RNAlib-2.6.0b
 
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soft_special.h
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1#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_SPECIAL_H
2#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_SPECIAL_H
3
38
39
51vrna_sc_mod_read_from_jsonfile(const char *filename,
52 vrna_md_t *md);
53
54
67 vrna_md_t *md);
68
69
77void
79
80
97int
99 const char *json,
100 const unsigned int *modification_sites);
101
102
120int
122 const char *json_file,
123 const unsigned int *modification_sites);
124
125
146int
148 const vrna_sc_mod_param_t params,
149 const unsigned int *modification_sites);
150
151
164int
166 const unsigned int *modification_sites);
167
168
181int
183 const unsigned int *modification_sites);
184
185
198int
200 const unsigned int *modification_sites);
201
202
215int
217 const unsigned int *modification_sites);
218
219
232int
234 const unsigned int *modification_sites);
235
236
250int
252 const unsigned int *modification_sites);
253
254
258#endif
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:156
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:203
struct vrna_sc_mod_param_s * vrna_sc_mod_param_t
Modified base parameter data structure.
Definition: soft_special.h:37
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_purine(vrna_fold_compound_t *fc, const unsigned int *modification_sites)
Add soft constraint callbacks for Purine (a.k.a. nebularine)
int vrna_sc_mod_jsonfile(vrna_fold_compound_t *fc, const char *json_file, const unsigned int *modification_sites)
Prepare soft constraint callbacks for modified base as specified in JSON string.
int vrna_sc_mod_json(vrna_fold_compound_t *fc, const char *json, const unsigned int *modification_sites)
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)
Add soft constraint callbacks for Pseudouridine.
int vrna_sc_mod_inosine(vrna_fold_compound_t *fc, const unsigned int *modification_sites)
Add soft constraint callbacks for Inosine.
int vrna_sc_mod_m6A(vrna_fold_compound_t *fc, const unsigned int *modification_sites)
Add soft constraint callbacks for N6-methyl-adenosine (m6A)
int vrna_sc_mod(vrna_fold_compound_t *fc, const vrna_sc_mod_param_t params, const unsigned int *modification_sites)
Prepare soft constraint callbacks for modified base as specified in JSON string.
int vrna_sc_mod_dihydrouridine(vrna_fold_compound_t *fc, const unsigned int *modification_sites)
Add soft constraint callbacks for dihydrouridine.
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_7DA(vrna_fold_compound_t *fc, const unsigned int *modification_sites)
Add soft constraint callbacks for 7-deaza-adenosine (7DA)
Definition: sc_cb_intern.h:21