# NOT RUN {
# }
# NOT RUN {
## load example data
pdbfile <- system.file("examples/hivp.pdb", package="bio3d")
pdb <- read.pdb(pdbfile)
trtfile <- system.file("examples/hivp.dcd", package="bio3d")
trj <- read.dcd(trtfile, verbose=FALSE)
## split the trj example in two
num.of.frames <- dim(trj)[1]
trj1 <- trj[1:(num.of.frames/2),]
trj2 <- trj[((num.of.frames/2)+1):num.of.frames,]
## Lets work with Calpha atoms only
ca.inds <- atom.select(pdb, "calpha")
#noh.inds <- atom.select(pdb, "noh")
## calculate single contact map matrices
cms <- list()
cms[[1]] <- cmap(trj1[,ca.inds$xyz], pcut=0.3, scut=0, dcut=7, mask.lower=FALSE)
cms[[2]] <- cmap(trj1[,ca.inds$xyz], pcut=0.3, scut=0, dcut=7, mask.lower=FALSE)
## calculate average contact matrix
cm.filter <- filter.cmap(cms, cutoff.sims=2)
## plot the result
par(pty="s", mfcol=c(1,3))
plot.cmap(cms[[1]])
plot.cmap(cms[[2]])
plot.cmap(cm.filter)
# }
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