Bios2cor (version 2.2.1)

angles.plot: plots the time evolution of the dihedral angles in top pairs

Description

Given an object of class 'structure' and names of dihedral angles, creates plots of the dihedral angles as a function of frames in a pdf file.

Usage

angles.plot(dynamic_structure, angles, filepathroot=NULL)

Value

returns a pdf file containing the plots of the frame dependance of each element included in argument angles.

Arguments

dynamic_structure

Dihedral angle structure, result of the dynamic_structure function

angles

A vector containing the names of the dihedral angles to be visualized.Default is NULL (all the torsional angles of the dynamic_structure object are taken into account).

filepathroot

Root of the full path name for the output file. Default is NULL. In this case, the output file is named "ANGLES.pdf". When filepathroot is not NULL, a "_ANGLES.pdf" extention is added to the filepathroot name.

Author

Antoine GARNIER and Marie CHABBERT

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

  #Indicating file path for output files
  wd <- tempdir()
  #wd <- getwd()
  file <- file.path(wd,"test_dyn1") 

  #Reading pdb and dcd files
  pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor")
  trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor")
  
  #Creating dynamic_structure object for wanted frames
  wanted_frames <- seq(from= 1, to= 40, by= 2)
  dynamic_structure <- dynamic_structure(pdb, trj, wanted_frames)

  #Calculating circular correlation between dihedral angles of selected residues 
  wanted_residues <- c("H","N","Q","F","Y","W")
  dihed_corr <- dynamic_circular(dynamic_structure, wanted_residues)

  #Selecting a correlation matrix
  dihed_corr <- dihed_corr$Zscore
  
  #Selecting angles of interest (here from the "top_pairs_analysis" function)
  top_angles <- top_pairs_analysis(dihed_corr, top= 25, file)
  my_angles <- unlist(top_angles$positions)
  
  #Creating plots of the time evolution of the dihedral angles 
  evol_angles <- angles.plot(dynamic_structure, my_angles, file)