Functions and data structures for secondary structure soft constraints. More...

Detailed Description

Functions and data structures for secondary structure soft constraints.

Soft-constraints are used to change position specific contributions in the recursions by adding bonuses/penalties in form of pseudo free energies to certain loop configurations.

Collaboration diagram for Soft Constraints:

Files
file	soft.h
	Functions and data structures for secondary structure soft constraints.

Data Structures
struct	vrna_sc_s
	The soft constraints data structure. More...

Typedefs
typedef struct vrna_sc_s	vrna_sc_t
	Typename for the soft constraints data structure vrna_sc_s.

typedef int(	vrna_callback_sc_energy) (int i, int j, int k, int l, unsigned char d, void *data)
	Callback to retrieve pseudo energy contribution for soft constraint feature. More...

typedef FLT_OR_DBL(	vrna_callback_sc_exp_energy) (int i, int j, int k, int l, unsigned char d, void *data)
	Callback to retrieve pseudo energy contribution as Boltzmann Factors for soft constraint feature. More...

typedef vrna_basepair_t *(	vrna_callback_sc_backtrack) (int i, int j, int k, int l, unsigned char d, void *data)
	Callback to retrieve auxiliary base pairs for soft constraint feature. More...

Functions
void	vrna_sc_init (vrna_fold_compound_t *vc)
	Initialize an empty soft constraints data structure within a vrna_fold_compound_t. More...

void	vrna_sc_set_bp (vrna_fold_compound_t vc, const FLT_OR_DBL *constraints, unsigned int options)
	Set soft constraints for paired nucleotides. More...

void	vrna_sc_add_bp (vrna_fold_compound_t *vc, int i, int j, FLT_OR_DBL energy, unsigned int options)
	Add soft constraints for paired nucleotides. More...

void	vrna_sc_set_up (vrna_fold_compound_t vc, const FLT_OR_DBL constraints, unsigned int options)
	Set soft constraints for unpaired nucleotides. More...

void	vrna_sc_add_up (vrna_fold_compound_t *vc, int i, FLT_OR_DBL energy, unsigned int options)
	Add soft constraints for unpaired nucleotides. More...

void	vrna_sc_remove (vrna_fold_compound_t *vc)
	Remove soft constraints from vrna_fold_compound_t. More...

void	vrna_sc_free (vrna_sc_t *sc)
	Free memory occupied by a vrna_sc_t data structure. More...

void	vrna_sc_add_data (vrna_fold_compound_t vc, void data, vrna_callback_free_auxdata *free_data)
	Add an auxiliary data structure for the generic soft constraints callback function. More...

void	vrna_sc_add_f (vrna_fold_compound_t vc, vrna_callback_sc_energy f)
	Bind a function pointer for generic soft constraint feature (MFE version) More...

void	vrna_sc_add_bt (vrna_fold_compound_t vc, vrna_callback_sc_backtrack f)
	Bind a backtracking function pointer for generic soft constraint feature. More...

void	vrna_sc_add_exp_f (vrna_fold_compound_t vc, vrna_callback_sc_exp_energy exp_f)
	Bind a function pointer for generic soft constraint feature (PF version) More...

Data Structure Documentation

struct vrna_sc_s

The soft constraints data structure.

Collaboration diagram for vrna_sc_s:

Data Fields
int **	energy_up
	Energy contribution for stretches of unpaired nucleotides.

FLT_OR_DBL **	exp_energy_up
	Boltzmann Factors of the energy contributions for unpaired sequence stretches.

int *	up_storage
	Storage container for energy contributions per unpaired nucleotide.

vrna_sc_bp_storage_t **	bp_storage
	Storage container for energy contributions per base pair.

int *	energy_stack
	Pseudo Energy contribution per base pair involved in a stack.

FLT_OR_DBL *	exp_energy_stack
	Boltzmann weighted pseudo energy contribution per nucleotide involved in a stack.

vrna_callback_sc_energy *	f
	A function pointer used for pseudo energy contribution in MFE calculations. More...

vrna_callback_sc_backtrack *	bt
	A function pointer used to obtain backtraced base pairs in loop regions that were altered by soft constrained pseudo energy contributions. More...

vrna_callback_sc_exp_energy *	exp_f
	A function pointer used for pseudo energy contribution boltzmann factors in PF calculations. More...

void *	data
	A pointer to the data object provided for for pseudo energy contribution functions of the generic soft constraints feature.

int *	energy_bp
	Energy contribution for base pairs.

