Soft Constraints

Functions and data structures for secondary structure soft constraints.

Introduction 

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.

Note

For the sake of memory efficiency, we do not implement a loop context aware version of soft constraints. The static soft constraints as implemented only distinguish unpaired from paired nucleotides. This is usually sufficient for most use-case scenarios. However, similar to hard constraints, an abstract soft constraints implementation using a callback mechanism exists, that allows for any soft constraint that is compatible with the RNA folding grammar. Thus, loop contexts and even individual derivation rules can be addressed separately for maximum flexibility in soft-constraints application.

Common API symbols 

Typedefs

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

Enums

enum vrna_sc_type_e

The type of a soft constraint.

Values:

enumerator VRNA_SC_DEFAULT: Default Soft Constraints.

enumerator VRNA_SC_WINDOW

Soft Constraints suitable for local structure prediction using window approach.

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_prepare(vrna_fold_compound_t *fc, unsigned int options): #include <ViennaRNA/constraints/soft.h>
Prepare soft constraints.

int vrna_sc_update(vrna_fold_compound_t *fc, unsigned int i, unsigned int options): #include <ViennaRNA/constraints/soft.h>
Update/prepare soft constraints for sliding-window computations.

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

struct vrna_sc_bp_storage_t

#include <ViennaRNA/constraints/soft.h>

A base pair constraint.

Public Members

unsigned int interval_start

unsigned int interval_end

int e

struct vrna_sc_s

#include <ViennaRNA/constraints/soft.h>

The soft constraints data structure.

Common data fields

const vrna_sc_type_e type: Type of the soft constraints data structure.

unsigned int n: Length of the sequence this soft constraints data structure belongs to.

unsigned char state: Current state of the soft constraints data structure.

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.

Global structure prediction data fields

int *energy_bp: Energy contribution for base pairs.

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

Local structure prediction data fields

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)

User-defined data fields

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

Public Members

union vrna_sc_s.[anonymous] [anonymous]

Constraints for Unpaired Positions 

Functions

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

#include <ViennaRNA/constraints/soft.h>

Set soft constraints for unpaired nucleotides in comparative structure predictions.

Use this function to set soft constraints for unpaired nucleotides for each sequence in the multiple sequence alignment (MSA). The constraints are provided as 0-based array of 1-based array with the actual pseudo energies, where the first dimension corresponds to the number (0-based) of the respective sequence in the alignment. If no constraints are provided for a particular sequence \( s \) in the MSA, the corresponding entry must be set to NULL.

See also

vrna_sc_set_up_comparative_seq(), vrna_sc_add_up_comparative(), vrna_sc_set_bp_comparative(), vrna_sc_add_stack_comparative(), vrna_sc_set_stack_comparative(), vrna_sc_set_up()

Note

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

Warning

Pseudo energies for all sequences must be provided in sequence coordinates rather than alignment coordinates!

Parameters:

fc – The vrna_fold_compound_t the soft constraints are associated with
constraints – A 0-based array of 1-based arrays with pseudo free energies in \( kcal / mol \)
options – The options flag indicating how/where to store the soft constraints

Returns:

The number of sequences in the MSA constraints have been applied to

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

#include <ViennaRNA/constraints/soft.h>

Set soft constraints for unpaired nucleotides in comparative structure predictions.

This is a convenience wrapper for vrna_sc_set_up_comparative() where only one particular sequence s is provided with constraints.

See also

vrna_sc_set_up_comparative(), vrna_sc_add_up_comparative_seq(), vrna_sc_set_bp_comparative_seq(), vrna_sc_add_stack_comparative_seq(), vrna_sc_set_stack_comparative_seq(), vrna_sc_set_up()

Note

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

Warning

Pseudo energies for all sequences must be provided in sequence coordinates rather than alignment coordinates!

Parameters:

fc – The vrna_fold_compound_t the soft constraints are associated with
s – The 0-based number of the sequence in the alignment the constraints are provided for
constraints – A 1-based arrays with pseudo free energies in \( kcal / mol \)
options – The options flag indicating how/where to store the soft constraints

Returns:

The number of sequences in the MSA constraints have been applied to

int vrna_sc_add_up(vrna_fold_compound_t *fc, unsigned 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.

int vrna_sc_add_up_comparative(vrna_fold_compound_t *fc, unsigned int *is, const FLT_OR_DBL *energies, unsigned int options)

#include <ViennaRNA/constraints/soft.h>

Add soft constraints for unpaired nucleotides in comparative structure predictions.

