RNAlib-2.4.4
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 
5 
24 void vrna_constraints_add_SHAPE(vrna_fold_compound_t *vc,
25  const char *shape_file,
26  const char *shape_method,
27  const char *shape_conversion,
28  int verbose,
29  unsigned int constraint_type);
30 
31 void vrna_constraints_add_SHAPE_ali(vrna_fold_compound_t *vc,
32  const char *shape_method,
33  const char **shape_files,
34  const int *shape_file_association,
35  int verbose,
36  unsigned int constraint_type);
63  const double *reactivities,
64  double m,
65  double b,
66  unsigned int options);
67 
81  const char **shape_files,
82  const int *shape_file_association,
83  double m,
84  double b,
85  unsigned int options);
86 
110  const double *reactivities,
111  double b,
112  double default_value,
113  const char *shape_conversion,
114  unsigned int options);
115 
128 int vrna_sc_SHAPE_parse_method( const char *method_string,
129  char *method,
130  float *param_1,
131  float *param_2);
132 
147 int vrna_sc_SHAPE_to_pr(const char *shape_conversion,
148  double *values,
149  int length,
150  double default_value);
151 
152 #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: fold_compound.h:131
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...