Types
This module provides the basic garbage-collected wrapper types used in nimna. It contains the following important type definitions:
- Compound (Compound)
- The core type of the nimna API. It represents a fully parameterized nucleic acid sequence, to be folded and analysed using the procedures in nimna. Internally, it stores a pointer to a vrna_fold_compound_t object of the ViennaRNA API, as well as a set of flags, to track the object's status to only perform necessary recomputations and return precomupted results otherwise.
- Compound2D (Compound)
- Same as Compound, but used for two-dimensional folding, i.e. folding with respect to two reference sequences.
- CompoundComparative (Compound)
- Same as Compound, but used for comparative folding of multiple sequences, i.e. of a multiple sequence Alignment.
- Alignment (Alignment)
- Represents a multiple sequence alignment, storing a list of sequences and their identifying names, together with a consensus secondary structure.
- Suboptimals (Suboptimals)
- Represents a list of suboptimal folds of a sequence.
- InteractionList (InteractionList)
- Represents a list of base interactions, those being base pairings, or G-quadruplexes.
- Settings (Settings)
- Represents a set of settings to be used for folding. For the set of available parameters, see the ViennaRNA documentation.
- Probabilities (Probabilities)
- The a view into the base pair probability matrix of a Compound, generated using partition function folding. As long as it is alive, its parent Compound may not be garbage collected. This is useful for assessing the probability of certain base-pairs existing, for example for fitness functions for nucleic acid design.
Types
Compound = ref object of RootObj vfc*: ptr VrnaFoldCompoundT ## \ ## A pointer to the underlying memory. hasPf*: bool ## \ ## Flag indicating whether the ``Compound`` has undergone \ ## partition function folding. isD*: bool ## \ ## Flag indicating whether the ``Compound`` is a dimer.
- Represents a sequence of DNA or RNA together with folding parameters and results.
Compound2D = ref object of Compound
- Represents a sequence of DNA or RNA together with folding parameters folding results, and a pair of reference structures.
CompoundComparative = ref object of Compound
- Represents a sequence alignment of DNAs or RNAs with folding parameters and results.
Alignment = ref object algn*: cstringArray cnames*: cstringArray id*: cstring structure*: cstring nSeqs*: int
- Represents a multiple sequence alignment.
DimerEnergies = VrnaDimerPfS
Fold = VrnaSuboptSolutionT
Suboptimals = ref object len*: int ## \ ## The size of the set of suboptimal solutions. so*: ptr Fold ## \ ## The underlying memory.
- Represents a set of suboptimal solutions to a sequence folding problem.
MfeSolution = VrnaSolTwoDt
- Represents a secondary structure and energy at a single position in secondary structure space.
PfSolution = VrnaSolTwoD_pfT
- Represents a partition function at a single position in secondary structure space.
MfeSolutions = ref object mfe*: ptr MfeSolution
- A set of solutions to the minimum free energy folding problem.
PfSolutions = ref object pf*: ptr PfSolution
- A set of solutions to the partition function folding problem.
InteractionList = ref object of RootObj pl*: ptr VrnaPlistT len*: int nitems*: int
- Represents a list of base interactions.
PairList = ref object of InteractionList
- Represents a list of base pairing interactions
GQuadList = ref object of InteractionList
- Represents a list of G-quadruplex interactions.
PairListItem = VrnaPlistT
Settings = VrnaMdT
- Represents a set of conditions for folding, such as for example temperature.
Parameters = VrnaParamT
- Represents a set of folding parameters, computed from Settings.
ScaledParameters = VrnaExpParamT
- Represents a set of partition function folding parameters, computed from Settings.
ConstraintOption = distinct cuint
- Represents the way a constraint on folding is stored and interpreted.
UnstructuredOption = distinct cuint
- Represents the kinds of motifs a ligand can bind to.
Probabilities = ref object parent*: Compound bppm*: ptr Flt_Or_Dbl
- Represents the base pair probability matrix of a Compound
MotifError = object of Exception
Consts
vcNoHeader = 0
vcDb = 16384
vcdbEnforceBp = 32768
vcdbPipe = 65536
vcdbDot = 131072
vcdbX = 262144
vcdbAngBrack = 524288
vcdbRndBrack = 1048576
vcdbIntramol = 2097152
vcdbIntermol = 4194304
vcdbGquad = 8388608
vcdbDefault = 16728064
vccExtLoop = 1
vccHpLoop = 2
vccIntLoop = 4
vccIntLoopEnc = 8
vccMbLoop = 16
vccMbLoopEnc = 32
vccEnforce = 64
vccNoRemove = 128
vccAllLoops = 63
vcmDefault = 0
vudExtLoop = 1
vudHpLoop = 2
vudIntLoop = 4
vudMbLoop = 8
vudMotif = 16
vudAllLoops = 15