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constraints_SHAPE.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H
2 #define VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H
3
4 #include <ViennaRNA/data_structures.h>
5
45 int vrna_sc_add_SHAPE_deigan( vrna_fold_compound_t *vc,
46 const double *reactivities,
47 double m,
48 double b,
49 unsigned int options);
50
63 int vrna_sc_add_SHAPE_deigan_ali( vrna_fold_compound_t *vc,
64 const char **shape_files,
65 const int *shape_file_association,
66 double m,
67 double b,
68 unsigned int options);
69
92 int vrna_sc_add_SHAPE_zarringhalam( vrna_fold_compound_t *vc,
93 const double *reactivities,
94 double b,
95 double default_value,
96 const char *shape_conversion,
97 unsigned int options);
98
111 int vrna_sc_SHAPE_parse_method( const char *method_string,
112 char *method,
113 float *param_1,
114 float *param_2);
115
130 int vrna_sc_SHAPE_to_pr(const char *shape_conversion,
131 double *values,
132 int length,
133 double default_value);
134
135 #endif
vrna_sc_SHAPE_parse_method
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 ...
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:424
vrna_sc_SHAPE_to_pr
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.
data_structures.h
vrna_sc_add_SHAPE_zarringhalam
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)
vrna_sc_add_SHAPE_deigan
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)
vrna_sc_add_SHAPE_deigan_ali
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...