Nothing
"sse.bridges" <- function(sse, type="helix", hbond=TRUE,
energy.cut=-1.0 ) {
if(missing(sse))
stop("sse missing")
if(is.null(sse$hbonds))
stop("sse$hbonds does not exists. run dssp with 'resno=FALSE' and 'full=TRUE'")
natoms <- nrow(sse$hbonds)
if(type=="helix") {
sse2 <- sse$helix
stype <- "H"
lim <- 4
}
if(type=="sheet") {
sse2 <- sse$sheet
stype <- "S"
lim <- 2
}
if(length(sse2$start)==0)
return(NULL)
## character array of SSE membership
simple.sse <- sse$sse
simple.sse[ !(sse$sse %in% c("H", "E", "G", "I")) ] <- "L"
simple.sse[ sse$sse %in% c("E") ] <- "S"
simple.sse[ sse$sse %in% c("H", "I", "G") ] <- "H"
inds <- NULL
for ( i in 1:(natoms-lim) ) {
if(simple.sse[i]!=stype)
next;
paired <- NULL
if(type=="helix") {
paired <- i+4
if(simple.sse[paired]!=stype)
next;
}
if (type=="sheet") {
## bridge pair info
paired <- sse$hbonds[i,c("BP1", "BP2")]
paired <- paired[ !is.na(paired) ]
if(length(paired)==0)
next;
}
if(hbond) {
## H-bond info
resid <- sse$hbonds[i, c(3,5,7,9)]
energ <- sse$hbonds[i, c(4,6,8,10)]
energ <- energ[ !is.na(resid) ]
resid <- resid[ !is.na(resid) ]
inds.tmp <- which(resid %in% paired)
resid <- resid[inds.tmp]
energ <- energ[inds.tmp]
dups <- duplicated(resid)
resid <- resid[ !dups ]
energ <- energ[ !dups ]
if(length(resid)==0)
next;
for( j in 1:length(resid) ) {
if(energ[j] < energy.cut)
inds <- c(inds, i, resid[j])
}
}
else {
for ( j in 1:length(paired) ) {
inds <- c(inds, i, paired[j])
}
}
}
if(length(inds)==0)
return(NULL)
mat <- matrix(inds, ncol=2, byrow=T)
mat <- t(apply(mat, 1, sort))
pair.ids <- apply(mat, 1, function(x) paste(x, collapse="-"))
mat <- matrix(mat[!duplicated(pair.ids), ], ncol=2)
return(mat)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.