Incorporate RNAplex model with seed heuristic

[martin-raden]

• include RNAplex model
• enable seed heuristic
• enable nested + pseudoknot accessibilities

[martin-raden]

accessibility computation models to be tested

• RNAplex
• Accessfold
• NUPACK-based

[martin-raden]

concerning NUPACK

NUPACK enables the computation of (position-wise) unpaired probabilities. These could be incorporated in a AccessFold-like approach to incorporate pseudoknotted intramolecular structure into the interaction prediction.

Two options:

• read Pu values from NUPACK ppairs output file
• use NUPACK library for direct computation (check if possible)