Soft Constraints

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.

Typedefs

typedef struct vrna_sc_s vrna_sc_t: #include <ViennaRNA/constraints/soft.h>
Typename for the soft constraints data structure vrna_sc_s.

typedef int (*vrna_sc_f)(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.

Param i:: Left (5’) delimiter position of substructure
Param j:: Right (3’) delimiter position of substructure
Param k:: Left delimiter of decomposition
Param l:: Right delimiter of decomposition
Param d:: Decomposition step indicator
Param data:: Auxiliary data
Return:: Pseudo energy contribution in deka-kalories per mol

typedef FLT_OR_DBL (*vrna_sc_exp_f)(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).

Param i:: Left (5’) delimiter position of substructure
Param j:: Right (3’) delimiter position of substructure
Param k:: Left delimiter of decomposition
Param l:: Right delimiter of decomposition
Param d:: Decomposition step indicator
Param data:: Auxiliary data
Return:: Pseudo energy contribution in deka-kalories per mol

typedef vrna_basepair_t *(*vrna_sc_bt_f)(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.

Param i:: Left (5’) delimiter position of substructure
Param j:: Right (3’) delimiter position of substructure
Param k:: Left delimiter of decomposition
Param l:: Right delimiter of decomposition
Param d:: Decomposition step indicator
Param data:: Auxiliary data
Return:: List of additional base pairs

Functions

void vrna_sc_init(vrna_fold_compound_t *fc)

#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.

SWIG Wrapper Notes:: This function is attached as method sc_init() to objects of type fold_compound. See, e.g. RNA.fold_compound.sc_init() in the Python API .

Note

Accepts vrna_fold_compound_t of type VRNA_FC_TYPE_SINGLE and VRNA_FC_TYPE_COMPARATIVE

Parameters:

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

int vrna_sc_set_bp(vrna_fold_compound_t *fc, const FLT_OR_DBL **constraints, unsigned int options)

#include <ViennaRNA/constraints/soft.h>

Set soft constraints for paired nucleotides.

SWIG Wrapper Notes:: This function is attached as method sc_set_bp() to objects of type fold_compound. See, e.g. RNA.fold_compound.sc_set_bp() in the Python API .

Note

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

Parameters:

fc – The vrna_fold_compound_t the soft constraints are associated with
constraints – A two-dimensional array of pseudo free energies in \( kcal / mol \)
options – The options flag indicating how/where to store the soft constraints

Returns:

Non-zero on successful application of the constraint, 0 otherwise.

int vrna_sc_add_bp(vrna_fold_compound_t *fc, int i, int j, FLT_OR_DBL energy, unsigned int options)

#include <ViennaRNA/constraints/soft.h>

Add soft constraints for paired nucleotides.

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:

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 \( 1 \leq i < j \leq n \):

fold_compound.sc_add_bp(matrix, options)

In both variants, the optional argument options defaults to VRNA_OPTION_DEFAULT. See, e.g. RNA.fold_compound.sc_add_bp() in the Python API .

Parameters:

fc – 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 \( kcal / mol \)
options – The options flag indicating how/where to store the soft constraints

Returns:

Non-zero on successful application of the constraint, 0 otherwise.

int vrna_sc_set_up(vrna_fold_compound_t *fc, const FLT_OR_DBL *constraints, unsigned int options)

#include <ViennaRNA/constraints/soft.h>

Set soft constraints for unpaired nucleotides.

SWIG Wrapper Notes:: This function is attached as method sc_set_up() to objects of type fold_compound. See, e.g. RNA.fold_compound.sc_set_up() in the Python API .

Note

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

Parameters:

fc – The vrna_fold_compound_t the soft constraints are associated with
constraints – A vector of pseudo free energies in \( kcal / mol \)
options – The options flag indicating how/where to store the soft constraints

Returns:

Non-zero on successful application of the constraint, 0 otherwise.

int vrna_sc_add_up(vrna_fold_compound_t *fc, int i, FLT_OR_DBL energy, unsigned int options)

#include <ViennaRNA/constraints/soft.h>

Add soft constraints for unpaired nucleotides.

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 \(i \) with the corresponding energy value:

fold_compound.sc_add_up(i, energy, options)

or an entire vector that stores free energy contributions for each nucleotide \(i \) with \( 1 \leq i \leq n \):

fold_compound.sc_add_bp(vector, options)

In both variants, the optional argument options defaults to VRNA_OPTION_DEFAULT. See, e.g. RNA.fold_compound.sc_add_up() in the Python API .

Parameters:

fc – 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 \( kcal / mol \)
options – The options flag indicating how/where to store the soft constraints

Returns:

Non-zero on successful application of the constraint, 0 otherwise.

void vrna_sc_remove(vrna_fold_compound_t *fc)

#include <ViennaRNA/constraints/soft.h>

Remove soft constraints from vrna_fold_compound_t.

SWIG Wrapper Notes:: This function is attached as method sc_remove() to objects of type fold_compound. See, e.g. RNA.fold_compound.sc_remove() in the Python API .

Note

Accepts vrna_fold_compound_t of type VRNA_FC_TYPE_SINGLE and VRNA_FC_TYPE_COMPARATIVE

Parameters:

fc – The vrna_fold_compound_t possibly containing soft constraints

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

int vrna_sc_add_data(vrna_fold_compound_t *fc, void *data, vrna_auxdata_free_f free_data)

#include <ViennaRNA/constraints/soft.h>

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

SWIG Wrapper Notes:: This function is attached as method sc_add_data() to objects of type fold_compound. See, e.g. RNA.fold_compound.sc_add_data() in the Python API .

Parameters:

fc – 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)

Returns:

Non-zero on successful binding the data (and free-function), 0 otherwise

int vrna_sc_add_f(vrna_fold_compound_t *fc, vrna_sc_f 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 \( 1 dacal/mol = 10 cal/mol \).

SWIG Wrapper Notes:: This function is attached as method sc_add_f() to objects of type fold_compound. See, e.g. RNA.fold_compound.sc_add_f() in the Python API .

Parameters:

fc – 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

Returns:

Non-zero on successful binding the callback function, 0 otherwise

int vrna_sc_add_bt(vrna_fold_compound_t *fc, vrna_sc_bt_f 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.

SWIG Wrapper Notes:: This function is attached as method sc_add_bt() to objects of type fold_compound. See, e.g. RNA.fold_compound.sc_add_bt() in the Python API .

Parameters:

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

Returns:

Non-zero on successful binding the callback function, 0 otherwise

int vrna_sc_add_exp_f(vrna_fold_compound_t *fc, vrna_sc_exp_f 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 \( cal/mol \).

SWIG Wrapper Notes:: This function is attached as method sc_add_exp_f() to objects of type fold_compound. See, e.g. RNA.fold_compound.sc_add_exp_f() in the Python API .

Parameters:

fc – 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

Returns:

Non-zero on successful binding the callback function, 0 otherwise

struct vrna_sc_s

#include <ViennaRNA/constraints/soft.h>

The soft constraints data structure.

Public Members

const vrna_sc_type_e type

unsigned int n

unsigned char state

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_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)

union vrna_sc_s.[anonymous] [anonymous]

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_sc_f f

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

See also

vrna_sc_add_f()

vrna_sc_bt_f 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_sc_exp_f exp_f

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

See also

vrna_sc_add_exp_f()

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

vrna_auxdata_prepare_f prepare_data

vrna_auxdata_free_f free_data