1#ifndef VIENNA_RNA_PACKAGE_LOOPS_MULTIBRANCH_H
2#define VIENNA_RNA_PACKAGE_LOOPS_MULTIBRANCH_H
9#ifdef VRNA_WARN_DEPRECATED
10# if defined(DEPRECATED)
13# if defined(__clang__)
14# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
15# elif defined(__GNUC__)
16# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
18# define DEPRECATED(func, msg) func
21# define DEPRECATED(func, msg) func
69E_ml_rightmost_stem(
int i,
190#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
225 if (si1 >= 0 && sj1 >= 0)
226 energy += P->mismatchM[type][si1][sj1];
228 energy += P->dangle5[type][si1];
230 energy += P->dangle3[type][sj1];
233 energy += P->TerminalAU;
235 energy += P->MLintern[type];
250exp_E_MLstem(
int type,
257 if (si1 >= 0 && sj1 >= 0)
258 energy = P->expmismatchM[type][si1][sj1];
260 energy = P->expdangle5[type][si1];
262 energy = P->expdangle3[type][sj1];
265 energy *= P->expTermAU;
267 energy *= P->expMLintern[type];
Various data structures and pre-processor macros.
The Basic Fold Compound API.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition basic.h:43
Base pair stack element.
Definition basic.h:143
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition basic.h:110
The datastructure that contains temperature scaled energy parameters.
Definition basic.h:57
struct vrna_mx_pf_aux_ml_s * vrna_mx_pf_aux_ml_t
Auxiliary helper arrays for fast exterior loop computations.
Definition multibranch.h:98
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)
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
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 .
Functions to deal with sets of energy parameters.
General utility- and helper-functions used throughout the ViennaRNA Package.