BioInf.RNAfold.Energy

A set of energy functions that are modelled after the ViennaRNA package, Version 2 (with d=2).

As part of the design, we could have (i) either continued giving many parameters or (ii) have fewer parameters that require input of the (Primary,Index,Index) type. Since the compilation speed of the grammars using these functions depends on the number of arguments (in case (i) compilation takes minutes!), this approach has benefits for testing the fusion library.

This means compilation is a lot faster, but runtime is not 2.8x slower but 3.5x slower.

Documentation

hairpinF :: Vienna2004 -> (Nuc :!: Nuc) -> ((Primary :!: Int) :!: Int) -> (Nuc :!: Nuc) -> Int

Hairpin structures. Hairpins with less than 3 unpaired nucleotides are forbidden.

NOTE (xs,i,j) is indeed *only* the unpaired stretch. Hence, the length is j-i+1, as given.

TODO Activate tabulated hairpin structures.

tinyloopF :: Vienna2004 -> ((Primary :!: Int) :!: Int) -> Int -> ((Primary :!: Int) :!: Int) -> Int

Tiny loops are small interior loops. This includes canonical stacks without any unpaired nucleotides, and small, tabulated interior loops.

bulgeLF :: Vienna2004 -> ((Primary :!: Int) :!: Int) -> Int -> (Nuc :!: Nuc) -> Int

A left bulge (....[[...]]) which four unpaired nucleotides in the bulge. the left bulge ls will be given six nucleotides (note, ls is the complete input, use li and lj as the first and last included nucleotide index), the two outer ones being for the outer and inner loop. On the right, we have rp and r which are nucleotides. ls!(Z:.li) and r form the outer Vienna pair. rp and ls!(Z:.lj) form the inner pair.

bulgeRF :: Vienna2004 -> (Nuc :!: Nuc) -> Int -> ((Primary :!: Int) :!: Int) -> Int

A right bulge ([[...]]....). See bulgeLF for how this works.

iloopN1F :: Vienna2004 -> ((Primary :!: Int) :!: Int) -> Int -> ((Primary :!: Int) :!: Int) -> Int

An interior loop with N unpaired nucleotides to the left and 1 unpaired nucleotide to the right. The regions ls and rs each have 2 nucleotides more than are unpaired. These first and last nucleotides form the last paired or first pairs in the stacks around the loop.

iloop1NF :: Vienna2004 -> ((Primary :!: Int) :!: Int) -> Int -> ((Primary :!: Int) :!: Int) -> Int

1xN interior loops.

iloopIF :: Vienna2004 -> ((Primary :!: Int) :!: Int) -> Int -> ((Primary :!: Int) :!: Int) -> Int

iloopOF :: Vienna2004 -> (Nuc :!: Nuc) -> Int -> (Nuc :!: Nuc) -> Int

multiIF :: Vienna2004 -> Int -> Int -> Int

multiOF :: Vienna2004 -> (Nuc :!: Nuc) -> Int -> (Nuc :!: Nuc) -> Int

regionStemF :: Vienna2004 -> Nuc -> Int -> Int

justStemF :: Vienna2004 -> (Nuc :!: Nuc) -> Int -> (Nuc :!: Nuc) -> Int

bsF :: Int -> Int -> Int

rSF :: Nuc -> Int -> Int

bcF :: Int -> Int -> Int

ssF :: Int -> Int

cmF :: Int -> Int -> Int

nilF :: Bool -> Int

iD :: a -> a

h :: Monad m => Stream m Int -> m Int

terminalAU :: Num a => a -> ViennaPair -> a