RNAlib-2.2.0
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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_DBL( | vrna_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... | |
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.
i | Left (5') delimiter position of substructure |
j | Right (3') delimiter position of substructure |
k | |
l | |
d | Decomposition step indicator |
data | Auxiliary data |
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.
i | Left (5') delimiter position of substructure |
j | Right (3') delimiter position of substructure |
k | |
l | |
d | Decomposition step indicator |
data | Auxiliary data |
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.
i | Left (5') delimiter position of substructure |
j | Right (3') delimiter position of substructure |
k | |
l | |
d | Decomposition step indicator |
data | Auxiliary data |
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 in
, where
.
vc | The fold compound the generalized soft constraint function should be bound to |
f | A pointer to the function that evaluates the generalized soft constraint feature |
data | A 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.
vc | The fold compound the generalized soft constraint function should be bound to |
f | A 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 as Boltzmann factor, i.e.
. The required unit for
is
.
vc | The fold compound the generalized soft constraint function should be bound to |
exp_f | A pointer to the function that evaluates the generalized soft constraint feature |
data | A 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 , taken from Jenison et al. 1994
vc | The vrna_fold_compound_t the motif is applied to |
seq | The sequence motif (may be interspaced by '&' character |
structure | The structure motif (may be interspaced by '&' character |
energy | The free energy of the motif (e.g. binding free energy) |
options | Options indicating whether to use the motif in MFE prediction, and/or PF predictions |