RNAlib-2.4.10
external.h
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1 #ifndef VIENNA_RNA_PACKAGE_LOOPS_EXTERNAL_H
2 #define VIENNA_RNA_PACKAGE_LOOPS_EXTERNAL_H
3 
6 
7 #ifdef VRNA_WARN_DEPRECATED
8 # if defined(DEPRECATED)
9 # undef DEPRECATED
10 # endif
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)))
15 # else
16 # define DEPRECATED(func, msg) func
17 # endif
18 #else
19 # define DEPRECATED(func, msg) func
20 #endif
21 
58 int
59 vrna_E_ext_stem(unsigned int type,
60  int n5d,
61  int n3d,
62  vrna_param_t *p);
63 
64 
84 int
86  int i,
87  int j);
88 
89 
90 int
91 vrna_E_ext_loop_5(vrna_fold_compound_t *fc);
92 
93 
94 int
95 vrna_E_ext_loop_3(vrna_fold_compound_t *fc,
96  int i);
97 
98 
99 /* End basic interface */
115 typedef struct vrna_mx_pf_aux_el_s *vrna_mx_pf_aux_el_t;
116 
117 
136 vrna_exp_E_ext_stem(unsigned int type,
137  int n5d,
138  int n3d,
139  vrna_exp_param_t *p);
140 
141 
142 struct vrna_mx_pf_aux_el_s *
143 vrna_exp_E_ext_fast_init(vrna_fold_compound_t *fc);
144 
145 
146 void
147 vrna_exp_E_ext_fast_rotate(struct vrna_mx_pf_aux_el_s *aux_mx);
148 
149 
150 void
151 vrna_exp_E_ext_fast_free(struct vrna_mx_pf_aux_el_s *aux_mx);
152 
153 
155 vrna_exp_E_ext_fast(vrna_fold_compound_t *fc,
156  int i,
157  int j,
158  struct vrna_mx_pf_aux_el_s *aux_mx);
159 
160 
161 void
162 vrna_exp_E_ext_fast_update(vrna_fold_compound_t *fc,
163  int j,
164  struct vrna_mx_pf_aux_el_s *aux_mx);
165 
166 
167 /* End partition function interface */
181 int
182 vrna_BT_ext_loop_f5(vrna_fold_compound_t *fc,
183  int *k,
184  int *i,
185  int *j,
186  vrna_bp_stack_t *bp_stack,
187  int *stack_count);
188 
189 
190 int
191 vrna_BT_ext_loop_f3(vrna_fold_compound_t *fc,
192  int *k,
193  int maxdist,
194  int *i,
195  int *j,
196  vrna_bp_stack_t *bp_stack,
197  int *stack_count);
198 
199 
200 int
201 vrna_BT_ext_loop_f3_pp(vrna_fold_compound_t *fc,
202  int *i,
203  int maxdist);
204 
205 
210 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
211 
263 DEPRECATED(int E_Stem(int type,
264  int si1,
265  int sj1,
266  int extLoop,
267  vrna_param_t *P),
268  "This function is obsolete");
269 
270 
271 DEPRECATED(int E_ExtLoop(int type,
272  int si1,
273  int sj1,
274  vrna_param_t *P),
275  "Use vrna_E_ext_stem() instead");
276 
277 
285 DEPRECATED(FLT_OR_DBL exp_E_ExtLoop(int type,
286  int si1,
287  int sj1,
288  vrna_exp_param_t *P),
289  "Use vrna_exp_E_ext_stem() instead");
290 
291 
300 DEPRECATED(FLT_OR_DBL exp_E_Stem(int type,
301  int si1,
302  int sj1,
303  int extLoop,
304  vrna_exp_param_t *P),
305  "This function is obsolete");
306 
307 
308 #endif
309 
315 #endif
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:102
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:143
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)