RNAlib-2.2.7
constraints_SHAPE.h
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1 #ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H
2 #define VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H
3 
5 
46  const double *reactivities,
47  double m,
48  double b,
49  unsigned int options);
50 
64  const char **shape_files,
65  const int *shape_file_association,
66  double m,
67  double b,
68  unsigned int options);
69 
91  const double *reactivities,
92  double b,
93  double default_value,
94  const char *shape_conversion,
95  unsigned int options);
96 
109 int vrna_sc_SHAPE_parse_method( const char *method_string,
110  char *method,
111  float *param_1,
112  float *param_2);
113 
128 int vrna_sc_SHAPE_to_pr(const char *shape_conversion,
129  double *values,
130  int length,
131  double default_value);
132 
133 #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 most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
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)
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_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...