RNAlib-2.3.1
part_func_up.h
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1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_UP_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_UP_H
3 
5 
6 #define RNA_UP_MODE_1 1U
7 #define RNA_UP_MODE_2 2U
8 #define RNA_UP_MODE_3 4U
9 
60 pu_contrib *pf_unstru(char *sequence,
61  int max_w);
62 
105 interact *pf_interact(const char *s1,
106  const char *s2,
107  pu_contrib *p_c,
108  pu_contrib *p_c2,
109  int max_w,
110  char *cstruc,
111  int incr3,
112  int incr5);
113 
117 void free_interact(interact *pin);
118 
122 int Up_plot(pu_contrib *p_c,
123  pu_contrib *p_c_sh,
124  interact *pint,
125  char *ofile,
126  int **unpaired_values,
127  char *select_contrib,
128  char *head,
129  unsigned int mode);
130 
134 pu_contrib *get_pu_contrib_struct( unsigned int n,
135  unsigned int w);
136 
141 
142 void
143 free_pu_contrib(pu_contrib *pu);
144 
149 #endif
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.
contributions to p_u
Definition: data_structures.h:237
Various data structures and pre-processor macros.
interaction data structure for RNAup
Definition: data_structures.h:249
void free_interact(interact *pin)
Frees the output of function pf_interact().
void free_pu_contrib_struct(pu_contrib *pu)
Frees the output of function pf_unstru().
pu_contrib * pf_unstru(char *sequence, int max_w)
Calculate the partition function over all unpaired regions of a maximal length.