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 :: ByteString
- nucleotide1 :: Char
- pdbnumber1 :: Int
- chain1 :: ByteString
- seqpos1 :: Int
- nucleotide2 :: Char
- pdbnumber2 :: Int
- chain2 :: ByteString
- seqpos2 :: Int
- data LinFR3D = LinFR3D {
- pdbID :: ByteString
- sequence :: ByteString
- pairs :: [(Int, Int, String)]
- linearizeFR3D :: FR3D -> LinFR3D
Documentation
Encapsulates all the basepairs information.
FR3D | |
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A single basepair in a basepair system.
Basepair | |
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Linearized FR3D format.
LinFR3D | |
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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).