RNAlib-2.2.7
constraints.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_H
2 #define VIENNA_RNA_PACKAGE_CONSTRAINTS_H
3 
5 
6 /* include all structure constraint related headers */
11 #include <ViennaRNA/ligand.h>
12 
35 #define VRNA_CONSTRAINT_FILE 0
36 
43 #define VRNA_CONSTRAINT_SOFT_MFE 0
44 
51 #define VRNA_CONSTRAINT_SOFT_PF VRNA_OPTION_PF
52 
65 #define VRNA_DECOMP_PAIR_HP 1
66 
80 #define VRNA_DECOMP_PAIR_IL 2
81 
95 #define VRNA_DECOMP_PAIR_ML 3
96 
110 #define VRNA_DECOMP_ML_ML_ML 5
111 
125 #define VRNA_DECOMP_ML_STEM 4
126 
140 #define VRNA_DECOMP_ML_ML 6
141 
156 #define VRNA_DECOMP_ML_UP 11
157 
172 #define VRNA_DECOMP_ML_ML_STEM 20
173 
188 #define VRNA_DECOMP_ML_COAXIAL 13
189 
204 #define VRNA_DECOMP_EXT_EXT 9
205 
220 #define VRNA_DECOMP_EXT_UP 8
221 
235 #define VRNA_DECOMP_EXT_STEM 14
236 
250 #define VRNA_DECOMP_EXT_EXT_EXT 15
251 
266 #define VRNA_DECOMP_EXT_STEM_EXT 16
267 
274 #define VRNA_DECOMP_EXT_STEM_OUTSIDE 17
275 
290 #define VRNA_DECOMP_EXT_EXT_STEM 18
291 
307 #define VRNA_DECOMP_EXT_EXT_STEM1 19
308 
353  const char *constraint,
354  unsigned int options);
355 
356 #endif
Find a vector of perturbation energies that minimizes the discripancies between predicted and observe...
Functions for incorporation of ligands binding to haipirn and interior loop motifs.
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:390
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.