RNAlib-2.2.7

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

+ Collaboration diagram for Soft Constraints:

Files

file  constraints_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, char d, void *data)
 Callback to retrieve pseudo energy contribution for soft constraint feature. More...
 
typedef FLT_OR_DBLvrna_callback_sc_exp_energy) (int i, int j, int k, int l, 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, 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_add_bp (vrna_fold_compound_t *vc, const FLT_OR_DBL **constraints, unsigned int options)
 Add soft constraints for paired nucleotides. More...
 
void vrna_sc_add_up (vrna_fold_compound_t *vc, const FLT_OR_DBL *constraints, 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...
 

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.


Data Structure Documentation

struct vrna_sc_s

The soft constraints data structure.

Data Fields

int ** energy_up
 Energy contribution for stretches of unpaired nucleotides.
 
int * energy_bp
 Energy contribution for base pairs.
 
FLT_OR_DBL ** exp_energy_up
 Boltzmann Factors of the energy contributions for unpaired sequence stretches.
 
FLT_OR_DBLexp_energy_bp
 Boltzmann Factors of the energy contribution for base pairs.
 
int * energy_stack
 Pseudo Energy contribution per base pair involved in a stack.
 
FLT_OR_DBLexp_energy_stack
 Boltzmann weighted pseudo energy contribution per nucleotide involved in a stack.
 
vrna_callback_sc_energyf
 A function pointer used for pseudo energy contribution in MFE calculations. More...
 
vrna_callback_sc_backtrackbt
 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_energyexp_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.
 

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()

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, 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.

See also
VRNA_DECOMP_PAIR_HP, VRNA_DECOMP_PAIR_IL, VRNA_DECOMP_PAIR_ML, VRNA_DECOMP_ML_ML_ML, VRNA_DECOMP_ML_STEM, VRNA_DECOMP_ML_ML, VRNA_DECOMP_ML_UP, VRNA_DECOMP_ML_ML_STEM, VRNA_DECOMP_ML_COAXIAL, VRNA_DECOMP_EXT_EXT, VRNA_DECOMP_EXT_UP, VRNA_DECOMP_EXT_STEM, VRNA_DECOMP_EXT_EXT_EXT, VRNA_DECOMP_EXT_STEM_EXT, VRNA_DECOMP_EXT_EXT_STEM, VRNA_DECOMP_EXT_EXT_STEM1, vrna_sc_add_f(), vrna_sc_add_exp_f(), vrna_sc_add_bt(), vrna_sc_add_data()
Parameters
iLeft (5') delimiter position of substructure
jRight (3') delimiter position of substructure
kLeft delimiter of decomposition
lRight delimiter of decomposition
dDecomposition step indicator
dataAuxiliary 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, 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.

See also
VRNA_DECOMP_PAIR_HP, VRNA_DECOMP_PAIR_IL, VRNA_DECOMP_PAIR_ML, VRNA_DECOMP_ML_ML_ML, VRNA_DECOMP_ML_STEM, VRNA_DECOMP_ML_ML, VRNA_DECOMP_ML_UP, VRNA_DECOMP_ML_ML_STEM, VRNA_DECOMP_ML_COAXIAL, VRNA_DECOMP_EXT_EXT, VRNA_DECOMP_EXT_UP, VRNA_DECOMP_EXT_STEM, VRNA_DECOMP_EXT_EXT_EXT, VRNA_DECOMP_EXT_STEM_EXT, VRNA_DECOMP_EXT_EXT_STEM, VRNA_DECOMP_EXT_EXT_STEM1, vrna_sc_add_exp_f(), vrna_sc_add_f(), vrna_sc_add_bt(), vrna_sc_add_data()
Parameters
iLeft (5') delimiter position of substructure
jRight (3') delimiter position of substructure
kLeft delimiter of decomposition
lRight delimiter of decomposition
dDecomposition step indicator
dataAuxiliary 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, char d, void *data)

#include <ViennaRNA/constraints_soft.h>

Callback to retrieve auxiliary base pairs for soft constraint feature.

See also
VRNA_DECOMP_PAIR_HP, VRNA_DECOMP_PAIR_IL, VRNA_DECOMP_PAIR_ML, VRNA_DECOMP_ML_ML_ML, VRNA_DECOMP_ML_STEM, VRNA_DECOMP_ML_ML, VRNA_DECOMP_ML_UP, VRNA_DECOMP_ML_ML_STEM, VRNA_DECOMP_ML_COAXIAL, VRNA_DECOMP_EXT_EXT, VRNA_DECOMP_EXT_UP, VRNA_DECOMP_EXT_STEM, VRNA_DECOMP_EXT_EXT_EXT, VRNA_DECOMP_EXT_STEM_EXT, VRNA_DECOMP_EXT_EXT_STEM, VRNA_DECOMP_EXT_EXT_STEM1, vrna_sc_add_bt(), vrna_sc_add_f(), vrna_sc_add_exp_f(), vrna_sc_add_data()
Parameters
iLeft (5') delimiter position of substructure
jRight (3') delimiter position of substructure
kLeft delimiter of decomposition
lRight delimiter of decomposition
dDecomposition step indicator
dataAuxiliary 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_VC_TYPE_SINGLE and VRNA_VC_TYPE_ALIGNMENT
See also
vrna_sc_add_bp(), vrna_sc_add_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
vcThe vrna_fold_compound_t where an empty soft constraint feature is to be added to
void vrna_sc_add_bp ( vrna_fold_compound_t vc,
const FLT_OR_DBL **  constraints,
unsigned int  options 
)

#include <ViennaRNA/constraints_soft.h>

Add soft constraints for paired nucleotides.

Parameters
vcThe vrna_fold_compound_t the soft constraints are associated with
constraintsA two-dimensional array of pseudo free energies in $ kcal / mol $
optionsThe options flag indicating how/where to store the soft constraints
void vrna_sc_add_up ( vrna_fold_compound_t vc,
const FLT_OR_DBL constraints,
unsigned int  options 
)

#include <ViennaRNA/constraints_soft.h>

Add soft constraints for unpaired nucleotides.

Parameters
vcThe vrna_fold_compound_t the soft constraints are associated with
constraintsA vector of pseudo free energies in $ kcal / mol $
optionsThe options flag indicating how/where to store the soft constraints
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_VC_TYPE_SINGLE and VRNA_VC_TYPE_ALIGNMENT
Parameters
vcThe 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
scThe 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
vcThe fold compound the generic soft constraint function should be bound to
dataA pointer to the data structure that holds required data for function 'f'
free_dataA pointer to a function that free's the memory occupied by (Maybe NULL)
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 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
vcThe fold compound the generic soft constraint function should be bound to
fA pointer to the function that evaluates the generic soft constraint feature
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 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
vcThe fold compound the generic soft constraint function should be bound to
fA pointer to the function that returns additional base pairs
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 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
vcThe fold compound the generic soft constraint function should be bound to
exp_fA pointer to the function that evaluates the generic soft constraint feature