Biobase.Secondary.Isostericity

Provides detailed information on isostericity of RNA basepairs. All data is extracted from csv files which were created from supplemental files in:

Frequency and isostericity of RNA base pairs
Jesse Stombaugh, Craig L. Zirbel, Eric Westhof, and Neocles B. Leontis
Nucl. Acids Res. (2009)
doi:10.1093nargkp011

Documentation

class IsostericityLookup a where

Methods to determine the isostericity classes for a given basepair type, or alternatively which basepair types are in a certain isostericity class.

TODO This requires a major cleanup: right now we are handling Strings as class descriptors, but we should really be newtype-wrapping or create enum data constructors.

Methods

getClasses :: a -> [String]

To which classes does a basepair+type belong

inClass :: String -> [a]

What basepairs+type are in a particular class

Instances

IsostericityLookup (ExtPair n)

For extended basepairs, we take the default mapping and go from there.

TODO inClass missing

Defined in Biobase.Secondary.Isostericity

Methods

getClasses :: ExtPair n -> [String]

inClass :: String -> [ExtPair n]

IsostericityLookup (Pair n)

Normal basepairs are assumed to have cWW basepairing.

TODO inClass missing

Defined in Biobase.Secondary.Isostericity

Methods

getClasses :: Pair n -> [String]

inClass :: String -> [Pair n]

default data

defaultIsostericityMap :: forall k (n :: k). Map (ExtPair n) [String]

The default isostericity mapping.

mkIsostericityMap :: forall k (n :: k). [[[String]]] -> Map (ExtPair n) [String]

Mapping of (pair,pairtype) to isostericity class.

mkIsostericityList :: [[[String]]] -> [(ExtPair n, [String])]

Process CSV list-of-lists to get the isostericity data.

parsedCSV :: [[[Field]]]

Simple parsing of raw CSV data.

Raw embeddings

detailedCSV :: ByteString

Raw CSV data, embedded into the library.