RNAPlot                 Generic RNA Secondary Structure Plotting
                        Function
RRNA-package            RNA secondary structure ploting
alignCoord              Alignment of secondary structure folds to 2
                        nucleotides.
aptPlotCT               RNA secondary structure plotting from CT files
backward                Internal function for moving through secondary
                        structures
bplfile                 Creates a bpl file from a coordinate file
circleCoord             Internal function for finding the coordinates
                        of NT's in a circle
ct2coord                Generate coordinate file
ct2knet                 creates a knet file from a CT file
forward                 Internal function for moving through secondary
                        structures
genCords                Internal function that generates coordinates
                        for a given loop starting and stopping at p1
                        and p2 respectfully
loadCoords              Loads a coordinate file into a data frame
loadCt                  Loads a CT file into an R data frame
loopLength              internal function that determines the length of
                        a loop
makeCt                  make a CT file from a structure and sequence
pseudoKnot              removes pseudoknots from a ct file
rotateS                 Internal function to rotate a single point
rotateV                 internal function to rotate a vector of points
stemCords               internal function that generates coordinates
                        for a stem
transformFold           Internal function to translate and rotate a
                        secondary structure plot
translate               internal function for translating points
