Bios2cor (version 1.2)

rotamer_circular: Circular correlation

Description

Calculates circular correlation scores between side chain dihedral angles during a molecular dynamics trajectory.

Usage

rotamer_circular(
    dynamic_struct,
    res_selection=
      c("C","I","L","M","V","R","H","K","D","E","N","Q","F","Y","W","T","S","P"),
    z_score= TRUE,
    auto_pairing= FALSE
  )

Arguments

dynamic_struct

Object of class 'structure' that is created by the dynamic_struct function

res_selection

Selection of amino acid types that will be taken into account in the covariation matrix. Allows to limit the analysis to a limited selection of amino acid types.

z_score

A logical value for Z-score normalisation of the covariation matrix. Default is TRUE.

auto_pairing

A logical value that maintains (TRUE) or removes (FALSE) covariation scores between dihedral angles within a same residue in the covariation matrix. DEFAULT is FALSE.

Value

A list of two elements : a matrix containing a covariation score for each pair of rotamer and its normalized version

Details

This function uses the cor.circular function from the circular package based on a circular version of the Pearson coeefficient.

References

Circular Statistics, from ``Topics in circular Statistics'' (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.

Examples

# NOT RUN {
  #Reading pdb file
  pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor")
  trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor")

  #conversion_file <- system.file("rotamer/dynameomics_rotameres.csv", package= "Bios2cor")

  wanted_residues <- c("H","N","Q","F","Y","W")
  
  wanted_frames <- seq(from= 1, to= 40, by= 2)
  dynamic_struct <- dynamic_struct(pdb, trj, wanted_frames)
    
  dihed_corr <- rotamer_circular(dynamic_struct, wanted_residues)
# }