Bios2cor (version 1.2)

rotamer_entropy: Entropy score

Description

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

Usage

rotamer_entropy(rotamers)

Arguments

rotamers

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

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).

Details

The entropy score S is computed by summing the number of rotameric changes over all frames, normalized to the number of frames.

Examples

# NOT RUN {
 #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_rotameres.csv", package= "Bios2cor")

  #Creating angle_conversion object
  wanted_frames <- seq(from= 1, to= 40, by= 5)
  dynamic_struct <- dynamic_struct(pdb, trj, wanted_frames)
  
  my_rotamers <- angle_conversion(dynamic_struct, conversion_file)
 
  #creating rotamer entropy object
  rotamer_entropy <- rotamer_entropy(my_rotamers)
# }