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_s * | vrna_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. | |
Specialized implementations that utilize the soft constraint callback mechanism.
,