RNAlib-2.4.14
SHAPE.h
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1 #ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H
2 #define VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H
3 
4 #include <ViennaRNA/fold_compound.h>
5 
23 void vrna_constraints_add_SHAPE(vrna_fold_compound_t *vc,
24  const char *shape_file,
25  const char *shape_method,
26  const char *shape_conversion,
27  int verbose,
28  unsigned int constraint_type);
29 
30 void vrna_constraints_add_SHAPE_ali(vrna_fold_compound_t *vc,
31  const char *shape_method,
32  const char **shape_files,
33  const int *shape_file_association,
34  int verbose,
35  unsigned int constraint_type);
61 int vrna_sc_add_SHAPE_deigan( vrna_fold_compound_t *vc,
62  const double *reactivities,
63  double m,
64  double b,
65  unsigned int options);
66 
79 int vrna_sc_add_SHAPE_deigan_ali( vrna_fold_compound_t *vc,
80  const char **shape_files,
81  const int *shape_file_association,
82  double m,
83  double b,
84  unsigned int options);
85 
108 int vrna_sc_add_SHAPE_zarringhalam( vrna_fold_compound_t *vc,
109  const double *reactivities,
110  double b,
111  double default_value,
112  const char *shape_conversion,
113  unsigned int options);
114 
127 int vrna_sc_SHAPE_parse_method( const char *method_string,
128  char *method,
129  float *param_1,
130  float *param_2);
131 
146 int vrna_sc_SHAPE_to_pr(const char *shape_conversion,
147  double *values,
148  int length,
149  double default_value);
150 
151 #endif
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
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.
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_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_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...
fold_compound.h
The Basic Fold Compound API.