RNAlib-2.3.1

Energy evaluation of multibranch loops for MFE and partition function calculations. More...

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Functions

int E_mb_loop_stack (int i, int j, vrna_fold_compound_t *vc)
 Evaluate energy of a multi branch helices stacking onto closing pair (i,j) More...
 
int vrna_BT_mb_loop (vrna_fold_compound_t *vc, int *i, int *j, int *k, int en, int *component1, int *component2)
 Backtrack the decomposition of a multi branch loop closed by $ (i,j) $. More...
 

Detailed Description

Energy evaluation of multibranch loops for MFE and partition function calculations.

Function Documentation

int E_mb_loop_stack ( int  i,
int  j,
vrna_fold_compound_t vc 
)

Evaluate energy of a multi branch helices stacking onto closing pair (i,j)

Computes total free energy for coaxial stacking of (i.j) with (i+1.k) or (k+1.j-1)

int vrna_BT_mb_loop ( vrna_fold_compound_t vc,
int *  i,
int *  j,
int *  k,
int  en,
int *  component1,
int *  component2 
)

Backtrack the decomposition of a multi branch loop closed by $ (i,j) $.

Parameters
vcThe vrna_fold_compound_t filled with all relevant data for backtracking
i5' position of base pair closing the loop (will be set to 5' position of leftmost decomposed block upon successful backtracking)
j3' position of base pair closing the loop (will be set to 3' position of rightmost decomposed block upon successful backtracking)
kSplit position that delimits leftmost from rightmost block, [i,k] and [k+1, j], respectively. (Will be set upon successful backtracking)
enThe energy contribution of the substructure enclosed by $ (i,j) $
component1Type of leftmost block (1 = ML, 2 = C)
component2Type of rightmost block (1 = ML, 2 = C)
Returns
1, if backtracking succeeded, 0 otherwise.