dynamic_entropy: Variability score

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

Variability score

Description

Measures a "dynamic entropy" or variability score of each dihedral angle based on the number of rotameric changes during the molecular dynamics trajectory.

Usage

  dynamic_entropy(rotamers)

Arguments

rotamers

A character matrix of type 'rotamers' that is produced by the angle2rotamer function. The matrix indicates the rotameric state of each side chain dihedral angle for each frame of the trajectory.

Details

The "dynamic entropy" score S is computed by summing the number of rotameric changes over all frames, normalized to the number of frames. It is not a "true entropy" score but gives usefull information on variability of the dihedral angle during the MD simulation.

Value

A numeric vector containing a "dynamic entropy" score for each side chain dihedral angle during the trajectory. The score is comprised between 0 (no change in the rotameric state during the trajectory) and 1 (rotameric change for every frame of the trajectory).

Author(s)

Antoine GARNIER, Lea BELLENGER and Marie CHABBERT

Examples

  #Reading pdb and dcd files
  pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor")
  trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor")
 
  #Reading conversion file
  conversion_file <- system.file("rotamer/dynameomics_rotamers.csv", package= "Bios2cor")

  #Creating the dynamic_structure and rotamers objects
  wanted_frames <- seq(from = 1, t = 40, by = 5)
  dynamic_structure <- dynamic_structure(pdb, trj, wanted_frames)
  rotamers <- angle2rotamer(dynamic_structure, conversion_file)
 
  #creating the dynamic_entropy object
  dynamic_entropy <- dynamic_entropy(rotamers)

Bios2cor documentation built on April 4, 2025, 4:14 a.m.