part_func_up.h
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#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_UP_H
#define VIENNA_RNA_PACKAGE_PART_FUNC_UP_H
#include <ViennaRNA/data_structures.h>
#define RNA_UP_MODE_1 1U
#define RNA_UP_MODE_2 2U
#define RNA_UP_MODE_3 4U
pu_contrib *pf_unstru(char *sequence,
int max_w);
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);
void free_interact(interact *pin);
int Up_plot(pu_contrib *p_c,
pu_contrib *p_c_sh,
interact *pint,
char *ofile,
int **unpaired_values,
char *select_contrib,
char *head,
unsigned int mode);
pu_contrib *get_pu_contrib_struct( unsigned int n,
unsigned int w);
void free_pu_contrib_struct(pu_contrib *pu);
void
free_pu_contrib(pu_contrib *pu);
#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.