Bios2cor (version 2.2.1)

dynamic_structure: Creates the data structure for the analysis of side chain dihedral angles

Description

Given a structure pdb file, a trajectory dcd file and frame indices, gathers information on side chain dihedral angles in a unique structure. This structure will be used in correlation/covariation methods aimed at analyzing side chain rotational motions during molecular dynamics simulations.

Usage

dynamic_structure(pdb, trj, frames=NULL)

Value

Returns a list of class 'structure' with the following elements containing information on the sequence, structure, trajectory and side chain dihedral angles (values and names) of the protein during the simulation:

pdb

an object of class 'pdb' created by the read.pdbfunction from the bio3d package

dcd

A numeric matrix of xyz coordinates with a frame per row and a Cartesian coordinate per column. Created by the read.dcdfunction from the bio3d package

xyz

A numeric matrix of xyz coordinates with a frame per row and a Cartesian coordinate per column. For each frame, the protein coordinates have been fitted on the pdb structure using the fit.xyz from the bio3d package

tor

A numeric matrix of side chain dihedral angles with a frame per row and a dihedral angle per column. Contains only side chain dihedral angles. Created by the xyz2tor function from the bio3d package

tor.names

a character vector with the names of all side chain chi dihedral angles. They are written as "M.chiN" where M is the residue number and N the dihedral angle chi (chi1, chi2,...). Alanine and Glycine residues which do not have side chain dihedral angles are omitted.

tor.resno

a character vector with the residue number M of all side chain chi dihedral angles.

tor.angle

a character vector with the dihedral angle (chiN) of all side chain chi dihedral angles.

nb_torsions

a numeric value indicating the total number of dihedral angles

prot.seq

a character vector with the sequence of the protein

nb_residues

a numeric value indicating the number of residues in the protein

nb_frames

a numeric value indicating the total number of selected frames

frames

a numeric vector indicating the selected frames

Arguments

pdb

Filepath of the pdb file

trj

Filepath of trajectory file (dcd file)

frames

Indicates the selected frames for the analysis, created with the seq function (Usage: frames <-seq(from ,to , by= ). Default is NULL (all the frames of the trajectory are taken into account).

Author

Bruck TADDESE, Antoine GARNIER 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")
  
  #Creating dynamic_structure object for selected frames  
  wanted_frames <- seq(from = 1, to = 40, by = 2)
  dynamic_structure <- dynamic_structure(pdb, trj, wanted_frames)

  #Creating dynamic_structure object for all the frames  
  #dynamic_structure <- dynamic_structure(pdb, trj)