Bios2cor (version 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)

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).

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

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")
  
  #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)
# }