Bios2cor (version 1.2)

ang_evo_graph: Angle evolution graphs

Description

Given an object of class 'structure' and names of dihedral angles, creates graphs to monitor the evolution of the dihedral angles along the frames and organizes them in a pdf file.

Usage

ang_evo_graph(dynamic_struct, top_positions, filepath)

Arguments

dynamic_struct

Dihedral angle structure, result of the dynamic_struct function

top_positions

A vector containing the names of the dihedral angles in the top X pairs; Result of corr_contact function

filepath

Filepath for the output file

Value

returns a pdf file containing the graphs of the frame dependance of each element included in argument top_positions

Details

The object of class 'structure' contains the side chain dihedral angles (between -180 and 180) for each residue in the protein, for each frame of the molecular simulations. This function allows visualisation of the evolution of selected angles

Examples

# NOT RUN {
  #Reading pdb file
  pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor")
  trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor")
  
   
  #output file
  filepath <- "angles.pdf"
  
  #Calculating dynamic data (dihedral angles)
  wanted_frames <- seq(from= 1, to= 40, by= 2)
  dynamic_struct <- dynamic_struct(pdb, trj, wanted_frames)

  wanted_residues <- c("H","N","Q","F","Y","W")
  
    
  dihed_corr <- rotamer_circular(dynamic_struct, wanted_residues)
  dihed_corr <- dihed_corr$normalized
  
  #Select positions of interest (calculated from the "corr_contact" function or list)
  top_angles <- corr_contact(dihed_corr, top= 25, "contact_file.txt","top_scores.txt")
  my_angles <- unlist(top_angles$positions)
  
  #Creating ang_evol graph
  evol_angles <- ang_evo_graph(dynamic_struct, my_angles, filepath)
# }