1 #ifndef VIENNA_RNA_PACKAGE_MULTIBRANCH_LOOPS_H
2 #define VIENNA_RNA_PACKAGE_MULTIBRANCH_LOOPS_H
42 PRIVATE INLINE
int E_MLstem(
int type,
53 PRIVATE INLINE
FLT_OR_DBL exp_E_MLstem(
int type,
99 E_mb_loop_fast(
int i,
111 E_ml_rightmost_stem(
int i,
117 E_ml_stems_fast(
int i,
123 PRIVATE INLINE
int E_MLstem(
int type,
int si1,
int sj1,
vrna_param_t *P){
125 if(si1 >= 0 && sj1 >= 0){
126 energy += P->mismatchM[type][si1][sj1];
129 energy += P->dangle5[type][si1];
132 energy += P->dangle3[type][sj1];
136 energy += P->TerminalAU;
138 energy += P->MLintern[type];
146 exp_E_MLstem(
int type,
152 if(si1 >= 0 && sj1 >= 0){
153 energy = P->expmismatchM[type][si1][sj1];
156 energy = P->expdangle5[type][si1];
159 energy = P->expdangle3[type][sj1];
163 energy *= P->expTermAU;
165 energy *= P->expMLintern[type];
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
General utility- and helper-functions used throughout the ViennaRNA Package.
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)
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
Base pair stack element.
Definition: data_structures.h:192
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 .