RNAlib-2.4.3
constraints_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/data_structures.h>
5 
14 void vrna_constraints_add_SHAPE(vrna_fold_compound_t *vc,
15  const char *shape_file,
16  const char *shape_method,
17  const char *shape_conversion,
18  int verbose,
19  unsigned int constraint_type);
20 
21 void vrna_constraints_add_SHAPE_ali(vrna_fold_compound_t *vc,
22  const char *shape_method,
23  const char **shape_files,
24  const int *shape_file_association,
25  int verbose,
26  unsigned int constraint_type);
52 int vrna_sc_add_SHAPE_deigan( vrna_fold_compound_t *vc,
53  const double *reactivities,
54  double m,
55  double b,
56  unsigned int options);
57 
70 int vrna_sc_add_SHAPE_deigan_ali( vrna_fold_compound_t *vc,
71  const char **shape_files,
72  const int *shape_file_association,
73  double m,
74  double b,
75  unsigned int options);
76 
99 int vrna_sc_add_SHAPE_zarringhalam( vrna_fold_compound_t *vc,
100  const double *reactivities,
101  double b,
102  double default_value,
103  const char *shape_conversion,
104  unsigned int options);
105 
118 int vrna_sc_SHAPE_parse_method( const char *method_string,
119  char *method,
120  float *param_1,
121  float *param_2);
122 
137 int vrna_sc_SHAPE_to_pr(const char *shape_conversion,
138  double *values,
139  int length,
140  double default_value);
141 
142 #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: fold_compound.h:130
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
Various data structures and pre-processor macros.
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...