BiobaseTurner- Import Turner RNA parameters

Safe HaskellNone



The Turner2004 data structure reflects the RNA (and DNA) energy parameters known as the Turner 2004 data set.

In general, have a look here: where parameters are explained.

TODO need a Functor instance over elements e. Or alternatively, generic programming to capture stuff going on in e



newtype Energy Source

The actual Turner parameters return energies in Double format.


Energy Double 

type Turner2004 = Turner2004Model EnergySource

The Turner model with Energys.

data Turner2004Model e Source

The Turner energy tables. Parametrized over the storing vector type v and the actual element type e.




_stack :: !(Unboxed PP e)
_dangle3 :: !(Unboxed PN e)
_dangle5 :: !(Unboxed PN e)
_hairpinL :: !(Vector e)
_hairpinMM :: !(Unboxed PNN e)
_hairpinLookup :: !(Map Primary e)
_hairpinGGG :: !e
_hairpinCslope :: !e
_hairpinCintercept :: !e
_hairpinC3 :: !e
_bulgeL :: !(Vector e)
_bulgeSingleC :: !e
_iloop1x1 :: !(Unboxed PPNN e)
_iloop2x1 :: !(Unboxed PPNNN e)
_iloop2x2 :: !(Unboxed PPNNNN e)
_iloopMM :: !(Unboxed PNN e)
_iloop2x3MM :: !(Unboxed PNN e)
_iloop1xnMM :: !(Unboxed PNN e)
_iloopL :: !(Vector e)
_multiMM :: !(Unboxed PNN e)
_ninio :: !e
_maxNinio :: !e
_multiOffset :: !e
_multiNuc :: !e
_multiHelix :: !e
_multiAsym :: !e
_multiStrain :: !e
_extMM :: !(Unboxed PNN e)
_coaxial :: !(Unboxed PP e)
_coaxStack :: !(Unboxed PNN e)
_tStackCoax :: !(Unboxed PNN e)
_largeLoop :: !e
_termAU :: !e
_intermolecularInit :: !e


(Show e, Unbox e) => Show (Turner2004Model e) 

type PP = (((Z :. Nuc) :. Nuc) :. Nuc) :. NucSource

type PN = ((Z :. Nuc) :. Nuc) :. NucSource

type PNN = (((Z :. Nuc) :. Nuc) :. Nuc) :. NucSource

ninio :: forall e. Lens' (Turner2004Model e) eSource

emap :: (Unbox e, Unbox e') => (e -> e') -> Turner2004Model e -> Turner2004Model e'Source

Map a function over all e elements.