Partition function implementations for base pair distance classes. More...

Include dependency graph for 2Dpfold.h:

Data Structures
struct	vrna_sol_TwoD_pf_t
	Solution element returned from vrna_pf_TwoD() More...

struct	TwoDpfold_vars
	Variables compound for 2Dfold partition function folding. More...

Typedefs
typedef struct vrna_sol_TwoD_pf_t	vrna_sol_TwoD_pf_t
	Solution element returned from vrna_pf_TwoD() More...

Functions
vrna_sol_TwoD_pf_t *	vrna_pf_TwoD (vrna_fold_compound_t *vc, int maxDistance1, int maxDistance2)
	Compute the partition function for all distance classes. More...

char *	vrna_pbacktrack_TwoD (vrna_fold_compound_t *vc, int d1, int d2)
	Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. More...

char *	vrna_pbacktrack5_TwoD (vrna_fold_compound_t *vc, 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. More...

TwoDpfold_vars *	get_TwoDpfold_variables (const char seq, const char structure1, char *structure2, int circ)
	Get a datastructure containing all necessary attributes and global folding switches. More...

void	destroy_TwoDpfold_variables (TwoDpfold_vars *vars)
	Free all memory occupied by a TwoDpfold_vars datastructure. More...

vrna_sol_TwoD_pf_t *	TwoDpfoldList (TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)
	Compute the partition function for all distance classes. More...

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. More...

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. More...

Detailed Description

Partition function implementations for base pair distance classes.

Function Documentation

TwoDpfold_vars* get_TwoDpfold_variables	(	const char *	seq,
		const char *	structure1,
		char *	structure2,
		int	circ
	)

Get a datastructure containing all necessary attributes and global folding switches.

This function prepares all necessary attributes and matrices etc which are needed for a call of TwoDpfold() . A snapshot of all current global model switches (dangles, temperature and so on) is done and stored in the returned datastructure. Additionally, all matrices that will hold the partition function values are prepared.

Deprecated:: Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), and vrna_fold_compound_free() instead!

Parameters

seq	the RNA sequence in uppercase format with letters from the alphabet {AUCG}
structure1	the first reference structure in dot-bracket notation
structure2	the second reference structure in dot-bracket notation
circ	a switch indicating if the sequence is linear (0) or circular (1)

Returns: the datastructure containing all necessary partition function attributes

void destroy_TwoDpfold_variables ( TwoDpfold_vars * vars )

Free all memory occupied by a TwoDpfold_vars datastructure.

This function free's all memory occupied by a datastructure obtained from from get_TwoDpfold_variabless() or get_TwoDpfold_variables_from_MFE()

Deprecated:: Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), and vrna_fold_compound_free() instead!

See also: get_TwoDpfold_variables(), get_TwoDpfold_variables_from_MFE()

Parameters

vars	the datastructure to be free'd

vrna_sol_TwoD_pf_t* TwoDpfoldList	(	TwoDpfold_vars *	vars,
		int	maxDistance1,
		int	maxDistance2
	)

Compute the partition function for all distance classes.

This function computes the partition functions for all distance classes according the two reference structures specified in the datastructure 'vars'. Similar to TwoDfold() the arguments maxDistance1 and maxDistance2 specify the maximum distance to both reference structures. A value of '-1' in either of them makes the appropriate distance restrictionless, i.e. all basepair distancies to the reference are taken into account during computation. In case there is a restriction, the returned solution contains an entry where the attribute k=l=-1 contains the partition function for all structures exceeding the restriction. A values of INF in the attribute 'k' of the returned list denotes the end of the list

Deprecated:: Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), and vrna_fold_compound_free() instead!

See also: get_TwoDpfold_variables(), destroy_TwoDpfold_variables(), vrna_sol_TwoD_pf_t

Parameters

vars	the datastructure containing all necessary folding attributes and matrices
maxDistance1	the maximum basepair distance to reference1 (may be -1)
maxDistance2	the maximum basepair distance to reference2 (may be -1)

Returns: a list of partition funtions for the appropriate distance classes

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 TwoDpfold() preceding this function is mandatory!

Deprecated:: Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), vrna_pbacktrack_TwoD(), and vrna_fold_compound_free() instead!

See also: TwoDpfold()

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 TwoDpfold() preceding this function is mandatory!

Deprecated:: Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), vrna_pbacktrack5_TwoD(), and vrna_fold_compound_free() instead!

See also: TwoDpfold_pbacktrack(), TwoDpfold()

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

Data Structures

Typedefs

Functions

Detailed Description

Function Documentation