Nothing
"aa2index" <-
function (aa, index = "KYTJ820101", window = 1) {
if (!is.vector(aa))
stop("aa2index: non vector argument")
if (!is.numeric(window) || window < 1)
stop("aa2index: 'window' must be numeric and positive")
if (window >= length(aa))
stop("aa2index: 'window' must be smaller than the sequence length")
# Use LazyData to import data - changed Jul 23, 2013
# if (!exists("aa.index"))
# data(aa.index)
aa.index = bio3d::aa.index
if (is.numeric(index)) {
if (index > length(names(aa.index))) {
stop("aa2index: 'index' number does not exist")
}
} else {
if (!is.element(index, names(aa.index))) {
stop("aa2index: 'index' name does not exist")
}
}
x <- aa.index[[index]]$I[aa]
if (window == 1) {
y <- x
} else {
n <- length(x)
y <- rep(NA, n)
w <- ceiling(window/2)
if ( (window %% 2) == 0 ) {
from <- w
to <- n - w
y[from:to] <- sapply(from:to, function(i)
mean(x[(i - (w-1)):(i+w)], na.rm=TRUE))
if (from-1 > 0) {
y[1:(from-1)] <- sapply(1:(from-1), function(i)
mean(x[1: (i + w)], na.rm=TRUE))
}
y[(to+1):n] <- sapply((to+1):n, function(i)
mean(x[(i- (w-1)): n], na.rm=TRUE))
} else {
from <- w
to <- n - (w-1)
y[from:to] <- sapply(from:to, function(i)
mean(x[(i - (w-1)):(i + (w-1))], na.rm=TRUE))
y[1:(from-1)] <- sapply(1:(from-1), function(i)
mean(x[1: (i + (w-1))], na.rm=TRUE))
y[(to+1):n] <- sapply((to+1):n, function(i)
mean(x[(i - (w-1)): n], na.rm=TRUE))
}
y <- round(y,2)
names(y) <- aa
}
return(y)
}
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