Probabilities

This module implements Probabilities, an immutable view into a Compound's probability matrix. It holds a reference to its parent Compound to make sure it does not outlive it. The module provides accessors and iterators, so the Probability object handles just as an array would.

Example usage

We have an RNA sequence and want to know the probabilities of base pairing for some base pairs.

import strformat
import nimna

var
  c: Compound = ... # The RNA sequence in question.
  prob = c.probabilities

for idx in 0 ..< c.len div 2:
  let
    onStemProbability = prob[idx, c.len - idx]
  echo fmt"Probability for base pair on diagonal: {onStemProbability}"

Imports

RNA, nimna_types, nimna_cutils, nimna_compound, nimna_fold

Procs

proc `[]`(p: Probabilities; i, j: int): float {. raises: [IndexError], tags: [] .}: Bracket accessor for a set of Probabilities.
proc probabilities(c: Compound): Probabilities {. raises: [Exception, FieldError], tags: [] .}: Returns a Probabilities object for monitoring the base pair probabilities inside the Compound. If no probabilities exist, they will be computed.
proc prob(c: Compound; i, j: int): float {. raises: [IndexError, Exception, FieldError], tags: [] .}: Returns the probability of base-pairing at positions i and j in a Compound.

Iterators

iterator items(p: Probabilities): float {. raises: [IndexError], tags: [] .}: Iterates over all entries in the probability matrix.
iterator pairs(p: Probabilities): tuple[pos: tuple[i, j: int], val: float] {. raises: [IndexError], tags: [] .}: Iterates over all pairs of indices (i, j) and their corresponding base pairing probabilities val.
iterator triples(p: Probabilities): tuple[i, j: int, val: float] {. raises: [IndexError], tags: [] .}: Iterates over all triples of indices i, j and their corresponding base pairing probabilities val.
iterator positions(p: Probabilities): seq[float] {. raises: [IndexError], tags: [] .}: Iterates over all positions in the sequence corresponding to the Probabilities, returning a seq of their base pairing probabilities.

Templates

template len(p: Probabilities): int