write.rosetta.constraints <- function(restrictionVector,
table.location = NULL,
mode = "xlff"){
distanceTable <- read.table(table.location)
rownames(distanceTable) <- paste0(distanceTable$V4,
distanceTable$V5,
"-",
distanceTable$V8,
distanceTable$V9)
if (mode == "flat_linear") {
distanceTable$input <- apply(distanceTable, 1, function(line) {
paste("AtomPair",
line[5],
line[4],
line[9],
line[8],
"LINEAR_PENALTY",
as.numeric(line[14])/2,
0,
as.numeric(line[14])/2,
1,
collapse = " ")})
} else if (mode == "xlff") {
distanceTable$input <- apply(distanceTable, 1, function(line) {
paste("observed",
line[2],
line[3],
line[4],
line[6],
line[7],
line[8],
collapse = " ")})
}
distanceTable <- subset(distanceTable,
rownames(distanceTable) %in% restrictionVector,
select = "input")
return(distanceTable)
}
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