version 0.1

Initial code for enumerative structure prediction and design in the ToyFold-1D model.

• Brute-force enumeration of bead-based model for RNA folding
• Simple script to display RNA conformations
• Scoring of conformations based on Toyfold model -- pair energy, freezing upon forming helix, penalty for bending RNA
• Exact calculation of partition function and base pair probabilities, including pseudoknots.
• Exact calculation of mutate-and-map-seq 'data'
• Enumerative design of sequences that fold into target structures
• This version formed the basis for Python implementation being developed by Hannah Wayment-Steele, https://github.com/HWaymentSteele/pyFold-1D.
• Does not yet have fluctuation energy, Conformation object, nearest-neighbor decomposition, ligand binding.