1 #ifndef VIENNA_RNA_PACKAGE_LOOPS_MULTIBRANCH_H 2 #define VIENNA_RNA_PACKAGE_LOOPS_MULTIBRANCH_H 8 #ifdef VRNA_WARN_DEPRECATED 9 # if defined(DEPRECATED) 12 # if defined(__clang__) 13 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 14 # elif defined(__GNUC__) 15 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 17 # define DEPRECATED(func, msg) func 20 # define DEPRECATED(func, msg) func 24 # define INLINE inline 74 E_ml_rightmost_stem(
int i,
126 vrna_exp_E_ml_fast_qqm(
struct vrna_mx_pf_aux_ml_s *aux_mx);
130 vrna_exp_E_ml_fast_qqm1(
struct vrna_mx_pf_aux_ml_s *aux_mx);
204 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 238 if (si1 >= 0 && sj1 >= 0)
239 energy += P->mismatchM[type][si1][sj1];
241 energy += P->dangle5[type][si1];
243 energy += P->dangle3[type][sj1];
246 energy += P->TerminalAU;
248 energy += P->MLintern[type];
261 exp_E_MLstem(
int type,
268 if (si1 >= 0 && sj1 >= 0)
269 energy = P->expmismatchM[type][si1][sj1];
271 energy = P->expdangle5[type][si1];
273 energy = P->expdangle3[type][sj1];
276 energy *= P->expTermAU;
278 energy *= P->expMLintern[type];
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:56
Various data structures and pre-processor macros.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:101
struct vrna_mx_pf_aux_ml_s * vrna_mx_pf_aux_ml_t
Auxiliary helper arrays for fast exterior loop computations.
Definition: multibranch.h:103
int vrna_BT_mb_loop(vrna_fold_compound_t *fc, int *i, int *j, int *k, int en, int *component1, int *component2)
Backtrack the decomposition of a multi branch loop closed by .
int vrna_E_mb_loop_stack(vrna_fold_compound_t *fc, int i, int j)
Evaluate energy of a multi branch helices stacking onto closing pair (i,j)
Base pair stack element.
Definition: basic.h:142
Functions to deal with sets of energy parameters.
General utility- and helper-functions used throughout the ViennaRNA Package.