- An unpaired nucleotide to the right of an NMbr structure.
- An unpaired nucleotide to the right of an NMbr1 structure.
- EStem to Helix start
- Closes a multibranched loop and produces an extended structure at
- Multibranched loop helper table
- Backtracking of a multibranched stem with unpaired nucleotides to the
- Backtracking of at least two stems by finding one or more stems to the
- Backtrack a single stem in NMbr1. This stem is closed at (i,j).
Functions for handling non-triplet multibranched loops.
TODO We can do the loop-splitting thing again to speed up multibranched closing by x10.
- fUnpairedRight :: BaseF (NMbr -> Features (Vector (PairIdx, Double)))
- btUnpairedRight :: Params -> Primary -> NMbr -> NBT -> NBT
- fUnpairedRight1 :: BaseF (NMbr1 -> Features (Vector (PairIdx, Double)))
- btUnpairedRight1 :: Params -> Primary -> NMbr1 -> NBT -> NBT
- fMlHelix :: BaseF (EStem -> Features (Vector (ExtPairIdx, Double)))
- btMlHelix :: Params -> Primary -> NMult -> EStem -> ExtBT -> NBT
- fMlClose :: BaseF (NMultLoop -> ExtFeatures (Vector (PairIdx, Double)))
- btMlClose :: Params -> Primary -> EStem -> NMultLoop -> NBT -> ExtBT
- fMlLoop :: BaseF (NMbr -> NMbr1 -> Features (Vector (Int, Double)))
- btMlLoop :: Params -> Primary -> NMultLoop -> NMbr -> NMbr1 -> NBT -> NBT -> NBT
- fMlStem :: BaseF (NMult -> Features (Vector (Int, Double)))
- btMlStem :: Params -> Primary -> NMbr -> NMult -> NBT -> NBT
- fMlStems :: BaseF (NMbr -> NMult -> Features (Vector (Int, Double)))
- btMlStems :: Params -> Primary -> NMbr -> NMult -> NBT -> NBT -> NBT
- fMl1Stem :: BaseF (NMult -> Features (Vector ((Int, Int), Double)))
- btMl1Stem :: Params -> Primary -> NMbr1 -> NMult -> NBT -> NBT
An unpaired nucleotide to the right of an NMbr structure.
fUnpairedRight :: BaseF (NMbr -> Features (Vector (PairIdx, Double)))Source
Energy for having the rightmost nucleotide (at j) unpaired in NMBr.
btUnpairedRight :: Params -> Primary -> NMbr -> NBT -> NBTSource
Backtrack in NMbr if the nucleotide at j is unpaired.
An unpaired nucleotide to the right of an NMbr1 structure.
fUnpairedRight1 :: BaseF (NMbr1 -> Features (Vector (PairIdx, Double)))Source
Energy for having the rightmost nucleotide (at j) unpaired in NMBr1.
btUnpairedRight1 :: Params -> Primary -> NMbr1 -> NBT -> NBTSource
Backtrack NMbr1 if the nucleotide at j is unpaired.
EStem to Helix start
fMlHelix :: BaseF (EStem -> Features (Vector (ExtPairIdx, Double)))Source
A multibranched helix (except the closing one). (i,j) are closed by a basepair. Backtracking into the EStem reveals the type of pairing.
btMlHelix :: Params -> Primary -> NMult -> EStem -> ExtBT -> NBTSource
Backtracks from (i,j) in NMult into the extended-pairing EStem.
Closes a multibranched loop and produces an extended structure at
fMlClose :: BaseF (NMultLoop -> ExtFeatures (Vector (PairIdx, Double)))Source
Closes a multibranch loop.
TODO make completely triplet compliant
btMlClose :: Params -> Primary -> EStem -> NMultLoop -> NBT -> ExtBTSource
Backtrack from and extended annotation (ij,ext) into the helper table NMultLoop.
Multibranched loop helper table
fMlLoop :: BaseF (NMbr -> NMbr1 -> Features (Vector (Int, Double)))Source
Multibranched loop helper function that combines at least one stem with exactly one stem but does not add the closing energy from (i,j).
btMlLoop :: Params -> Primary -> NMultLoop -> NMbr -> NMbr1 -> NBT -> NBT -> NBTSource
Backtracking the multibranched loop.
Backtracking of a multibranched stem with unpaired nucleotides to the
fMlStem :: BaseF (NMult -> Features (Vector (Int, Double)))Source
Backtrack a single stem in NMbr, where the stem has zero or more unpaired nucleotides to the left.
btMlStem :: Params -> Primary -> NMbr -> NMult -> NBT -> NBTSource
Backtrack by trying to find a multilooped helix.
Backtracking of at least two stems by finding one or more stems to the
fMlStems :: BaseF (NMbr -> NMult -> Features (Vector (Int, Double)))Source
Add a stem to a multibranch table containing already at least one stem.
btMlStems :: Params -> Primary -> NMbr -> NMult -> NBT -> NBT -> NBTSource
Backtrack by finding the splitting index between an NMbr composite structure and a single multibranched stem NMult (which can contain unpaired nucleotides to the left).