Stochastic Backtracking of Structures from Distance Based Partitioning
[Distance based partitioning of the Secondary Structure Space, Stochastic backtracking in the Ensemble]

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

Collaboration diagram for Stochastic Backtracking of Structures from Distance Based Partitioning:

Functions
char *	TwoDpfold_pbacktrack (TwoDpfold_vars *vars, int d1, int d2)
	Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability.
char *	TwoDpfold_pbacktrack5 (TwoDpfold_vars *vars, int d1, int d2, unsigned int length)
	Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability.

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Detailed Description

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

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Function Documentation

char* TwoDpfold_pbacktrack	(	TwoDpfold_vars *	vars,
		int	d1,
		int	d2
	)

Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability.

If the argument 'd1' is set to '-1', the structure will be backtracked in the distance class where all structures exceeding the maximum basepair distance to either of the references reside.

Precondition:

The argument 'vars' must contain precalculated partition function matrices, i.e. a call to TwoDpfoldList() preceding this function is mandatory!

See also:

TwoDpfoldList()

Parameters:

[in]	vars	the datastructure containing all necessary folding attributes and matrices
[in]	d1	the distance to reference1 (may be -1)
[in]	d2	the distance to reference2

Returns:

A sampled secondary structure in dot-bracket notation

char* TwoDpfold_pbacktrack5	(	TwoDpfold_vars *	vars,
		int	d1,
		int	d2,
		unsigned int	length
	)

Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability.

This function does essentially the same as TwoDpfold_pbacktrack with the only difference that partial structures, i.e. structures beginning from the 5' end with a specified length of the sequence, are backtracked

Note:

This function does not work (since it makes no sense) for circular RNA sequences!

Precondition:

The argument 'vars' must contain precalculated partition function matrices, i.e. a call to TwoDpfoldList() preceding this function is mandatory!

See also:

TwoDpfold_pbacktrack(), TwoDpfoldList()

Parameters:

[in]	vars	the datastructure containing all necessary folding attributes and matrices
[in]	d1	the distance to reference1 (may be -1)
[in]	d2	the distance to reference2
[in]	length	the length of the structure beginning from the 5' end

Returns:

A sampled secondary structure in dot-bracket notation