1 #ifndef VIENNA_RNA_PACKAGE_LOOPS_EXTERNAL_H 2 #define VIENNA_RNA_PACKAGE_LOOPS_EXTERNAL_H 7 #ifdef VRNA_WARN_DEPRECATED 8 # if defined(DEPRECATED) 11 # if defined(__clang__) 12 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 13 # elif defined(__GNUC__) 14 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 16 # define DEPRECATED(func, msg) func 19 # define DEPRECATED(func, msg) func 142 struct vrna_mx_pf_aux_el_s *
147 vrna_exp_E_ext_fast_rotate(
struct vrna_mx_pf_aux_el_s *aux_mx);
151 vrna_exp_E_ext_fast_free(
struct vrna_mx_pf_aux_el_s *aux_mx);
158 struct vrna_mx_pf_aux_el_s *aux_mx);
164 struct vrna_mx_pf_aux_el_s *aux_mx);
210 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 263 DEPRECATED(
int E_Stem(
int type,
268 "This function is obsolete");
271 DEPRECATED(
int E_ExtLoop(
int type,
275 "Use vrna_E_ext_stem() instead");
289 "Use vrna_exp_E_ext_stem() instead");
305 "This function is obsolete");
int vrna_E_ext_loop(vrna_fold_compound_t *fc, int i, int j)
Evaluate the free energy of a base pair in the exterior loop.
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.
struct vrna_mx_pf_aux_el_s * vrna_mx_pf_aux_el_t
Auxiliary helper arrays for fast exterior loop computations.
Definition: external.h:115
FLT_OR_DBL exp_E_Stem(int type, int si1, int sj1, int extLoop, vrna_exp_param_t *P)
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:101
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.
int vrna_E_ext_stem(unsigned int type, int n5d, int n3d, vrna_param_t *p)
Evaluate a stem branching off the exterior loop.
Base pair stack element.
Definition: basic.h:142
Functions to deal with sets of energy parameters.
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)
FLT_OR_DBL exp_E_ExtLoop(int type, int si1, int sj1, vrna_exp_param_t *P)