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part_func_up.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_UP_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_UP_H
3
4 #include <ViennaRNA/data_structures.h>
5
6 #define RNA_UP_MODE_1 1U
7 #define RNA_UP_MODE_2 2U
8 #define RNA_UP_MODE_3 4U
9
55 pu_contrib *pf_unstru(char *sequence,
56 int max_w);
57
100 interact *pf_interact(const char *s1,
101 const char *s2,
102 pu_contrib *p_c,
103 pu_contrib *p_c2,
104 int max_w,
105 char *cstruc,
106 int incr3,
107 int incr5);
108
112 void free_interact(interact *pin);
113
117 int Up_plot(pu_contrib *p_c,
118 pu_contrib *p_c_sh,
119 interact *pint,
120 char *ofile,
121 int **unpaired_values,
122 char *select_contrib,
123 char *head,
124 unsigned int mode);
125
129 pu_contrib *get_pu_contrib_struct( unsigned int n,
130 unsigned int w);
131
135 void free_pu_contrib_struct(pu_contrib *pu);
136
137 void
138 free_pu_contrib(pu_contrib *pu);
139
144 #endif
pf_interact
interact * pf_interact(const char *s1, const char *s2, pu_contrib *p_c, pu_contrib *p_c2, int max_w, char *cstruc, int incr3, int incr5)
Calculates the probability of a local interaction between two sequences.
pu_contrib
contributions to p_u
Definition: data_structures.h:207
data_structures.h
interact
interaction data structure for RNAup
Definition: data_structures.h:219
free_interact
void free_interact(interact *pin)
Frees the output of function pf_interact().
free_pu_contrib_struct
void free_pu_contrib_struct(pu_contrib *pu)
Frees the output of function pf_unstru().
pf_unstru
pu_contrib * pf_unstru(char *sequence, int max_w)
Calculate the partition function over all unpaired regions of a maximal length.