1#ifndef VIENNA_RNA_PACKAGE_LOOPS_EXTERNAL_H
2#define VIENNA_RNA_PACKAGE_LOOPS_EXTERNAL_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
211#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
268DEPRECATED(
int E_Stem(
int type,
273 "This function is obsolete. Use vrna_E_ext_stem() or E_MLstem() instead");
276DEPRECATED(
int E_ExtLoop(
int type,
280 "Use vrna_E_ext_stem() instead");
294 "Use vrna_exp_E_ext_stem() instead");
310 "This function is obsolete");
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
FLT_OR_DBL exp_E_ExtLoop(int type, int si1, int sj1, vrna_exp_param_t *P)
int E_Stem(int type, int si1, int sj1, int extLoop, vrna_param_t *P)
Compute the energy contribution of a stem branching off a loop-region.
FLT_OR_DBL exp_E_Stem(int type, int si1, int sj1, int extLoop, vrna_exp_param_t *P)
FLT_OR_DBL vrna_exp_E_ext_stem(unsigned int type, int n5d, int n3d, vrna_exp_param_t *p)
Evaluate a stem branching off the exterior loop (Boltzmann factor version)
int vrna_E_ext_stem(unsigned int type, int n5d, int n3d, vrna_param_t *p)
Evaluate a stem branching off the exterior loop.
int vrna_eval_ext_stem(vrna_fold_compound_t *fc, int i, int j)
Evaluate the free energy of a base pair in the exterior loop.
struct vrna_mx_pf_aux_el_s * vrna_mx_pf_aux_el_t
Auxiliary helper arrays for fast exterior loop computations.
Definition: external.h:116
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148
Functions to deal with sets of energy parameters.