RNAlib-2.4.14
external.h
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1 #ifndef VIENNA_RNA_PACKAGE_LOOPS_EXTERNAL_H
2 #define VIENNA_RNA_PACKAGE_LOOPS_EXTERNAL_H
3 
4 #include <ViennaRNA/datastructures/basic.h>
5 #include <ViennaRNA/fold_compound.h>
6 #include <ViennaRNA/params/basic.h>
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 
59 int
60 vrna_E_ext_stem(unsigned int type,
61  int n5d,
62  int n3d,
63  vrna_param_t *p);
64 
65 
85 int
86 vrna_E_ext_loop(vrna_fold_compound_t *fc,
87  int i,
88  int j);
89 
90 
91 int
92 vrna_E_ext_loop_5(vrna_fold_compound_t *fc);
93 
94 
95 int
96 vrna_E_ext_loop_3(vrna_fold_compound_t *fc,
97  int i);
98 
99 
100 /* End basic interface */
116 typedef struct vrna_mx_pf_aux_el_s *vrna_mx_pf_aux_el_t;
117 
118 
136 FLT_OR_DBL
137 vrna_exp_E_ext_stem(unsigned int type,
138  int n5d,
139  int n3d,
140  vrna_exp_param_t *p);
141 
142 
143 struct vrna_mx_pf_aux_el_s *
144 vrna_exp_E_ext_fast_init(vrna_fold_compound_t *fc);
145 
146 
147 void
148 vrna_exp_E_ext_fast_rotate(struct vrna_mx_pf_aux_el_s *aux_mx);
149 
150 
151 void
152 vrna_exp_E_ext_fast_free(struct vrna_mx_pf_aux_el_s *aux_mx);
153 
154 
155 FLT_OR_DBL
156 vrna_exp_E_ext_fast(vrna_fold_compound_t *fc,
157  int i,
158  int j,
159  struct vrna_mx_pf_aux_el_s *aux_mx);
160 
161 
162 void
163 vrna_exp_E_ext_fast_update(vrna_fold_compound_t *fc,
164  int j,
165  struct vrna_mx_pf_aux_el_s *aux_mx);
166 
167 
168 /* End partition function interface */
182 int
183 vrna_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 
191 int
192 vrna_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 
201 int
202 vrna_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 
268 DEPRECATED(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273  "This function is obsolete.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 
276 DEPRECATED(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 
290 DEPRECATED(FLT_OR_DBL exp_E_ExtLoop(int type,
291  int si1,
292  int sj1,
293  vrna_exp_param_t *P),
294  "Use vrna_exp_E_ext_stem() instead");
295 
296 
305 DEPRECATED(FLT_OR_DBL exp_E_Stem(int type,
306  int si1,
307  int sj1,
308  int extLoop,
309  vrna_exp_param_t *P),
310  "This function is obsolete");
311 
312 
313 #endif
314 
320 #endif
vrna_E_ext_loop
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.
FLT_OR_DBL
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
basic.h
Various data structures and pre-processor macros.
vrna_mx_pf_aux_el_t
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
exp_E_Stem
FLT_OR_DBL exp_E_Stem(int type, int si1, int sj1, int extLoop, vrna_exp_param_t *P)
vrna_exp_param_s
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:103
E_Stem
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.
vrna_E_ext_stem
int vrna_E_ext_stem(unsigned int type, int n5d, int n3d, vrna_param_t *p)
Evaluate a stem branching off the exterior loop.
vrna_bp_stack_s
Base pair stack element.
Definition: basic.h:143
basic.h
Functions to deal with sets of energy parameters.
fold_compound.h
The Basic Fold Compound API.
vrna_exp_E_ext_stem
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)
exp_E_ExtLoop
FLT_OR_DBL exp_E_ExtLoop(int type, int si1, int sj1, vrna_exp_param_t *P)