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
224 if (si1 >= 0 && sj1 >= 0)
225 energy += P->mismatchM[type][si1][sj1];
227 energy += P->dangle5[type][si1];
229 energy += P->dangle3[type][sj1];
232 energy += P->TerminalAU;
234 energy += P->MLintern[type];
247exp_E_MLstem(
int type,
254 if (si1 >= 0 && sj1 >= 0)
255 energy = P->expmismatchM[type][si1][sj1];
257 energy = P->expdangle5[type][si1];
259 energy = P->expdangle3[type][sj1];
262 energy *= P->expTermAU;
264 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:103
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:148
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.