RNAlib-2.4.0
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 
25 typedef struct {
26  FLT_OR_DBL *qq;
27  FLT_OR_DBL *qq1;
28 
29  int qqu_size;
30  FLT_OR_DBL **qqu;
32 
33 
52 int E_ExtLoop(int type,
53  int si1,
54  int sj1,
55  vrna_param_t *P);
56 
57 
63 FLT_OR_DBL exp_E_ExtLoop(int type,
64  int si1,
65  int sj1,
66  vrna_exp_param_t *P);
67 
68 
114 int E_Stem(int type,
115  int si1,
116  int sj1,
117  int extLoop,
118  vrna_param_t *P);
119 
120 
129 FLT_OR_DBL exp_E_Stem(int type,
130  int si1,
131  int sj1,
132  int extLoop,
133  vrna_exp_param_t *P);
134 
135 
136 int
137 E_ext_loop(int i,
138  int j,
140 
141 
142 int
143 vrna_E_ext_loop_5(vrna_fold_compound_t *vc);
144 
145 
146 int
147 vrna_E_ext_loop_3(vrna_fold_compound_t *fc,
148  int i);
149 
150 
151 int
152 vrna_BT_ext_loop_f5(vrna_fold_compound_t *vc,
153  int *k,
154  int *i,
155  int *j,
156  vrna_bp_stack_t *bp_stack,
157  int *stack_count);
158 
159 
160 int
161 vrna_BT_ext_loop_f3(vrna_fold_compound_t *vc,
162  int *k,
163  int maxdist,
164  int *i,
165  int *j,
166  vrna_bp_stack_t *bp_stack,
167  int *stack_count);
168 
169 
170 int
171 vrna_BT_ext_loop_f3_pp(vrna_fold_compound_t *fc,
172  int *i,
173  int maxdist);
174 
175 
177 vrna_exp_E_ext_fast_init(vrna_fold_compound_t *vc);
178 
179 
180 void
181 vrna_exp_E_ext_fast_rotate(vrna_fold_compound_t *vc,
182  vrna_mx_pf_aux_el_t *aux_mx);
183 
184 
185 void
186 vrna_exp_E_ext_fast_free(vrna_fold_compound_t *vc,
187  vrna_mx_pf_aux_el_t *aux_mx);
188 
189 
191 vrna_exp_E_ext_fast(vrna_fold_compound_t *vc,
192  int i,
193  int j,
194  vrna_mx_pf_aux_el_t *aux_mx);
195 
196 
202 #endif
FLT_OR_DBL exp_E_Stem(int type, int si1, int sj1, int extLoop, vrna_exp_param_t *P)
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:48
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:463
int E_Stem(int type, int si1, int sj1, int extLoop, vrna_param_t *P)
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:57
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 exp_E_ExtLoop(int type, int si1, int sj1, vrna_exp_param_t *P)
Base pair stack element.
Definition: data_structures.h:229
int E_ExtLoop(int type, int si1, int sj1, vrna_param_t *P)
Auxiliary helper arrays for fast exterior loop computations.
Definition: exterior_loops.h:25