RNAlib-2.6.0a
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
24vrna_constraints_add_SHAPE(vrna_fold_compound_t *vc,
25 const char *shape_file,
26 const char *shape_method,
27 const char *shape_conversion,
28 int verbose,
29 unsigned int constraint_type);
30
31
32void
33vrna_constraints_add_SHAPE_ali(vrna_fold_compound_t *vc,
34 const char *shape_method,
35 const char **shape_files,
36 const int *shape_file_association,
37 int verbose,
38 unsigned int constraint_type);
39
40
66int
68 const double *reactivities,
69 double m,
70 double b,
71 unsigned int options);
72
73
86int
88 const char **shape_files,
89 const int *shape_file_association,
90 double m,
91 double b,
92 unsigned int options);
93
94
117int
119 const double *reactivities,
120 double b,
121 double default_value,
122 const char *shape_conversion,
123 unsigned int options);
124
125
138int
139vrna_sc_SHAPE_parse_method(const char *method_string,
140 char *method,
141 float *param_1,
142 float *param_2);
143
144
159int
160vrna_sc_SHAPE_to_pr(const char *shape_conversion,
161 double *values,
162 int length,
163 double default_value);
164
165
166#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:156