RNAlib-2.2.0
+ Collaboration diagram for Generalized Soft Constraints:

Macros

#define VRNA_DECOMP_PAIR_HP   1
 Generalized constraint folding flag indicating hairpin loop decomposition step.
 
#define VRNA_DECOMP_PAIR_IL   2
 Generalized constraint folding flag indicating interior loop decomposition step.
 

Typedefs

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_add_f (vrna_fold_compound_t *vc, vrna_callback_sc_energy *f)
 Bind a function pointer for generalized 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 generalized 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 generalized soft constraint feature (PF version) More...
 
int vrna_sc_add_hi_motif (vrna_fold_compound_t *vc, const char *seq, const char *structure, FLT_OR_DBL energy, unsigned int options)
 Add soft constraints for hairpin or interior loop binding motif. More...
 

Detailed Description

Typedef Documentation

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

#include <ViennaRNA/constraints.h>

Callback to retrieve pseudo energy contribution for soft constraint feature.

Parameters
iLeft (5') delimiter position of substructure
jRight (3') delimiter position of substructure
k
l
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.h>

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

Parameters
iLeft (5') delimiter position of substructure
jRight (3') delimiter position of substructure
k
l
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.h>

Callback to retrieve auxiliary base pairs for soft constraint feature.

Parameters
iLeft (5') delimiter position of substructure
jRight (3') delimiter position of substructure
k
l
dDecomposition step indicator
dataAuxiliary data
Returns
List of additional base pairs

Function Documentation

void vrna_sc_add_f ( vrna_fold_compound_t vc,
vrna_callback_sc_energy f 
)

#include <ViennaRNA/constraints.h>

Bind a function pointer for generalized 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 generalized soft constraint feature has to return a pseudo free energy $ \hat{E} $ in $ dacal/mol $, where $ 1 dacal/mol = 10 cal/mol $.

Parameters
vcThe fold compound the generalized soft constraint function should be bound to
fA pointer to the function that evaluates the generalized soft constraint feature
dataA pointer to the data structure that holds required data for function 'f'
void vrna_sc_add_bt ( vrna_fold_compound_t vc,
vrna_callback_sc_backtrack f 
)

#include <ViennaRNA/constraints.h>

Bind a backtracking function pointer for generalized 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 generalized 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.

Parameters
vcThe fold compound the generalized 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.h>

Bind a function pointer for generalized 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 generalized 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 $.

Parameters
vcThe fold compound the generalized soft constraint function should be bound to
exp_fA pointer to the function that evaluates the generalized soft constraint feature
dataA pointer to the data structure that holds required data for function 'f'
int vrna_sc_add_hi_motif ( vrna_fold_compound_t vc,
const char *  seq,
const char *  structure,
FLT_OR_DBL  energy,
unsigned int  options 
)

#include <ViennaRNA/ligand.h>

Add soft constraints for hairpin or interior loop binding motif.

Here is an example that adds a theophylline binding motif. Free energy contribution is derived from $k_d = 0.32 \mu mol / l $, taken from Jenison et al. 1994

"GAUACCAG&CCCUUGGCAGC",
"(...((((&)...)))...)",
-9.22,
Parameters
vcThe vrna_fold_compound_t the motif is applied to
seqThe sequence motif (may be interspaced by '&' character
structureThe structure motif (may be interspaced by '&' character
energyThe free energy of the motif (e.g. binding free energy)
optionsOptions indicating whether to use the motif in MFE prediction, and/or PF predictions
Returns
non-zero value if application of the motif using soft constraints was successful