# Distance based partitioning of the Secondary Structure Space
[Classified Dynamic Programming]

Compute Thermodynamic properties for a Distance Class Partitioning of the Secondary Structure Space. More...

Collaboration diagram for Distance based partitioning of the Secondary Structure Space:

## Modules
| Calculating MFE representatives of a Distance Based Partitioning

| Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures.
| Calculate Partition Functions of a Distance Based Partitioning

| Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures.
| Stochastic Backtracking of Structures from Distance Based Partitioning

| Contains functions related to stochastic backtracking from a specified distance class.

## Detailed Description

Compute Thermodynamic properties for a Distance Class Partitioning of the Secondary Structure Space.

All functions related to this group implement the basic recursions for MFE folding, partition function computation and stochastic backtracking with a classified dynamic programming approach. The secondary structure space is divided into partitions according to the base pair distance to two given reference structures and all relevant properties are calculated for each of the resulting partitions

See also:
  For further details have a look into lorenz:2009