FLT_OR_DBL *	exp_energy_bp
	Boltzmann Factors of the energy contribution for base pairs.

int **	energy_bp_local
	Energy contribution for base pairs (sliding window approach)

FLT_OR_DBL **	exp_energy_bp_local
	Boltzmann Factors of the energy contribution for base pairs (sliding window approach)

Field Documentation

vrna_callback_sc_energy* vrna_sc_s::f

A function pointer used for pseudo energy contribution in MFE calculations.

See also: vrna_sc_add_f()

vrna_callback_sc_backtrack* vrna_sc_s::bt

A function pointer used to obtain backtraced base pairs in loop regions that were altered by soft constrained pseudo energy contributions.

See also: vrna_sc_add_bt()

vrna_callback_sc_exp_energy* vrna_sc_s::exp_f

A function pointer used for pseudo energy contribution boltzmann factors in PF calculations.

See also: vrna_sc_add_exp_f()

Typedef Documentation

typedef int( vrna_callback_sc_energy) (int i, int j, int k, int l, unsigned char d, void *data)

#include <ViennaRNA/constraints/soft.h>

Callback to retrieve pseudo energy contribution for soft constraint feature.

This is the prototype for callback functions used by the folding recursions to evaluate generic soft constraints. The first four parameters passed indicate the delimiting nucleotide positions of the decomposition, and the parameter denotes the decomposition step. The last parameter data is the auxiliary data structure associated to the hard constraints via vrna_sc_add_data(), or NULL if no auxiliary data was added.

Notes on Callback Functions:: This callback enables one to add (pseudo-)energy contributions to individual decompositions of the secondary structure.

Parameters

i	Left (5') delimiter position of substructure
j	Right (3') delimiter position of substructure
k	Left delimiter of decomposition
l	Right delimiter of decomposition
d	Decomposition step indicator
data	Auxiliary data

Returns: Pseudo energy contribution in deka-kalories per mol

typedef FLT_OR_DBL( vrna_callback_sc_exp_energy) (int i, int j, int k, int l, unsigned char d, void *data)

#include <ViennaRNA/constraints/soft.h>

Callback to retrieve pseudo energy contribution as Boltzmann Factors for soft constraint feature.

This is the prototype for callback functions used by the partition function recursions to evaluate generic soft constraints. The first four parameters passed indicate the delimiting nucleotide positions of the decomposition, and the parameter denotes the decomposition step. The last parameter data is the auxiliary data structure associated to the hard constraints via vrna_sc_add_data(), or NULL if no auxiliary data was added.

Notes on Callback Functions:: This callback enables one to add (pseudo-)energy contributions to individual decompositions of the secondary structure (Partition function variant, i.e. contributions must be returned as Boltzmann factors).

Parameters

i	Left (5') delimiter position of substructure
j	Right (3') delimiter position of substructure
k	Left delimiter of decomposition
l	Right delimiter of decomposition
d	Decomposition step indicator
data	Auxiliary data

Returns: Pseudo energy contribution in deka-kalories per mol

typedef vrna_basepair_t*( vrna_callback_sc_backtrack) (int i, int j, int k, int l, unsigned char d, void *data)

#include <ViennaRNA/constraints/soft.h>

Callback to retrieve auxiliary base pairs for soft constraint feature.

Notes on Callback Functions:: This callback enables one to add auxiliary base pairs in the backtracking steps of hairpin- and interior loops.

Parameters

i	Left (5') delimiter position of substructure
j	Right (3') delimiter position of substructure
k	Left delimiter of decomposition
l	Right delimiter of decomposition
d	Decomposition step indicator
data	Auxiliary data

Returns: List of additional base pairs

Function Documentation

void vrna_sc_init ( vrna_fold_compound_t * vc )

#include <ViennaRNA/constraints/soft.h>

Initialize an empty soft constraints data structure within a vrna_fold_compound_t.

This function adds a proper soft constraints data structure to the vrna_fold_compound_t data structure. If soft constraints already exist within the fold compound, they are removed.

