.
pb_ref : dict
The definition of the protein blocks.
"""
pb_seq = ""
# Transform the dict into a numpy array with the right order
ref = numpy.array([pb_ref[key] for key in sorted(pb_ref)])
# iterate over all residues
for res in sorted(dihedrals):
angles = []
# try to get all eight angles required for PB assignement
try:
angles.append(dihedrals[res-2]["psi"])
angles.append(dihedrals[res-1]["phi"])
angles.append(dihedrals[res-1]["psi"])
angles.append(dihedrals[res ]["phi"])
angles.append(dihedrals[res ]["psi"])
angles.append(dihedrals[res+1]["phi"])
angles.append(dihedrals[res+1]["psi"])
angles.append(dihedrals[res+2]["phi"])
# check for bad angles
# (error while calculating torsion: missing atoms)
if None in angles:
pb_seq += "Z"
continue
# cannot get required angles (Nter, Cter or missign residues)
# -> cannot assign PB
# jump to next residue
except KeyError:
pb_seq += "Z"
continue
# Compute the RMSD between all reference angles and angles of the current residue
# (16*8)*(1,8) vectorization
# Note (ref - ang + 180) % 360 - 180) ensure the real difference between 2 angles
rmsda = numpy.sum(((ref - angles + 180) % 360 - 180)**2, axis=1)
# Find the PB with the lowest RMSD
pb_seq += PB.NAMES[numpy.argmin(rmsda)]
return pb_seq