RNAlib-2.2.0-RC3
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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. | |
#define | VRNA_SC_GEN_MFE (char)1 |
A flag passed to the generalized soft constraints pre-, and post- functions to indicate Minimum Free Energy (MFE) processing. More... | |
#define | VRNA_SC_GEN_PF (char)2 |
A flag passed to the generalized soft constraints pre-, and post- functions to indicate Partition function (PF) processing. More... | |
Functions | |
void | vrna_sc_add_f (vrna_fold_compound *vc, int(*f)(int, int, int, int, char, void *), void *data) |
Bind a function pointer for generalized soft constraint feature (MFE version) More... | |
void | vrna_sc_add_bt (vrna_fold_compound *vc, PAIR *(*f)(int, int, int, int, char, void *)) |
Bind a backtracking function pointer for generalized soft constraint feature. More... | |
void | vrna_sc_add_exp_f (vrna_fold_compound *vc, FLT_OR_DBL(*exp_f)(int, int, int, int, char, void *), void *data) |
Bind a function pointer for generalized soft constraint feature (PF version) More... | |
void | vrna_sc_add_pre (vrna_fold_compound *vc, void(*pre)(vrna_fold_compound *, char)) |
Add a pre-processing function for the generalized soft constraints feature. More... | |
void | vrna_sc_add_post (vrna_fold_compound *vc, void(*post)(vrna_fold_compound *, char)) |
Add a post-processing function for the generalized soft constraints feature. More... | |
#define VRNA_SC_GEN_MFE (char)1 |
A flag passed to the generalized soft constraints pre-, and post- functions to indicate Minimum Free Energy (MFE) processing.
This flag is passed as second argument to the pre-, and post- processing funtions that are bound to the vrna_sc_t structure via vrna_sc_add_pre(), and vrna_sc_add_post(), respectively. Use it in your implementation of the pre-, and post-processing functions to determine the mode of action required for corresponding pre-, and post- processing of data available to the function.
#define VRNA_SC_GEN_PF (char)2 |
A flag passed to the generalized soft constraints pre-, and post- functions to indicate Partition function (PF) processing.
This flag is passed as second argument to the pre-, and post- processing funtions that are bound to the vrna_sc_t structure via vrna_sc_add_pre(), and vrna_sc_add_post(), respectively. Use it in your implementation of the pre-, and post-processing functions to determine the mode of action required for corresponding pre-, and post- processing of data available to the function.
void vrna_sc_add_f | ( | vrna_fold_compound * | vc, |
int(*)(int, int, int, int, char, void *) | f, | ||
void * | data | ||
) |
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. 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 * | vc, |
PAIR *(*)(int, int, int, int, char, void *) | f | ||
) |
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. 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 PAIR 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 * | vc, |
FLT_OR_DBL(*)(int, int, int, int, char, void *) | exp_f, | ||
void * | data | ||
) |
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. 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' |
void vrna_sc_add_pre | ( | vrna_fold_compound * | vc, |
void(*)(vrna_fold_compound *, char) | pre | ||
) |
Add a pre-processing function for the generalized soft constraints feature.
vc | The fold compound the generalized soft constraint function should be bound to |
pre | A pointer to the pre-processing function |
void vrna_sc_add_post | ( | vrna_fold_compound * | vc, |
void(*)(vrna_fold_compound *, char) | post | ||
) |
Add a post-processing function for the generalized soft constraints feature.
vc | The fold compound the generalized soft constraint function should be bound to |
post | A pointer to the post-processing function |