Note: Accepts vrna_fold_compound_t of type VRNA_FC_TYPE_SINGLE and VRNA_FC_TYPE_COMPARATIVE

See also: vrna_sc_set_bp(), vrna_sc_set_up(), vrna_sc_add_SHAPE_deigan(), vrna_sc_add_SHAPE_zarringhalam(), vrna_sc_remove(), vrna_sc_add_f(), vrna_sc_add_exp_f(), vrna_sc_add_pre(), vrna_sc_add_post()

Parameters

vc	The vrna_fold_compound_t where an empty soft constraint feature is to be added to

SWIG Wrapper Notes:: This function is attached as method sc_init() to objects of type fold_compound

void vrna_sc_set_bp	(	vrna_fold_compound_t *	vc,
		const FLT_OR_DBL **	constraints,
		unsigned int	options
	)

#include <ViennaRNA/constraints/soft.h>

Set soft constraints for paired nucleotides.

Note: This function replaces any pre-exisitng soft constraints with the ones supplied in constraints.

See also: vrna_sc_add_bp(), vrna_sc_set_up(), vrna_sc_add_up()

Parameters

vc	The vrna_fold_compound_t the soft constraints are associated with
constraints	A two-dimensional array of pseudo free energies in
options	The options flag indicating how/where to store the soft constraints

SWIG Wrapper Notes:: This function is attached as method sc_set_bp() to objects of type fold_compound

void vrna_sc_add_bp	(	vrna_fold_compound_t *	vc,
		int	i,
		int	j,
		FLT_OR_DBL	energy,
		unsigned int	options
	)

#include <ViennaRNA/constraints/soft.h>

Add soft constraints for paired nucleotides.

See also: vrna_sc_set_bp(), vrna_sc_set_up(), vrna_sc_add_up()

Parameters

vc	The vrna_fold_compound_t the soft constraints are associated with
i	The 5' position of the base pair the soft constraint is added for
j	The 3' position of the base pair the soft constraint is added for
energy	The free energy (soft-constraint) in
options	The options flag indicating how/where to store the soft constraints

SWIG Wrapper Notes:

This function is attached as an overloaded method sc_add_bp() to objects of type fold_compound. The method either takes arguments for a single base pair (i,j) with the corresponding energy value:

1 fold_compound.sc_add_bp(i, j, energy, options)

or an entire 2-dimensional matrix with dimensions n x n that stores free energy contributions for any base pair (i,j) with $1 \leq i < j \leq n$ :

1 fold_compound.sc_add_bp(matrix, options)

In both variants, the options argument is optional can may be omitted.

void vrna_sc_set_up	(	vrna_fold_compound_t *	vc,
		const FLT_OR_DBL *	constraints,
		unsigned int	options
	)

#include <ViennaRNA/constraints/soft.h>

Set soft constraints for unpaired nucleotides.

Note: This function replaces any pre-exisitng soft constraints with the ones supplied in constraints.

See also: vrna_sc_add_up(), vrna_sc_set_bp(), vrna_sc_add_bp()

Parameters

vc	The vrna_fold_compound_t the soft constraints are associated with
constraints	A vector of pseudo free energies in
options	The options flag indicating how/where to store the soft constraints

SWIG Wrapper Notes:: This function is attached as method sc_set_up() to objects of type fold_compound

void vrna_sc_add_up	(	vrna_fold_compound_t *	vc,
		int	i,
		FLT_OR_DBL	energy,
		unsigned int	options
	)

#include <ViennaRNA/constraints/soft.h>

Add soft constraints for unpaired nucleotides.

See also: vrna_sc_set_up(), vrna_sc_add_bp(), vrna_sc_set_bp()

Parameters

vc	The vrna_fold_compound_t the soft constraints are associated with
i	The nucleotide position the soft constraint is added for
energy	The free energy (soft-constraint) in
options	The options flag indicating how/where to store the soft constraints

SWIG Wrapper Notes:: This function is attached as an overloaded method sc_add_up() to objects of type fold_compound. The method either takes arguments for a single nucleotide with the corresponding energy value:
1 fold_compound.sc_add_up(i, energy, options)
or an entire vector that stores free energy contributions for each nucleotide with $1 \leq i \leq n$ :
1 fold_compound.sc_add_bp(vector, options)
In both variants, the options argument is optional can may be omitted.

void vrna_sc_remove ( vrna_fold_compound_t * vc )

#include <ViennaRNA/constraints/soft.h>

Remove soft constraints from vrna_fold_compound_t.

