RNAlib-2.2.9

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constraints.h
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1 #ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_H
2 #define VIENNA_RNA_PACKAGE_CONSTRAINTS_H
3
4 #include <ViennaRNA/data_structures.h>
5
6 /* include all structure constraint related headers */
7 #include <ViennaRNA/constraints_hard.h>
8 #include <ViennaRNA/constraints_soft.h>
9 #include <ViennaRNA/constraints_SHAPE.h>
10 #include <ViennaRNA/perturbation_fold.h>
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
352 void vrna_constraints_add(vrna_fold_compound_t *vc,
353 const char *constraint,
354 unsigned int options);
355
356 #endif
perturbation_fold.h
Find a vector of perturbation energies that minimizes the discripancies between predicted and observe...
ligand.h
Functions for incorporation of ligands binding to haipirn and interior loop motifs.
vrna_constraints_add
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.
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:424
data_structures.h
constraints_SHAPE.h
This module provides function to incorporate SHAPE reactivity data into the folding recursions by mea...
constraints_hard.h
Functions and data structures for handling of secondary structure hard constraints.
constraints_soft.h
Functions and data structures for secondary structure soft constraints.