| Safe Haskell | None |
|---|
Biobase.Turner
Description
The Turner2004 data structure reflects the RNA (and DNA) energy
parameters known as the Turner 2004 data set.
In general, have a look here: http://rna.urmc.rochester.edu/NNDB/turner04/index.html 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 = Energy Double
- type Turner2004 = Turner2004Model Energy
- data Turner2004Model e = Turner2004Model {
- _stack :: !(Unboxed PP e)
- _dangle3 :: !(Unboxed PN e)
- _dangle5 :: !(Unboxed PN e)
- _hairpinL :: !(Vector e)
- _hairpinMM :: !(Unboxed PNN e)
- _hairpinLookup :: !(Map ByteString 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
- type PP = (((Z :. Nuc) :. Nuc) :. Nuc) :. Nuc
- type PN = ((Z :. Nuc) :. Nuc) :. Nuc
- type PNN = (((Z :. Nuc) :. Nuc) :. Nuc) :. Nuc
- type PPNN = (PP :. Nuc) :. Nuc
- type PPNNN = PPNN :. Nuc
- type PPNNNN = PPNNN :. Nuc
- termAU :: forall e. Lens' (Turner2004Model e) e
- tStackCoax :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)
- stack :: forall e. Lens' (Turner2004Model e) (Unboxed PP e)
- ninio :: forall e. Lens' (Turner2004Model e) e
- multiStrain :: forall e. Lens' (Turner2004Model e) e
- multiOffset :: forall e. Lens' (Turner2004Model e) e
- multiNuc :: forall e. Lens' (Turner2004Model e) e
- multiMM :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)
- multiHelix :: forall e. Lens' (Turner2004Model e) e
- multiAsym :: forall e. Lens' (Turner2004Model e) e
- maxNinio :: forall e. Lens' (Turner2004Model e) e
- largeLoop :: forall e. Lens' (Turner2004Model e) e
- intermolecularInit :: forall e. Lens' (Turner2004Model e) e
- iloopMM :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)
- iloopL :: forall e. Lens' (Turner2004Model e) (Vector e)
- iloop2x3MM :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)
- iloop2x2 :: forall e. Lens' (Turner2004Model e) (Unboxed PPNNNN e)
- iloop2x1 :: forall e. Lens' (Turner2004Model e) (Unboxed PPNNN e)
- iloop1xnMM :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)
- iloop1x1 :: forall e. Lens' (Turner2004Model e) (Unboxed PPNN e)
- hairpinMM :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)
- hairpinLookup :: forall e. Lens' (Turner2004Model e) (Map ByteString e)
- hairpinL :: forall e. Lens' (Turner2004Model e) (Vector e)
- hairpinGGG :: forall e. Lens' (Turner2004Model e) e
- hairpinCslope :: forall e. Lens' (Turner2004Model e) e
- hairpinCintercept :: forall e. Lens' (Turner2004Model e) e
- hairpinC3 :: forall e. Lens' (Turner2004Model e) e
- extMM :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)
- dangle5 :: forall e. Lens' (Turner2004Model e) (Unboxed PN e)
- dangle3 :: forall e. Lens' (Turner2004Model e) (Unboxed PN e)
- coaxial :: forall e. Lens' (Turner2004Model e) (Unboxed PP e)
- coaxStack :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)
- bulgeSingleC :: forall e. Lens' (Turner2004Model e) e
- bulgeL :: forall e. Lens' (Turner2004Model e) (Vector e)
- emap :: (Unbox e, Unbox e') => (e -> e') -> Turner2004Model e -> Turner2004Model e'
Documentation
The actual Turner parameters return energies in Double format.
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.
Constructors
| Turner2004Model | |
Fields
| |
Instances
| (Show e, Unbox e) => Show (Turner2004Model e) |
termAU :: forall e. Lens' (Turner2004Model e) eSource
tStackCoax :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)Source
ninio :: forall e. Lens' (Turner2004Model e) eSource
multiStrain :: forall e. Lens' (Turner2004Model e) eSource
multiOffset :: forall e. Lens' (Turner2004Model e) eSource
multiNuc :: forall e. Lens' (Turner2004Model e) eSource
multiHelix :: forall e. Lens' (Turner2004Model e) eSource
multiAsym :: forall e. Lens' (Turner2004Model e) eSource
maxNinio :: forall e. Lens' (Turner2004Model e) eSource
largeLoop :: forall e. Lens' (Turner2004Model e) eSource
intermolecularInit :: forall e. Lens' (Turner2004Model e) eSource
iloopL :: forall e. Lens' (Turner2004Model e) (Vector e)Source
iloop2x3MM :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)Source
iloop1xnMM :: forall e. Lens' (Turner2004Model e) (Unboxed PNN e)Source
hairpinLookup :: forall e. Lens' (Turner2004Model e) (Map ByteString e)Source
hairpinL :: forall e. Lens' (Turner2004Model e) (Vector e)Source
hairpinGGG :: forall e. Lens' (Turner2004Model e) eSource
hairpinCslope :: forall e. Lens' (Turner2004Model e) eSource
hairpinCintercept :: forall e. Lens' (Turner2004Model e) eSource
hairpinC3 :: forall e. Lens' (Turner2004Model e) eSource
bulgeSingleC :: forall e. Lens' (Turner2004Model e) eSource
bulgeL :: forall e. Lens' (Turner2004Model e) (Vector e)Source
emap :: (Unbox e, Unbox e') => (e -> e') -> Turner2004Model e -> Turner2004Model e'Source
Map a function over all e elements.