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\name{angles.plot}
\Rdversion{1.1}
\alias{angles.plot}
\title{
plots the time evolution of the dihedral angles in top pairs
}
\description{
Given an object of class 'structure' and names of dihedral angles, creates plots of the dihedral angles as a function of frames in a pdf file.
}
\usage{
angles.plot(dynamic_structure, filepathroot, angles)
}
\arguments{
\item{dynamic_structure}{
Dihedral angle structure, result of the \code{dynamic_structure} function
}
\item{angles}{
A vector containing the names of the dihedral angles to be visualized.Default is NULL (all the torsional angles of the dynamic_structure object are taken into account).
}
\item{filepathroot}{
Root of the full path name for the output file. If NULL, an output file "ANGLES.pdf" is created in tempdir(). If not NULL, a "_ANGLES.pdf" extention is added to the filepathroot.
}
}
\details{
The object of class 'structure' contains the side chain dihedral angles (between -180 and 180) for each residue in the protein, for each frame of the molecular simulations. This function allows visualisation of the evolution of selected angles.
}
\value{
returns a pdf file containing the plots of the frame dependance of each element included in argument \code{angles}.
}
\author{
Antoine GARNIER and Marie CHABBERT
}
\examples{
#Indicating file path for output files
out <- tempdir()
file <- file.path(out,"test_dyn1")
#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 wanted frames
wanted_frames <- seq(from= 1, to= 40, by= 2)
dynamic_structure <- dynamic_structure(pdb, trj, wanted_frames)
#Calculating circular correlation between dihedral angles of selected residues
wanted_residues <- c("H","N","Q","F","Y","W")
dihed_corr <- dynamic_circular(dynamic_structure, wanted_residues)
#Selecting a correlation matrix
dihed_corr <- dihed_corr$Zscore
#Selecting angles of interest (here from the "top_pairs_analysis" function)
top_angles <- top_pairs_analysis(dihed_corr, top= 25, file)
my_angles <- unlist(top_angles$positions)
#Creating plots of the time evolution of the dihedral angles
evol_angles <- angles.plot(dynamic_structure, file, my_angles)
}
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