RNAlib-2.6.3
 
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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 *fc,
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 *fc,
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
70int
72 const double *reactivities,
73 double m,
74 double b,
75 unsigned int options);
76
77
90int
92 const char **shape_files,
93 const int *shape_file_association,
94 double m,
95 double b,
96 unsigned int options);
97
98
126int
128 const double *reactivities,
129 double b,
130 double default_value,
131 const char *shape_conversion,
132 unsigned int options);
133
134
147int
148vrna_sc_SHAPE_parse_method(const char *method_string,
149 char *method,
150 float *param_1,
151 float *param_2);
152
153
169int
170vrna_sc_SHAPE_to_pr(const char *shape_conversion,
171 double *values,
172 int length,
173 double default_value);
174
175
176#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 *fc, 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_zarringhalam(vrna_fold_compound_t *fc, 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)
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_deigan(vrna_fold_compound_t *fc, const double *reactivities, double m, double b, unsigned int options)
Add SHAPE reactivity data as soft constraints (Deigan et al. method)
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168