Use this function to add soft constraints for unpaired nucleotides for each sequence in the multiple sequence alignment (MSA). The constraints are provided as 0-based array of pseudo energies, one for each sequence in the MSA. If no constraints are provided for a particular sequence, the corrsponding is value must be 0.

See also

vrna_sc_set_up_comparative_seq(), vrna_sc_add_up_comparative(), vrna_sc_set_bp_comparative(), vrna_sc_add_stack_comparative(), vrna_sc_set_stack_comparative(), vrna_sc_add_up()

Warning

Pseudo energies for all sequences must be provided in sequence coordinates rather than alignment coordinates!

Parameters:

fc – The vrna_fold_compound_t the soft constraints are associated with
is – A 0-based array of nucleotide positions the soft constraint is added for
energies – A 0-based array of free energies (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_add_up_comparative_seq(vrna_fold_compound_t *fc, unsigned int s, unsigned int i, const FLT_OR_DBL energy, unsigned int options)

#include <ViennaRNA/constraints/soft.h>

Add soft constraints for unpaired nucleotides in comparative structure predictions.

This is a convenience wrapper for vrna_sc_add_up_comparative() where only one particular sequence s is provided with constraints.

See also

vrna_sc_set_up_comparative_seq(), vrna_sc_add_up_comparative(), vrna_sc_set_bp_comparative(), vrna_sc_add_stack_comparative(), vrna_sc_set_stack_comparative(), vrna_sc_add_up()

Warning

Pseudo energies for all sequences must be provided in sequence coordinates rather than alignment coordinates!

Parameters:

fc – The vrna_fold_compound_t the soft constraints are associated with
s – The 0-based number of the sequence in the alignment the constraints are provided for
i – The 1-based nucleotide position the soft constraint is added for
energy – The free energies (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.

Constraints for Base Pairs 

Functions

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

#include <ViennaRNA/constraints/soft.h>

Set soft constraints for paired nucleotides in comparative structure predictions.

Similar to vrna_sc_set_bp() this function allows to set soft constraints \( e_{i,j}^\mathrm{BP} \) for all base pairs \( (i, j) \) at once using a 1-based upper-triangular matrix \( E_\mathrm{BP} \). Since this function is supposed to be used for comparative structure predictions over a multiple sequence alignment (MSA), a 0-based array of matrices must be supplied as parameter constraints. If no constraints are to be used for sequence \( s \) in the MSA, the corresponding entry may be set to NULL.

See also

vrna_sc_set_bp_comparative_seq(), vrna_sc_add_bp_comparative(), vrna_sc_set_up_comparative(), vrna_sc_add_up_comparative(), vrna_sc_set_stack_comparative(), vrna_sc_add_stack_comparative(), vrna_sc_set_bp()

Note

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

Warning

Currently, base pair constraints must be provided in alignment coordinates rather than sequence coordinates! This may change in the future!

Parameters:

fc – The vrna_fold_compound_t the soft constraints are associated with
constraints – A 0-based array of 1-based two-dimensional arrays with pseudo free energies in \( kcal / mol \)
options – The options flag indicating how/where to store the soft constraints

Returns:

The number of sequences in the MSA constraints have been applied to

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

#include <ViennaRNA/constraints/soft.h>

Set soft constraints for paired nucleotides in comparative structure predictions.

This is a convenience wrapper for vrna_sc_set_bp_comparative() where only one particular sequence s is provided with constraints.

See also

vrna_sc_set_bp_comparative(), vrna_sc_add_bp_comparative(), vrna_sc_set_up_comparative_seq(), vrna_sc_add_up_comparative_seq(), vrna_sc_set_stack_comparative_seq(), vrna_sc_add_stack_comparative_seq(), vrna_sc_set_bp()

Note

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

Warning

This function not only re-sets the constraints for sequence s in the MSA but will also remove all constraints for all other sequences!

Warning

Currently, base pair constraints must be provided in alignment coordinates rather than sequence coordinates! This may change in the future!

