RNAlib-2.3.2
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 
62 FLT_OR_DBL exp_E_ExtLoop( int type,
63  int si1,
64  int sj1,
65  vrna_exp_param_t *P);
66 
112 int E_Stem( int type,
113  int si1,
114  int sj1,
115  int extLoop,
116  vrna_param_t *P);
117 
126 FLT_OR_DBL exp_E_Stem(int type,
127  int si1,
128  int sj1,
129  int extLoop,
130  vrna_exp_param_t *P);
131 
132 
133 int
134 E_ext_loop( int i,
135  int j,
137 
138 void
139 E_ext_loop_5( vrna_fold_compound_t *vc);
140 
141 int
142 vrna_BT_ext_loop_f5(vrna_fold_compound_t *vc,
143  int *k,
144  int *i,
145  int *j,
146  vrna_bp_stack_t *bp_stack,
147  int *stack_count);
148 
149 
151 vrna_exp_E_ext_fast_init(vrna_fold_compound_t *vc);
152 
153 
154 void
155 vrna_exp_E_ext_fast_rotate( vrna_fold_compound_t *vc,
156  vrna_mx_pf_aux_el_t *aux_mx);
157 
158 
159 void
160 vrna_exp_E_ext_fast_free( vrna_fold_compound_t *vc,
161  vrna_mx_pf_aux_el_t *aux_mx);
162 
163 
165 vrna_exp_E_ext_fast(vrna_fold_compound_t *vc,
166  int i,
167  int j,
168  vrna_mx_pf_aux_el_t *aux_mx);
169 
175 #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:454
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:55
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:99
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:222
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