1 #ifndef VIENNA_RNA_PACKAGE_MULTIBRANCH_LOOPS_H 2 #define VIENNA_RNA_PACKAGE_MULTIBRANCH_LOOPS_H 60 PRIVATE INLINE
int E_MLstem(
int type,
72 PRIVATE INLINE
FLT_OR_DBL exp_E_MLstem(
int type,
128 E_ml_rightmost_stem(
int i,
219 if (si1 >= 0 && sj1 >= 0)
220 energy += P->mismatchM[type][si1][sj1];
222 energy += P->dangle5[type][si1];
224 energy += P->dangle3[type][sj1];
227 energy += P->TerminalAU;
229 energy += P->MLintern[type];
236 exp_E_MLstem(
int type,
243 if (si1 >= 0 && sj1 >= 0)
244 energy = P->expmismatchM[type][si1][sj1];
246 energy = P->expdangle5[type][si1];
248 energy = P->expdangle3[type][sj1];
251 energy *= P->expTermAU;
253 energy *= P->expMLintern[type];
Auxiliary helper arrays for fast exterior loop computations.
Definition: multibranch_loops.h:32
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:48
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:463
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:57
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 data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:101
int vrna_E_mb_loop_stack(vrna_fold_compound_t *vc, int i, int j)
Evaluate energy of a multi branch helices stacking onto closing pair (i,j)
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:229