Enforcing 180 degrees turns in structures

[shanilpanara]

Summary

In order to explore unstable structures, we want to enforce 180 degree turns between two crossovers (i.e. 180, 540, 900... etc) whether or not this is the natural twist configuration.

We will therefore need a way to control this.

[shanilpanara]

achieved in https://github.com/shanilpanara/origamiUROP/pull/46/commits/6d453b84b110a68cdcbf55d0365624b6aeca4cc1 @debeshmandal

Summary

1. Find closest half turn for the number of nucleotides
   • i.e. 0.5, 1.5, 2.5
2. Calculate angle and convert to radians, e.g.:
   • 0.5 = 180° rotation spread between n-1 bonds
   • 1.5 = 540° rotation spread between n-1 bonds
   • 2.5 = 900° rotation spread between n-1 bonds

Variables

• n -> number of nucleotides
• bp_per_turn -> generally set to 10.45
• round_to_multiple -> a function which does what it says on the tin
• enforce_180 -> either True or False

---

Code added directly into generate_helix()

    if enforce_180 and not n == 1:
        half_turns = round_to_multiple(n/bp_per_turn, 0.5, 1)
        # minus one because for x nt there will only be x-1 bonds
        angle = np.radians(360*half_turns / (n-1) )
    else:
        angle = 0.626