Parameters:

fc – The vrna_fold_compound_t the soft constraints are associated with
s – The 0-based number of the sequence in the alignment the constraints are provided for
constraints – A 1-based two-dimensional array of pseudo free energies in \( kcal / mol \)
options – The options flag indicating how/where to store the soft constraints

Returns:

The number of sequences in the MSA constraints have been applied to

int vrna_sc_add_bp(vrna_fold_compound_t *fc, unsigned int i, unsigned 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_add_bp_comparative(vrna_fold_compound_t *fc, unsigned int *is, unsigned int *js, const FLT_OR_DBL *energies, unsigned int options)

#include <ViennaRNA/constraints/soft.h>

Add soft constraints for paired nucleotides in comparative structure predictions.

Similar to vrna_sc_add_bp(), this function allows to add soft constraints \( e_{i,j}^\mathrm{BP} \) for all base pairs \( (i, j) \) in the multiple sequence alignment (MSA). The actual pairing partners \( i \) and \( j \) for each sequence in the MSA are provided in the form of 0-based arrays as parameters is and js. The corresponding energy contributions are provided as 0-based array in parameter energies. If no constraint is provided for sequence \( s \) in the MSA, the corresponding is value must be set to 0.

See also

vrna_sc_add_bp_comparative_seq(), vrna_sc_set_bp_comparative(), vrna_sc_set_up_comparative(), vrna_sc_add_up_comparative(), vrna_sc_set_stack_comparative(), vrna_sc_add_stack_comparative(), vrna_sc_add_bp()

Note

Consecutive calls of this function with the same is and js accumulate to corresponding energies values, i.e. energies are added up onto each other.

Warning

Currently, base pair constraints must be provided in alignment coordinates rather than sequence coordinates! This may change in the future!

Parameters:

fc – The vrna_fold_compound_t the soft constraints are associated with
is – A 0-based array of 5’ position of the base pairs the soft constraint is added for
js – A 0-based array of 3’ position of the base pairs the soft constraint is added for
energies – A 0-based array of free energies (soft-constraint) in \( kcal / mol \)
options – The options flag indicating how/where to store the soft constraints

Returns:

The number of sequences in the MSA constraints have been applied to

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

#include <ViennaRNA/constraints/soft.h>

Add soft constraints for paired nucleotides in comparative structure predictions.

This is a convenience wrapper for vrna_sc_add_bp_comparative() where only one particular sequence s is provided with constraints.

See also

vrna_sc_add_bp_comparative(), vrna_sc_set_bp_comparative_seq(), vrna_sc_set_up_comparative_seq(), vrna_sc_add_up_comparative_seq(), vrna_sc_set_stack_comparative_seq(), vrna_sc_add_stack_comparative_seq(), vrna_sc_add_bp()

Note

Consecutive calls of this function with the same i and j accumulate to corresponding energies values, i.e. energies are added up onto each other.

Warning

Currently, base pair constraints must be provided in alignment coordinates rather than sequence coordinates! This may change in the future!

Parameters:

fc – The vrna_fold_compound_t the soft constraints are associated with
s – The 0-based number of the sequence in the alignment the constraints are provided for
i – 5’ position of the base pairs the soft constraint is added for
j – 3’ position of the base pairs the soft constraint is added for
energy – Free energy (soft-constraint) in \( kcal / mol \)
options – The options flag indicating how/where to store the soft constraints

Returns:

The number of sequences in the MSA constraints have been applied to

Constraints for Stacked Base Pairs 

Functions

int vrna_sc_set_stack(vrna_fold_compound_t *fc, const FLT_OR_DBL *constraints, unsigned int options): #include <ViennaRNA/constraints/soft.h>

int vrna_sc_set_stack_comparative(vrna_fold_compound_t *fc, const FLT_OR_DBL **constraints, unsigned int options): #include <ViennaRNA/constraints/soft.h>

int vrna_sc_set_stack_comparative_seq(vrna_fold_compound_t *fc, unsigned int s, const FLT_OR_DBL *constraints, unsigned int options): #include <ViennaRNA/constraints/soft.h>

int vrna_sc_add_stack(vrna_fold_compound_t *fc, unsigned int i, FLT_OR_DBL energy, unsigned int options): #include <ViennaRNA/constraints/soft.h>

int vrna_sc_add_stack_comparative(vrna_fold_compound_t *fc, unsigned int *is, const FLT_OR_DBL *energies, unsigned int options): #include <ViennaRNA/constraints/soft.h>

int vrna_sc_add_stack_comparative_seq(vrna_fold_compound_t *fc, unsigned int s, unsigned int i, FLT_OR_DBL energy, unsigned int options): #include <ViennaRNA/constraints/soft.h>

