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# Bios2cor is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# See the GNU General Public License at:
# http://www.gnu.org/licenses/
#
angles.plot <- function(dynamic_structure, filepathroot, angles=NULL){
if (missing(dynamic_structure))
stop("A 'dynamic_structure' object is required")
if (is.null(angles)){
angles <- dynamic_structure$tor.names
}
if (is.null(filepathroot)) {
final_filepath <- paste(tempdir(), "/ANGLES.pdf",sep="")
final_csv <- paste(tempdir(), "/ANGLES.csv",sep="")
} else {
final_filepath <- paste(filepathroot, "_ANGLES.pdf",sep="")
final_csv <- paste(filepathroot, "_ANGLES.csv",sep="")
}
#Importing torsional and angles data
tor <- dynamic_structure$tor
nb_frames <- length(tor[,1])
nb_angles <- length(angles)
frames <- dynamic_structure$frames
#Generating ordered plots
nb_max_figures <- 35
nb_col <- 5
pdf(final_filepath)
#save user's parameters to reset them on exit
oldpar <- par(no.readonly = TRUE)
on.exit(par(oldpar))
layout(matrix(1:nb_max_figures, ncol= nb_col, byrow= TRUE)) # plot up to 7 rows of 5 figures / page
#Setting the margins of the graph in inches (mai)
par(mai= c(0.25, 0.25, 0.2, 0.2))
#Alphanumerical graph ordering
graph_order <- c(1:nb_angles)
graph_order <- sort(unlist(as.integer(lapply(strsplit(angles, "\\."), "[[", 1))), index.return= TRUE)$ix
for(i in graph_order){
angle_name <- angles[i]
dihedral_angles <- tor[, angle_name]
plot(x= 1:nb_frames, y= dihedral_angles, cex= 0.1, xlab= "frames", ylab="dihedral angles", main= angle_name)
}
dev.off()
tor <- tor[,angles]
write.csv(cbind(frames,round(tor, digits=2)), file = final_csv)
}
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