RNAlib-2.5.1
external.h
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1#ifndef VIENNA_RNA_PACKAGE_LOOPS_EXTERNAL_H
2#define VIENNA_RNA_PACKAGE_LOOPS_EXTERNAL_H
3
7
8#ifdef VRNA_WARN_DEPRECATED
9# if defined(DEPRECATED)
10# undef DEPRECATED
11# endif
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)))
16# else
17# define DEPRECATED(func, msg) func
18# endif
19#else
20# define DEPRECATED(func, msg) func
21#endif
22
59int
60vrna_E_ext_stem(unsigned int type,
61 int n5d,
62 int n3d,
63 vrna_param_t *p);
64
65
85int
87 int i,
88 int j);
89
90
91int
92vrna_E_ext_loop_5(vrna_fold_compound_t *fc);
93
94
95int
96vrna_E_ext_loop_3(vrna_fold_compound_t *fc,
97 int i);
98
99
100/* End basic interface */
116typedef struct vrna_mx_pf_aux_el_s *vrna_mx_pf_aux_el_t;
117
118
137vrna_exp_E_ext_stem(unsigned int type,
138 int n5d,
139 int n3d,
141
142
144vrna_exp_E_ext_fast_init(vrna_fold_compound_t *fc);
145
146
147void
148vrna_exp_E_ext_fast_rotate(vrna_mx_pf_aux_el_t aux_mx);
149
150
151void
152vrna_exp_E_ext_fast_free(vrna_mx_pf_aux_el_t aux_mx);
153
154
156vrna_exp_E_ext_fast(vrna_fold_compound_t *fc,
157 int i,
158 int j,
159 vrna_mx_pf_aux_el_t aux_mx);
160
161
162void
163vrna_exp_E_ext_fast_update(vrna_fold_compound_t *fc,
164 int j,
165 vrna_mx_pf_aux_el_t aux_mx);
166
167
168/* End partition function interface */
182int
183vrna_BT_ext_loop_f5(vrna_fold_compound_t *fc,
184 int *k,
185 int *i,
186 int *j,
187 vrna_bp_stack_t *bp_stack,
188 int *stack_count);
189
190
191int
192vrna_BT_ext_loop_f3(vrna_fold_compound_t *fc,
193 int *k,
194 int maxdist,
195 int *i,
196 int *j,
197 vrna_bp_stack_t *bp_stack,
198 int *stack_count);
199
200
201int
202vrna_BT_ext_loop_f3_pp(vrna_fold_compound_t *fc,
203 int *i,
204 int maxdist);
205
206
211#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
212
268DEPRECATED(int E_Stem(int type,
269 int si1,
270 int sj1,
271 int extLoop,
272 vrna_param_t *P),
273 "This function is obsolete. Use vrna_E_ext_stem() or E_MLstem() instead");
274
275
276DEPRECATED(int E_ExtLoop(int type,
277 int si1,
278 int sj1,
279 vrna_param_t *P),
280 "Use vrna_E_ext_stem() instead");
281
282
290DEPRECATED(FLT_OR_DBL exp_E_ExtLoop(int type,
291 int si1,
292 int sj1,
294 "Use vrna_exp_E_ext_stem() instead");
295
296
305DEPRECATED(FLT_OR_DBL exp_E_Stem(int type,
306 int si1,
307 int sj1,
308 int extLoop,
310 "This function is obsolete");
311
312
313#endif
314
320#endif
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.