Detailed Description

Collaboration diagram for Distance Based Partitioning of the Secondary Structure Space:

Modules
	Computing 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.

	Computing 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.

Files
file	2Dfold.h
	MFE structures for base pair distance classes.

file	2Dpfold.h
	Partition function implementations for base pair distance classes.

Modules