Motif

This module implements structured and unstructured sequence-motif based constraints. It works just like soft constraints, by assigning a free energy to a sequence motif.

Example usage

Let's say we have an RNA sequence containing an aptamer with known fold and free energy of binding. We want to add that aptamer as a motif constraint.

The aptamer structure and sequence:

structure ASCII art:

  5'  3'
  C---G
  G---C
 A    U C G G 5'
A    /  | | |
 A  A   G C C 3'

sequence:
         v
CGAAAAGCC&GGCUCG
        ---
structure:
         v
((...((((&))))))
        ---
          \_ `&` indicates a sequence split.

import nimna

# The aptamer's binding free energy.
const energy = -2.37 # kcal / mol

var
  c: Compound = ... # The Compound.

# Set the constraint:
c.preferMotif("CGAAAAGCC&GGCUCG",
              "((...((((&))))))",
              energy)