1 #ifndef VIENNA_RNA_PACKAGE_MULTIBRANCH_LOOPS_H
2 #define VIENNA_RNA_PACKAGE_MULTIBRANCH_LOOPS_H
45 PRIVATE INLINE
int E_MLstem(
int type,
56 PRIVATE INLINE
FLT_OR_DBL exp_E_MLstem(
int type,
102 E_mb_loop_fast(
int i,
114 E_ml_rightmost_stem(
int i,
120 E_ml_stems_fast(
int i,
126 PRIVATE INLINE
int E_MLstem(
int type,
int si1,
int sj1,
vrna_param_t *P){
128 if(si1 >= 0 && sj1 >= 0){
129 energy += P->mismatchM[type][si1][sj1];
132 energy += P->dangle5[type][si1];
135 energy += P->dangle3[type][sj1];
139 energy += P->TerminalAU;
141 energy += P->MLintern[type];
149 exp_E_MLstem(
int type,
155 if(si1 >= 0 && sj1 >= 0){
156 energy = P->expmismatchM[type][si1][sj1];
159 energy = P->expdangle5[type][si1];
162 energy = P->expdangle3[type][sj1];
166 energy *= P->expTermAU;
168 energy *= P->expMLintern[type];
int E_mb_loop_stack(int i, int j, vrna_fold_compound_t *vc)
Evaluate energy of a multi branch helices stacking onto closing pair (i,j)
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:44
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:397
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:55
General utility- and helper-functions used throughout the ViennaRNA Package.
Various data structures and pre-processor macros.
Functions to deal with sets of energy parameters.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:99
int vrna_BT_mb_loop(vrna_fold_compound_t *vc, int *i, int *j, int *k, int en, int *component1, int *component2)
Backtrack the decomposition of a multi branch loop closed by .
Base pair stack element.
Definition: data_structures.h:199