Generic implementation 

Typedefs

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 int (*vrna_sc_direct_f)(vrna_fold_compound_t *fc, int i, int j, int k, int l, void *data): #include <ViennaRNA/constraints/soft.h>

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 FLT_OR_DBL (*vrna_sc_exp_direct_f)(vrna_fold_compound_t *fc, int i, int j, int k, int l, void *data): #include <ViennaRNA/constraints/soft.h>

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 internal 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

DEPRECATED (typedef int(vrna_callback_sc_energy)(int i, int j, int k, int l, unsigned char d, void *data), "Use vrna_sc_f instead!"): #include <ViennaRNA/constraints/soft.h>

DEPRECATED (typedef FLT_OR_DBL(vrna_callback_sc_exp_energy)(int i, int j, int k, int l, unsigned char d, void *data), "Use vrna_sc_exp_f instead!"): #include <ViennaRNA/constraints/soft.h>

DEPRECATED (typedef vrna_basepair_t *(vrna_callback_sc_backtrack)(int i, int j, int k, int l, unsigned char d, void *data), "Use vrna_sc_bt_f instead"): #include <ViennaRNA/constraints/soft.h>

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_auxdata(vrna_fold_compound_t *fc, void *data, vrna_auxdata_prepare_f prepare_cb, vrna_auxdata_free_f free_cb): #include <ViennaRNA/constraints/soft.h>

int vrna_sc_set_data_comparative(vrna_fold_compound_t *fc, void **data, vrna_auxdata_free_f *free_data, unsigned int options): #include <ViennaRNA/constraints/soft.h>

int vrna_sc_set_data_comparative_seq(vrna_fold_compound_t *fc, unsigned int s, void *data, vrna_auxdata_free_f free_data, unsigned int options): #include <ViennaRNA/constraints/soft.h>

int vrna_sc_set_auxdata_comparative(vrna_fold_compound_t *fc, void **data, vrna_auxdata_prepare_f *prepare_cbs, vrna_auxdata_free_f *free_data, unsigned int options): #include <ViennaRNA/constraints/soft.h>

int vrna_sc_set_auxdata_comparative_seq(vrna_fold_compound_t *fc, unsigned int s, void *data, vrna_auxdata_prepare_f prepare_cb, vrna_auxdata_free_f free_data, unsigned int options): #include <ViennaRNA/constraints/soft.h>

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

size_t vrna_sc_multi_cb_add(vrna_fold_compound_t *fc, vrna_sc_direct_f cb, vrna_sc_exp_direct_f cb_exp, void *data, vrna_auxdata_prepare_f prepare_cb, vrna_auxdata_free_f free_cb, unsigned int decomp_type): #include <ViennaRNA/constraints/soft.h>

size_t vrna_sc_multi_cb_add_comparative(vrna_fold_compound_t *fc, vrna_sc_direct_f *cbs, vrna_sc_exp_direct_f *cbs_exp, void **datas, vrna_auxdata_prepare_f *prepare_cbs, vrna_auxdata_free_f *free_cbs, unsigned int *ds, unsigned int multi_params): #include <ViennaRNA/constraints/soft.h>

int vrna_sc_set_f_comparative(vrna_fold_compound_t *fc, vrna_sc_f *f, unsigned int options): #include <ViennaRNA/constraints/soft.h>

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

int vrna_sc_set_exp_f_comparative(vrna_fold_compound_t *fc, vrna_sc_exp_f *exp_f, unsigned int options): #include <ViennaRNA/constraints/soft.h>

Soft Constraints

Introduction

Common API symbols

Constraints for Unpaired Positions

Constraints for Base Pairs

Constraints for Stacked Base Pairs

Generic implementation

Introduction 

Common API symbols 

Constraints for Unpaired Positions 

Constraints for Base Pairs 

Constraints for Stacked Base Pairs 

Generic implementation 