1#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_SPECIAL_H
2#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_SPECIAL_H
52#define VRNA_SC_MOD_CHECK_FALLBACK 1
67#define VRNA_SC_MOD_CHECK_UNMOD 2
76#define VRNA_SC_MOD_SILENT 4
87#define VRNA_SC_MOD_DEFAULT (VRNA_SC_MOD_CHECK_FALLBACK | VRNA_SC_MOD_CHECK_UNMOD)
153 const unsigned int *modification_sites,
154 unsigned int options);
179 const char *json_file,
180 const unsigned int *modification_sites,
181 unsigned int options);
210 const unsigned int *modification_sites,
211 unsigned int options);
232 const unsigned int *modification_sites,
233 unsigned int options);
254 const unsigned int *modification_sites,
255 unsigned int options);
276 const unsigned int *modification_sites,
277 unsigned int options);
298 const unsigned int *modification_sites,
299 unsigned int options);
320 const unsigned int *modification_sites,
321 unsigned int options);
342 const unsigned int *modification_sites,
343 unsigned int options);
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
The data structure that contains the complete model details used throughout the calculations.
Definition model.h:245
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)
struct vrna_sc_mod_param_s * vrna_sc_mod_param_t
Modified base parameter data structure.
Definition soft_special.h:37
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)
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(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.
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.
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_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_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_inosine(vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options)
Add soft constraint callbacks for Inosine.
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.
int vrna_sc_mod_dihydrouridine(vrna_fold_compound_t *fc, const unsigned int *modification_sites, unsigned int options)
Add soft constraint callbacks for dihydrouridine.
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.
Definition sc_cb_intern.h:23