qvalue.qvalue

Q-Value Analysis

The Q-value is a measure of the fraction of native contacts conserved during a simulation. Native contacts are defined from the selected atoms in a reference structure. This module implements two primary Q-value calculation methods:

1. Wolynes Q: A weighted measure of native contact preservation.

   • Native contacts are defined without applying a specific distance cutoff.

   • Each contact is weighted using a Gaussian function centered on the reference structure’s inter-atomic distance and scaled by the sequence separation:

   \[q(t) = \frac{1}{N} \sum_{i,j} \exp\left(-\frac{(r_{ij} - r_{ij}^N)^2}{2\sigma_{ij}^2}\right)\]

   where: - \(r_{ij}\) is the distance between atoms \(i\) and \(j\) at time \(t\). - \(r_{ij}^N\) is the reference distance between atoms \(i\) and \(j\). - \(\sigma_{ij}\) is the separation in the sequence between residues \(i\) and \(j\).

2. Onuchic Q: Similar to Wolynes Q but applies additional constraints:

   • Excludes contacts with a sequence separation below a threshold.

   • Incorporates a distance cutoff to restrict the evaluation to native contacts.

   • \(\sigma_{ij}\) is the separation in the sequence between residues \(i\) and \(j\) plus 1.

Usage Example

from MDAnalysis import Universe
from qvalue_module import qValue
u = Universe("native.pdb", "trajectory.dcd")
q_calc = qValue(u)
q_calc.run()
q_wolynes = q_calc.results['Wolynes']['q_values']
q_onuchic = q_calc.results['Onuchic']['q_values']

Functions

get_rij(rij, rijn, seq_sep[, N, sigma_Exp])
qvalue_pair_interface_CB(rij, rijn, seq_sep)
qvalue_pair_onuchic(rij, rijn, seq_sep[, a, ...])	Onuchic Q value contribution for each pair of atoms.
qvalue_pair_wolynes(rij, rijn, seq_sep[, a, ...])	Wolynes Q value contribution for each pair of atoms.

Classes

qValue(universe[, reference_universe, ...])

Calculates Q-values (fraction of native contacts) across a trajectory by comparing inter-atomic distances in a trajectory to those in a reference structure.