RNAlib-2.4.4
exterior_loops.h
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1 #ifndef VIENNA_RNA_PACKAGE_EXTERIOR_LOOPS_H
2 #define VIENNA_RNA_PACKAGE_EXTERIOR_LOOPS_H
3 
5 #include <ViennaRNA/params.h>
6 
7 #ifdef VRNA_WARN_DEPRECATED
8 # if defined(__clang__)
9 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
10 # elif defined(__GNUC__)
11 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
12 # else
13 # define DEPRECATED(func, msg) func
14 # endif
15 #else
16 # define DEPRECATED(func, msg) func
17 #endif
18 
37 typedef struct {
38  FLT_OR_DBL *qq;
39  FLT_OR_DBL *qq1;
40 
41  int qqu_size;
42  FLT_OR_DBL **qqu;
44 
45 
63 int
64 vrna_E_ext_stem(unsigned int type,
65  int n5d,
66  int n3d,
67  vrna_param_t *p);
68 
69 
88 vrna_exp_E_ext_stem(unsigned int type,
89  int n5d,
90  int n3d,
91  vrna_exp_param_t *p);
92 
93 
94 int
95 vrna_E_ext_loop(vrna_fold_compound_t *vc,
96  int i,
97  int j);
98 
99 
100 int
101 vrna_E_ext_loop_5(vrna_fold_compound_t *vc);
102 
103 
104 int
105 vrna_E_ext_loop_3(vrna_fold_compound_t *fc,
106  int i);
107 
108 
109 int
110 vrna_BT_ext_loop_f5(vrna_fold_compound_t *vc,
111  int *k,
112  int *i,
113  int *j,
114  vrna_bp_stack_t *bp_stack,
115  int *stack_count);
116 
117 
118 int
119 vrna_BT_ext_loop_f3(vrna_fold_compound_t *vc,
120  int *k,
121  int maxdist,
122  int *i,
123  int *j,
124  vrna_bp_stack_t *bp_stack,
125  int *stack_count);
126 
127 
128 int
129 vrna_BT_ext_loop_f3_pp(vrna_fold_compound_t *fc,
130  int *i,
131  int maxdist);
132 
133 
135 vrna_exp_E_ext_fast_init(vrna_fold_compound_t *vc);
136 
137 
138 void
139 vrna_exp_E_ext_fast_rotate(vrna_fold_compound_t *vc,
140  vrna_mx_pf_aux_el_t *aux_mx);
141 
142 
143 void
144 vrna_exp_E_ext_fast_free(vrna_fold_compound_t *vc,
145  vrna_mx_pf_aux_el_t *aux_mx);
146 
147 
149 vrna_exp_E_ext_fast(vrna_fold_compound_t *vc,
150  int i,
151  int j,
152  vrna_mx_pf_aux_el_t *aux_mx);
153 
154 
155 void
156 vrna_exp_E_ext_fast_update(vrna_fold_compound_t *fc,
157  int j,
158  vrna_mx_pf_aux_el_t *aux_mx);
159 
160 
161 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
162 
209 DEPRECATED(int E_Stem(int type,
210  int si1,
211  int sj1,
212  int extLoop,
213  vrna_param_t *P),
214  "This function is obsolete");
215 
216 
217 DEPRECATED(int E_ExtLoop(int type,
218  int si1,
219  int sj1,
220  vrna_param_t *P),
221  "Use vrna_E_ext_stem() instead");
222 
223 
231 DEPRECATED(FLT_OR_DBL exp_E_ExtLoop(int type,
232  int si1,
233  int sj1,
234  vrna_exp_param_t *P),
235  "Use vrna_exp_E_ext_stem() instead");
236 
237 
246 DEPRECATED(FLT_OR_DBL exp_E_Stem(int type,
247  int si1,
248  int sj1,
249  int extLoop,
250  vrna_exp_param_t *P),
251  "This function is obsolete");
252 
253 
254 #endif
255 
261 #endif
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:131
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:56
FLT_OR_DBL exp_E_Stem(int type, int si1, int sj1, int extLoop, vrna_exp_param_t *P)
Various data structures and pre-processor macros.
Functions to deal with sets of energy parameters.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:101
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)
Base pair stack element.
Definition: data_structures.h:141
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_ExtLoop(int type, int si1, int sj1, vrna_exp_param_t *P)
int vrna_E_ext_stem(unsigned int type, int n5d, int n3d, vrna_param_t *p)
Evaluate a stem branching off the exterior loop.
Auxiliary helper arrays for fast exterior loop computations.
Definition: exterior_loops.h:37