Modules§
Structs§
- FIVE_
PRIME_ DE_ DELTA_ FES - Fasta
Record - HL_
TM_ DELTA_ FES - HashMap
- A hash map implemented with quadratic probing and SIMD lookup.
- IL_
TM_ DELTA_ FES - INIT_
HL_ DELTA_ FES - LogProb
MatPair OnSta - LogSs
PpfMats - LogSta
PpfMat Sets - LogSta
PpfMats - ML_
TM_ DELTA_ FES - MeaSs
- ONE_
VS_ MANY_ IL_ TM_ DELTA_ FES - Options
- A description of the options that a program can handle.
- Prob
MatPair OnSta - RIBOSUM_
85_ 60_ BA_ SCORE_ MAT - RIBOSUM_
85_ 60_ BPA_ SCORE_ MAT - SPECIAL_
HL_ DELTA_ FES - STACK_
DELTA_ FES - SaScoring
Params - StaFe
Params - Stem
Params - THREE_
PRIME_ DE_ DELTA_ FES - TWO_
VS_ 3_ IL_ TM_ DELTA_ FES
Constants§
- A
- AA
- AC
- AG
- AU
- BASE_
PAIRING_ LEFT_ BASE - BASE_
PAIRING_ RIGHT_ BASE - C
- CA
- CC
- CG
- COEFFICIENT_
4_ ALL_ C_ HL_ DELTA_ FE - COEFFICIENT_
4_ LOG_ EXTRAPOLATION_ OF_ INIT_ HL_ DELTA_ FE - COEFFICIENT_
4_ NINIO - COEFFICIENT_
4_ TERM_ OF_ NUM_ OF_ BRANCHING_ HELICES_ ON_ INIT_ ML_ DELTA_ FE - CONST_
4_ ALL_ C_ HL_ DELTA_ FE - CONST_
4_ INIT_ ML_ DELTA_ FE - CU
- G
- GA
- GAS_
CONST - GC
- GG
- GU
- HELIX_
AU_ OR_ GU_ END_ PENALTY_ DELTA_ FE - HELIX_
INTERMOLECULAR_ INIT_ DELTA_ FE - HELIX_
SYMMETRY_ PENALTY_ DELTA_ FE - HL_
GG_ FIRST_ MISMATCH_ BONUS_ DELTA_ FE - HL_
OF_ 3_ CS_ PENALTY_ DELTA_ FE - HL_
SPECIAL_ GU_ CLOSURE_ BONUS_ DELTA_ FE - HL_
UU_ OR_ GA_ FIRST_ MISMATCH_ BONUS_ DELTA_ FE - INFINITY
Deprecation planned - Infinity (∞).
Use
f64::INFINITYinstead. - INVERSE_
TEMPERATURE - K0
- KILO
- MAX_
2_ LOOP_ LEN - MAX_
LOOP_ LEN_ 4_ LOG_ EXTRAPOLATION_ OF_ INIT_ LOOP_ DELTA_ FE - MAX_
NINIO - MAX_
SPAN_ OF_ INDEX_ PAIR_ CLOSING_ IL - MIN_
HL_ LEN - MIN_
LOOP_ LEN_ 4_ LOG_ EXTRAPOLATION_ OF_ INIT_ HL_ DELTA_ FE - MIN_
SPAN_ OF_ INDEX_ PAIR_ CLOSING_ HL - MIN_
SPAN_ OF_ INDEX_ PAIR_ CLOSING_ ML - NEG_
INFINITY Deprecation planned - Negative infinity (−∞).
Use
f64::NEG_INFINITYinstead. - PSEUDO_
BASE - SEQ_
ALPHABET - TEMPERATURE
- U
- UA
- UC
- UG
- UNPAIRING_
BASE - UU
Functions§
- from_
utf8_ ⚠unchecked - Converts a slice of bytes to a string slice without checking that the string contains valid UTF-8.
- get_
2_ loop_ fe - get_
bpp_ mat - get_
bpp_ mat_ and_ nbpps - get_
hl_ fe - get_
log_ bpp_ mat - get_
log_ ss_ ppf_ mats - get_
log_ sta_ ppf_ 4d_ mats - get_
prob_ mat_ pairs_ on_ sta_ with_ rna_ id_ pairs - get_
seq_ len_ diff - invert_
bp - io_
algo_ 4_ log_ prob_ mat_ pair_ on_ rna_ sta - io_
algo_ 4_ prob_ mat_ pair_ on_ rna_ sta - is_
au_ or_ gu - is_
canonical - is_
rna_ base - logsumexp
- max
- Compares and returns the maximum of two values.
- mccaskill_
algo - min
- Compares and returns the minimum of two values.
- neofold
- pct_
of_ bpp_ and_ upp_ mat - print_
program_ usage - prob_
cons_ transformation_ of_ log_ prob_ mat_ pair_ on_ sta - remove_
small_ bpps_ from_ bpp_ mat - remove_
zeros_ from_ bpp_ mat
Type Aliases§
- Args
- BaScore
Mat - Base
- Base
Pair - Base
Quadruple - BpaScore
Mat - CaScore
Mat - Char
- Char
Pair - DeDelta
Fes - Energy
- EpsOf
Terms4 LogPf - EpsOf
Terms4 LogProb - ExpPart
OfTerm4 LogPf - ExpPart
OfTerm4 LogProb - FastaId
- Fasta
Records - Free
Energy - Hasher
- HlTm
Delta Fes - IlTm
Delta Fes - Init
HlDelta Fes - LogPartial
Pfs - LogPf
- LogPpf
Mat - LogProb
- LogProb3d
Mat - LogProb4d
Mat - LogProb
Mat - LogProb
MatPairs OnSta With RnaId Pairs - LogProb
Mats - LogProb
Seqs - LogProbs
- Mea
- MeaMat
- MeaSs
Char - MeaSs
Str - Meas
- MlTm
Delta Fes - Num
- Partition
Func - Pos
- PosPair
- PosPair
Seqs With PosPairs - PosPairs
- PosQuadruple
- PosSeqs
With Poss - PosTriple
- Poss
- Prob
- Prob1d
Mat - Prob3d
Mat - Prob4d
Mat - ProbMat
- Prob
Mats - Prob
SeqPair - Probs
- RnaId
- RnaId
Pair - SaScore
- Seq
- SeqPair
- SeqSlice
- Slice
OfEps OfTerms4 LogPf - Slice
OfEps OfTerms4 LogProb - Sparse
LogProb Mat - Sparse
Prob Mat - Special
HlDelta Fes - SsPair
- StaFe
Param Sets With RnaId Pairs - StaFree
Energy - Stack
Delta Fes