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\name{dynamic_structure}
\Rdversion{1.1}
\alias{dynamic_structure}
\title{
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{
\item{pdb}{
Filepath of the pdb file
}
\item{trj}{
Filepath of trajectory file (dcd file)
}
\item{frames}{
Indicates the selected frames for the analysis, created with the \code{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:
\item{pdb}{
an object of class 'pdb' created by the \code{read.pdb}function from the \code{bio3d} package
}
\item{dcd}{
A numeric matrix of xyz coordinates with a frame per row and a Cartesian coordinate per column. Created by the \code{read.dcd}function from the \code{bio3d} package
}
\item{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 \code{fit.xyz} from the \code{bio3d} package
}
\item{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 \code{xyz2tor} function from the \code{bio3d} package
}
\item{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.
}
\item{tor.resno}{
a character vector with the residue number M of all side chain chi dihedral angles.
}
\item{tor.angle}{
a character vector with the dihedral angle (chiN) of all side chain chi dihedral angles.
}
\item{nb_torsions}{
a numeric value indicating the total number of dihedral angles
}
\item{prot.seq}{
a character vector with the sequence of the protein
}
\item{nb_residues}{
a numeric value indicating the number of residues in the protein
}
\item{nb_frames}{
a numeric value indicating the total number of selected frames
}
\item{frames}{
a numeric vector indicating the selected frames
}
}
\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)
}
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