RNAlib-2.2.5
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 
40  const double *reactivities,
41  double m,
42  double b,
43  unsigned int options);
44 
58  const char **shape_files,
59  const int *shape_file_association,
60  double m,
61  double b,
62  unsigned int options);
63 
85  const double *reactivities,
86  double b,
87  double default_value,
88  const char *shape_conversion,
89  unsigned int options);
90 
103 int vrna_sc_SHAPE_parse_method( const char *method_string,
104  char *method,
105  float *param_1,
106  float *param_2);
107 
122 int vrna_sc_SHAPE_to_pr(const char *shape_conversion,
123  double *values,
124  int length,
125  double default_value);
126 
127 #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:397
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.
Various data structures and pre-processor macros.
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...