Bios2cor (version 1.2)

dynamic_struct: 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_struct(pdb, trj, frames)

Arguments

pdb

Filepath of protein description (pdb file)

trj

Filepath of trajectory file (dcd file)

frames

Stride length indicating the ratio of selected frames in dcd file

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,...). Positions for Alanine and Glycine residues which do not have side chain dihedral angles are omitted.

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 vector indicating the frames that are used (first, last, stride)

Examples

# NOT RUN {
   #Input files
  pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor")
  trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor")
  conversion_file <- system.file("rotamer/dynameomics_rotameres.csv", package= "Bios2cor")
  
  wanted_frames <- seq(from= 1, to= 40, by= 2)
  dynamic_struct <- dynamic_struct(pdb, trj, wanted_frames)
  
# }