RNAlib-2.3.2
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 1
58 
72 #define VRNA_DECOMP_PAIR_IL 2
73 
87 #define VRNA_DECOMP_PAIR_ML 3
88 
102 #define VRNA_DECOMP_ML_ML_ML 5
103 
117 #define VRNA_DECOMP_ML_STEM 4
118 
132 #define VRNA_DECOMP_ML_ML 6
133 
148 #define VRNA_DECOMP_ML_UP 11
149 
164 #define VRNA_DECOMP_ML_ML_STEM 20
165 
180 #define VRNA_DECOMP_ML_COAXIAL 13
181 
196 #define VRNA_DECOMP_ML_COAXIAL_ENC 22
197 
212 #define VRNA_DECOMP_EXT_EXT 9
213 
228 #define VRNA_DECOMP_EXT_UP 8
229 
243 #define VRNA_DECOMP_EXT_STEM 14
244 
258 #define VRNA_DECOMP_EXT_EXT_EXT 15
259 
274 #define VRNA_DECOMP_EXT_STEM_EXT 16
275 
282 #define VRNA_DECOMP_EXT_STEM_OUTSIDE 17
283 
298 #define VRNA_DECOMP_EXT_EXT_STEM 18
299 
315 #define VRNA_DECOMP_EXT_EXT_STEM1 19
316 
317 
318 #define VRNA_DECOMP_EXT_L 20
319 
320 
321 #define VRNA_DECOMP_EXT_EXT_L 21
322 
367  const char *constraint,
368  unsigned int options);
369 
370 #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:454
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...