1 #ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_H
2 #define VIENNA_RNA_PACKAGE_CONSTRAINTS_H
27 #define VRNA_CONSTRAINT_FILE 0
35 #define VRNA_CONSTRAINT_SOFT_MFE 0
43 #define VRNA_CONSTRAINT_SOFT_PF VRNA_OPTION_PF
57 #define VRNA_DECOMP_PAIR_HP 1
72 #define VRNA_DECOMP_PAIR_IL 2
87 #define VRNA_DECOMP_PAIR_ML 3
102 #define VRNA_DECOMP_ML_ML_ML 5
117 #define VRNA_DECOMP_ML_STEM 4
132 #define VRNA_DECOMP_ML_ML 6
148 #define VRNA_DECOMP_ML_UP 11
164 #define VRNA_DECOMP_ML_ML_STEM 20
180 #define VRNA_DECOMP_ML_COAXIAL 13
196 #define VRNA_DECOMP_EXT_EXT 9
212 #define VRNA_DECOMP_EXT_UP 8
227 #define VRNA_DECOMP_EXT_STEM 14
242 #define VRNA_DECOMP_EXT_EXT_EXT 15
258 #define VRNA_DECOMP_EXT_STEM_EXT 16
266 #define VRNA_DECOMP_EXT_STEM_OUTSIDE 17
282 #define VRNA_DECOMP_EXT_EXT_STEM 18
299 #define VRNA_DECOMP_EXT_EXT_STEM1 19
302 #define VRNA_DECOMP_EXT_L 20
305 #define VRNA_DECOMP_EXT_EXT_L 21
351 const char *constraint,
352 unsigned int options);
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:397
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...