RNAlib-2.2.0RC0
Constraining the Secondary Structure Recursions

This section covers all functions and variables related to the problem of incorporating secondary structure constraints into the folding recursions. More...

+ Collaboration diagram for Constraining the Secondary Structure Recursions:

Modules

 Hard Constraints
 
 Soft Constraints
 

Macros

#define VRNA_DECOMP_PAIR_HP   1
 Generalized constraint folding flag indicating hairpin loop decomposition step.
 
#define VRNA_DECOMP_PAIR_IL   2
 Generalized constraint folding flag indicating interior loop decomposition step.
 

Detailed Description

This section covers all functions and variables related to the problem of incorporating secondary structure constraints into the folding recursions.

Secondary Structure constraints can further be subdivided into so called Hard-Constraints and Soft-Constraints. Hard-Constraints directly influence the production rules used in the folding recursions by allowing, disallowing or enforcing certain decomposition steps. Soft-constraints on the other hand are used to change position specific contributions in the recursions by adding a bonus/penalty to certain loop configurations.