RNAlib-2.5.1
SHAPE.h
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1#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H
2#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H
3
5
23void vrna_constraints_add_SHAPE(vrna_fold_compound_t *vc,
24 const char *shape_file,
25 const char *shape_method,
26 const char *shape_conversion,
27 int verbose,
28 unsigned int constraint_type);
29
30void vrna_constraints_add_SHAPE_ali(vrna_fold_compound_t *vc,
31 const char *shape_method,
32 const char **shape_files,
33 const int *shape_file_association,
34 int verbose,
35 unsigned int constraint_type);
62 const double *reactivities,
63 double m,
64 double b,
65 unsigned int options);
66
80 const char **shape_files,
81 const int *shape_file_association,
82 double m,
83 double b,
84 unsigned int options);
85
109 const double *reactivities,
110 double b,
111 double default_value,
112 const char *shape_conversion,
113 unsigned int options);
114
127int vrna_sc_SHAPE_parse_method( const char *method_string,
128 char *method,
129 float *param_1,
130 float *param_2);
131
146int vrna_sc_SHAPE_to_pr(const char *shape_conversion,
147 double *values,
148 int length,
149 double default_value);
150
151#endif
int vrna_sc_SHAPE_parse_method(const char *method_string, char *method, float *param_1, float *param_2)
Parse a character string and extract the encoded SHAPE reactivity conversion method and possibly the ...
The Basic Fold Compound API.
int vrna_sc_add_SHAPE_deigan_ali(vrna_fold_compound_t *vc, const char **shape_files, const int *shape_file_association, double m, double b, unsigned int options)
Add SHAPE reactivity data from files as soft constraints for consensus structure prediction (Deigan e...
int vrna_sc_add_SHAPE_deigan(vrna_fold_compound_t *vc, const double *reactivities, double m, double b, unsigned int options)
Add SHAPE reactivity data as soft constraints (Deigan et al. method)
int vrna_sc_SHAPE_to_pr(const char *shape_conversion, double *values, int length, double default_value)
Convert SHAPE reactivity values to probabilities for being unpaired.
int vrna_sc_add_SHAPE_zarringhalam(vrna_fold_compound_t *vc, const double *reactivities, double b, double default_value, const char *shape_conversion, unsigned int options)
Add SHAPE reactivity data as soft constraints (Zarringhalam et al. method)
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148