dynamic_structure: Creates the data structure for the analysis of side chain...

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

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

Author(s)

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)

Bios2cor documentation built on April 4, 2025, 4:14 a.m.