| Safe Haskell | None |
|---|---|
| Language | Haskell2010 |
BioInf.ViennaRNA.Bindings
Contents
Description
Bindings to important functions in the ViennaRNA library.
TODO Anything here that is not thread-safe should internally use a mutex!
- mfe :: ByteString -> IO (Double, ByteString)
- mfeTemp :: Double -> ByteString -> IO (Double, ByteString)
- circmfe :: ByteString -> IO (Double, ByteString)
- eos :: ByteString -> ByteString -> IO Double
- eosTemp :: Double -> ByteString -> ByteString -> IO Double
- eosCirc :: ByteString -> ByteString -> IO Double
- part :: ByteString -> IO (Double, ByteString, Array (Int, Int) Double)
- partConstrained :: ByteString -> ByteString -> IO (Double, ByteString, Array (Int, Int) Double)
- circPart :: ByteString -> IO (Double, ByteString, Array (Int, Int) Double)
- circPartConstrained :: ByteString -> ByteString -> IO (Double, ByteString, Array (Int, Int) Double)
- centroidTemp :: Double -> ByteString -> IO (Double, ByteString, Double)
- coeos :: ByteString -> ByteString -> Int -> IO Double
- comfe :: ByteString -> Int -> IO (Double, ByteString)
- copart :: ByteString -> Int -> IO (CofoldF, ByteString, Array (Int, Int) Double)
- copartConstrained :: ByteString -> ByteString -> Int -> IO (CofoldF, ByteString, Array (Int, Int) Double)
- duplexFold :: ByteString -> ByteString -> IO Duplex
- data CofoldF = CofoldF {}
- data Duplex = Duplex {}
Documentation
mfe :: ByteString -> IO (Double, ByteString) Source #
Fold a sequence into an optimal secondary structure. Returns a pair of energy and structure.
mfeTemp :: Double -> ByteString -> IO (Double, ByteString) Source #
circmfe :: ByteString -> IO (Double, ByteString) Source #
eos :: ByteString -> ByteString -> IO Double Source #
Given a sequence and a structure, returns the energy of the sequence/structure pair.
eosTemp :: Double -> ByteString -> ByteString -> IO Double Source #
eosCirc :: ByteString -> ByteString -> IO Double Source #
Energy of a circular structure
part :: ByteString -> IO (Double, ByteString, Array (Int, Int) Double) Source #
Given a string, calculates the partition function for said string. Returns the ensemble energy, a string with where each nucleotide position is annotated with the strength of the potential pairing, and the whole base pair probability table.
partConstrained :: ByteString -> ByteString -> IO (Double, ByteString, Array (Int, Int) Double) Source #
circPartConstrained :: ByteString -> ByteString -> IO (Double, ByteString, Array (Int, Int) Double) Source #
centroidTemp :: Double -> ByteString -> IO (Double, ByteString, Double) Source #
Centroid structure
RNAcofold
coeos :: ByteString -> ByteString -> Int -> IO Double Source #
Energy of struct for cofolded structures.
comfe :: ByteString -> Int -> IO (Double, ByteString) Source #
mfe of co-folded structure
copart :: ByteString -> Int -> IO (CofoldF, ByteString, Array (Int, Int) Double) Source #
Cofolded partition function. Makes the set of different partfun values from cofoldF available.
copartConstrained :: ByteString -> ByteString -> Int -> IO (CofoldF, ByteString, Array (Int, Int) Double) Source #
duplexFold :: ByteString -> ByteString -> IO Duplex Source #
Fold a duplex structure
Constructors
| CofoldF | |
Constructors
| Duplex | |