| Safe Haskell | Safe-Infered |
|---|
Biobase.FR3D
Contents
Description
FR3D provides a very convenient library of explored RNA structures. We are mostly interested in the basepairs files. In contrast to the RNAstrand library or melting experiments, these data sets provide non-canonical RNA pairing.
NOTE that FR3D entries contain basepairs both in (i,j) as well as (j,i) orientation (with i<j).
- data FR3D = FR3D {
- pdbid :: ByteString
- chains :: [(ByteString, ByteString)]
- basepairs :: [Basepair]
- data Basepair = Basepair {
- interaction :: ExtPairAnnotation
- nucleotide1 :: Char
- pdbnumber1 :: Int
- chain1 :: ByteString
- seqpos1 :: Int
- nucleotide2 :: Char
- pdbnumber2 :: Int
- chain2 :: ByteString
- seqpos2 :: Int
- data LinFR3D = LinFR3D {
- pdbID :: ByteString
- sequence :: ByteString
- pairs :: [TriPair]
- type TriPair = (ExtPairIdx, ExtPair, Basepair)
- linearizeFR3D :: FR3D -> LinFR3D
- class RemoveDuplicatePairs a where
- removeDuplicatePairs :: a -> a
- checkFR3D :: FR3D -> Either (FR3D, [Basepair]) FR3D
- checkLinFR3D :: LinFR3D -> Either (LinFR3D, [TriPair]) LinFR3D
Documentation
Encapsulates all the basepairs information.
Constructors
| FR3D | |
Fields
| |
Instances
A single basepair in a basepair system.
Constructors
| Basepair | |
Fields
| |
Linearized FR3D format.
Constructors
| LinFR3D | |
Fields
| |
Instances
type TriPair = (ExtPairIdx, ExtPair, Basepair)Source
linearizeFR3D :: FR3D -> LinFR3DSource
The default format is a bit unwieldy; Linearization assumes that all sequences are in 5'->3' order; then produces one sequence with & separating the sequences and pairs reduced to (Int,Int,cWW).
class RemoveDuplicatePairs a whereSource
Methods
removeDuplicatePairs :: a -> aSource