Missing functionality from ViennaRNA

[marcom]

Some of these items might already work, but should still get their own testset in the tests/ dir.

ViennaRNA-2.5.0 and before

• default temperature for DNA params is 37 °C (like for RNA), change to better default

Callback functions

• subopt
• pbacktrack
• neighbours
• more?

Windowed predictions

See also: #9

• pf_window
• pf_window_channel
• bpp_window (using vrna_probs_window)
• bpp_window_channel
• zscore

Soft and hard constraints

• soft constraints
• hard constraints

G-quadruplexes

Duplex predictions

• strand concentrations?

Multistrand predictions

• strand concentrations

RNA-DNA hybrids

• only duplexes?

Grammar callbacks

• callbacks at various stages of recursions

ViennaRNA-2.6.0

https://github.com/ViennaRNA/ViennaRNA/releases/tag/v2.6.0

• energies for modified bases (uses soft constraints callback), energy parameter modifications stored as json
• adjust energies to different salt concentrations (Na+)
• new soft constraints multi-callback dispatcher