RNAlib-2.4.3
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 #define VRNA_DECOMP_PAIR_ML_EXT (unsigned char)23
89 
90 #define VRNA_DECOMP_PAIR_ML_OUTSIDE (unsigned char)4
91 
104 #define VRNA_DECOMP_ML_ML_ML (unsigned char)5
105 
119 #define VRNA_DECOMP_ML_STEM (unsigned char)6
120 
134 #define VRNA_DECOMP_ML_ML (unsigned char)7
135 
150 #define VRNA_DECOMP_ML_UP (unsigned char)8
151 
166 #define VRNA_DECOMP_ML_ML_STEM (unsigned char)9
167 
182 #define VRNA_DECOMP_ML_COAXIAL (unsigned char)10
183 
198 #define VRNA_DECOMP_ML_COAXIAL_ENC (unsigned char)11
199 
214 #define VRNA_DECOMP_EXT_EXT (unsigned char)12
215 
230 #define VRNA_DECOMP_EXT_UP (unsigned char)13
231 
245 #define VRNA_DECOMP_EXT_STEM (unsigned char)14
246 
260 #define VRNA_DECOMP_EXT_EXT_EXT (unsigned char)15
261 
276 #define VRNA_DECOMP_EXT_STEM_EXT (unsigned char)16
277 
284 #define VRNA_DECOMP_EXT_STEM_OUTSIDE (unsigned char)17
285 
300 #define VRNA_DECOMP_EXT_EXT_STEM (unsigned char)18
301 
317 #define VRNA_DECOMP_EXT_EXT_STEM1 (unsigned char)19
318 
319 #define VRNA_DECOMP_EXT_STEM_EXT1 (unsigned char)20
320 
321 #define VRNA_DECOMP_EXT_L (unsigned char)21
322 #define VRNA_DECOMP_EXT_EXT_L (unsigned char)22
323 
368  const char *constraint,
369  unsigned int options);
370 
371 
372 #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: fold_compound.h:130
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...