RNAlib-2.6.3
 
Loading...
Searching...
No Matches

Specialized implementations that utilize the soft constraint callback mechanism. More...

Go to the source code of this file.

Macros

#define VRNA_SC_MOD_CHECK_FALLBACK   1
 Check for sequence positions whether they resemble the fallback base.
 
#define VRNA_SC_MOD_CHECK_UNMOD   2
 Check for sequence positions whether they resemble the unmodified base.
 
#define VRNA_SC_MOD_SILENT   4
 Do not produce any warnings within the vrna_sc_mod*() functions.
 
#define VRNA_SC_MOD_DEFAULT   (VRNA_SC_MOD_CHECK_FALLBACK | VRNA_SC_MOD_CHECK_UNMOD)
 Default settings for the vrna_sc_mod*() functions.
 

Typedefs

typedef struct vrna_sc_mod_param_svrna_sc_mod_param_t
 Modified base parameter data structure.
 

Functions

vrna_sc_mod_param_t vrna_sc_mod_read_from_jsonfile (const char *filename, vrna_md_t *md)
 Parse and extract energy parameters for a modified base from a JSON file.
 
vrna_sc_mod_param_t vrna_sc_mod_read_from_json (const char *json, vrna_md_t *md)
 Parse and extract energy parameters for a modified base from a JSON string.
 
void vrna_sc_mod_parameters_free (vrna_sc_mod_param_t params)
 Release memory occupied by a modified base parameter data structure.
 
int vrna_sc_mod_json (vrna_fold_compound_t *fc, const char *json, const unsigned int *modification_sites, unsigned int options)
 Prepare soft constraint callbacks for modified base as specified in JSON string.
 
int vrna_sc_mod_jsonfile (vrna_fold_compound_t *fc, const char *json_file, const unsigned int *modification_sites, unsigned int options)
 Prepare soft constraint callbacks for modified base as specified in JSON string.
 
int vrna_sc_mod (vrna_fold_compound_t *fc, const vrna_sc_mod_param_t params, const unsigned int *modification_sites, unsigned int options)
 Prepare soft constraint callbacks for modified base as specified in JSON string.
 
int vrna_sc_mod_m6A (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options)
 Add soft constraint callbacks for N6-methyl-adenosine (m6A)
 
int vrna_sc_mod_pseudouridine (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options)
 Add soft constraint callbacks for Pseudouridine.
 
int vrna_sc_mod_inosine (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options)
 Add soft constraint callbacks for Inosine.
 
int vrna_sc_mod_7DA (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options)
 Add soft constraint callbacks for 7-deaza-adenosine (7DA)
 
int vrna_sc_mod_purine (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options)
 Add soft constraint callbacks for Purine (a.k.a. nebularine)
 
int vrna_sc_mod_dihydrouridine (vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options)
 Add soft constraint callbacks for dihydrouridine.
 

Detailed Description

Specialized implementations that utilize the soft constraint callback mechanism.

,