RNAlib-2.4.5
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 
106 #define VRNA_CONSTRAINT_FILE 0
107 
114 #define VRNA_CONSTRAINT_SOFT_MFE 0
115 
122 #define VRNA_CONSTRAINT_SOFT_PF VRNA_OPTION_PF
123 
136 #define VRNA_DECOMP_PAIR_HP (unsigned char)1
137 
151 #define VRNA_DECOMP_PAIR_IL (unsigned char)2
152 
166 #define VRNA_DECOMP_PAIR_ML (unsigned char)3
167 #define VRNA_DECOMP_PAIR_ML_EXT (unsigned char)23
168 
169 #define VRNA_DECOMP_PAIR_ML_OUTSIDE (unsigned char)4
170 
183 #define VRNA_DECOMP_ML_ML_ML (unsigned char)5
184 
198 #define VRNA_DECOMP_ML_STEM (unsigned char)6
199 
213 #define VRNA_DECOMP_ML_ML (unsigned char)7
214 
229 #define VRNA_DECOMP_ML_UP (unsigned char)8
230 
245 #define VRNA_DECOMP_ML_ML_STEM (unsigned char)9
246 
261 #define VRNA_DECOMP_ML_COAXIAL (unsigned char)10
262 
277 #define VRNA_DECOMP_ML_COAXIAL_ENC (unsigned char)11
278 
293 #define VRNA_DECOMP_EXT_EXT (unsigned char)12
294 
309 #define VRNA_DECOMP_EXT_UP (unsigned char)13
310 
324 #define VRNA_DECOMP_EXT_STEM (unsigned char)14
325 
339 #define VRNA_DECOMP_EXT_EXT_EXT (unsigned char)15
340 
355 #define VRNA_DECOMP_EXT_STEM_EXT (unsigned char)16
356 
363 #define VRNA_DECOMP_EXT_STEM_OUTSIDE (unsigned char)17
364 
379 #define VRNA_DECOMP_EXT_EXT_STEM (unsigned char)18
380 
396 #define VRNA_DECOMP_EXT_EXT_STEM1 (unsigned char)19
397 
398 #define VRNA_DECOMP_EXT_STEM_EXT1 (unsigned char)20
399 
400 #define VRNA_DECOMP_EXT_L (unsigned char)21
401 #define VRNA_DECOMP_EXT_EXT_L (unsigned char)22
402 
447  const char *constraint,
448  unsigned int options);
449 
450 
451 #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:131
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...