Note: Accepts vrna_fold_compound_t of type VRNA_FC_TYPE_SINGLE and VRNA_FC_TYPE_COMPARATIVE

Parameters

vc	The vrna_fold_compound_t possibly containing soft constraints

SWIG Wrapper Notes:: This function is attached as method sc_remove() to objects of type fold_compound

void vrna_sc_free ( vrna_sc_t * sc )

#include <ViennaRNA/constraints/soft.h>

Free memory occupied by a vrna_sc_t data structure.

Parameters

sc	The data structure to free from memory

void vrna_sc_add_data	(	vrna_fold_compound_t *	vc,
		void *	data,
		vrna_callback_free_auxdata *	free_data
	)

#include <ViennaRNA/constraints/soft.h>

Add an auxiliary data structure for the generic soft constraints callback function.

See also: vrna_sc_add_f(), vrna_sc_add_exp_f(), vrna_sc_add_bt()

Parameters

vc	The fold compound the generic soft constraint function should be bound to
data	A pointer to the data structure that holds required data for function 'f'
free_data	A pointer to a function that free's the memory occupied by `data` (Maybe NULL)

SWIG Wrapper Notes:: This function is attached as method sc_add_data() to objects of type fold_compound

void vrna_sc_add_f	(	vrna_fold_compound_t *	vc,
		vrna_callback_sc_energy *	f
	)

#include <ViennaRNA/constraints/soft.h>

Bind a function pointer for generic soft constraint feature (MFE version)

This function allows one to easily bind a function pointer and corresponding data structure to the soft constraint part vrna_sc_t of the vrna_fold_compound_t. The function for evaluating the generic soft constraint feature has to return a pseudo free energy $\hat{E}$ in $ dacal/mol $ , where $ 1 dacal/mol = 10 cal/mol $ .

See also: vrna_sc_add_data(), vrna_sc_add_bt(), vrna_sc_add_exp_f()

Parameters

vc	The fold compound the generic soft constraint function should be bound to
f	A pointer to the function that evaluates the generic soft constraint feature

SWIG Wrapper Notes:: This function is attached as method sc_add_f() to objects of type fold_compound

void vrna_sc_add_bt	(	vrna_fold_compound_t *	vc,
		vrna_callback_sc_backtrack *	f
	)

#include <ViennaRNA/constraints/soft.h>

Bind a backtracking function pointer for generic soft constraint feature.

This function allows one to easily bind a function pointer to the soft constraint part vrna_sc_t of the vrna_fold_compound_t. The provided function should be used for backtracking purposes in loop regions that were altered via the generic soft constraint feature. It has to return an array of vrna_basepair_t data structures, were the last element in the list is indicated by a value of -1 in it's i position.

See also: vrna_sc_add_data(), vrna_sc_add_f(), vrna_sc_add_exp_f()

Parameters

vc	The fold compound the generic soft constraint function should be bound to
f	A pointer to the function that returns additional base pairs

SWIG Wrapper Notes:: This function is attached as method sc_add_bt() to objects of type fold_compound

void vrna_sc_add_exp_f	(	vrna_fold_compound_t *	vc,
		vrna_callback_sc_exp_energy *	exp_f
	)

#include <ViennaRNA/constraints/soft.h>

Bind a function pointer for generic soft constraint feature (PF version)

This function allows one to easily bind a function pointer and corresponding data structure to the soft constraint part vrna_sc_t of the vrna_fold_compound_t. The function for evaluating the generic soft constraint feature has to return a pseudo free energy $\hat{E}$ as Boltzmann factor, i.e. $exp(- \hat{E} / kT)$ . The required unit for $ E $ is $ cal/mol $ .

See also: vrna_sc_add_bt(), vrna_sc_add_f(), vrna_sc_add_data()

Parameters

vc	The fold compound the generic soft constraint function should be bound to
exp_f	A pointer to the function that evaluates the generic soft constraint feature

SWIG Wrapper Notes:: This function is attached as method sc_add_exp_f() to objects of type fold_compound

Detailed Description

Files

Data Structures

Typedefs

Functions

Data Structure Documentation

Data Fields

Field Documentation

Typedef Documentation

Function Documentation