RNAlib-2.2.0c
vrna_hcT Struct Reference

The hard constraints data structure. More...

Data Fields

char * matrix
 Upper triangular matrix encoding where a base pair or unpaired nucleotide is allowed.
 
int * up_ext
 A linear array that holds the number of allowed unpaired nucleotides in an exterior loop.
 
int * up_hp
 A linear array that holds the number of allowed unpaired nucleotides in a hairpin loop.
 
int * up_int
 A linear array that holds the number of allowed unpaired nucleotides in an interior loop.
 
int * up_ml
 A linear array that holds the number of allowed unpaired nucleotides in a multi branched loop.
 

Detailed Description

The hard constraints data structure.

The content of this data structure determines the decomposition pattern used in the folding recursions. Attribute 'matrix' is used as source for the branching pattern of the decompositions during all folding recursions. Any entry in matrix[i,j] consists of the 6 LSB that allows to distinguish the following types of base pairs:

The four linear arrays 'up_xxx' provide the number of available unpaired nucleotides (including position i) 3' of each position in the sequence.

See Also
get_hard_constraints(), vrna_hc_free(), VRNA_HC_CONTEXT_EXT_LOOP, VRNA_HC_CONTEXT_HP_LOOP, VRNA_HC_CONTEXT_INT_LOOP, #VRNA_HC_CONTEXT_EXT_LOOP_ENC, VRNA_HC_CONTEXT_MB_LOOP, VRNA_HC_CONTEXT_MB_LOOP_ENC

The documentation for this struct was generated from the following file: