RNAlib-2.4.0
constraints.h
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1 #ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_H
2 #define VIENNA_RNA_PACKAGE_CONSTRAINTS_H
3 
5 
6 /* include all structure constraint related headers */
12 
27 #define VRNA_CONSTRAINT_FILE 0
28 
35 #define VRNA_CONSTRAINT_SOFT_MFE 0
36 
43 #define VRNA_CONSTRAINT_SOFT_PF VRNA_OPTION_PF
44 
57 #define VRNA_DECOMP_PAIR_HP (unsigned char)1
58 
72 #define VRNA_DECOMP_PAIR_IL (unsigned char)2
73 
87 #define VRNA_DECOMP_PAIR_ML (unsigned char)3
88 
89 #define VRNA_DECOMP_PAIR_ML_OUTSIDE (unsigned char)4
90 
103 #define VRNA_DECOMP_ML_ML_ML (unsigned char)5
104 
118 #define VRNA_DECOMP_ML_STEM (unsigned char)6
119 
133 #define VRNA_DECOMP_ML_ML (unsigned char)7
134 
149 #define VRNA_DECOMP_ML_UP (unsigned char)8
150 
165 #define VRNA_DECOMP_ML_ML_STEM (unsigned char)9
166 
181 #define VRNA_DECOMP_ML_COAXIAL (unsigned char)10
182 
197 #define VRNA_DECOMP_ML_COAXIAL_ENC (unsigned char)11
198 
213 #define VRNA_DECOMP_EXT_EXT (unsigned char)12
214 
229 #define VRNA_DECOMP_EXT_UP (unsigned char)13
230 
244 #define VRNA_DECOMP_EXT_STEM (unsigned char)14
245 
259 #define VRNA_DECOMP_EXT_EXT_EXT (unsigned char)15
260 
275 #define VRNA_DECOMP_EXT_STEM_EXT (unsigned char)16
276 
283 #define VRNA_DECOMP_EXT_STEM_OUTSIDE (unsigned char)17
284 
299 #define VRNA_DECOMP_EXT_EXT_STEM (unsigned char)18
300 
316 #define VRNA_DECOMP_EXT_EXT_STEM1 (unsigned char)19
317 
318 #define VRNA_DECOMP_EXT_STEM_EXT1 (unsigned char)20
319 
320 #define VRNA_DECOMP_EXT_L (unsigned char)21
321 #define VRNA_DECOMP_EXT_EXT_L (unsigned char)22
322 
367  const char *constraint,
368  unsigned int options);
369 
370 
371 #endif
Find a vector of perturbation energies that minimizes the discripancies between predicted and observe...
void vrna_constraints_add(vrna_fold_compound_t *vc, const char *constraint, unsigned int options)
Add constraints to a vrna_fold_compound_t data structure.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:463
Various data structures and pre-processor macros.
This module provides function to incorporate SHAPE reactivity data into the folding recursions by mea...
Functions and data structures for handling of secondary structure hard constraints.
Functions and data structures for secondary structure soft constraints.
Functions for incorporation of ligands binding to hairpin and interior loop motifs using the soft con...