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RNAlib-2.3.4
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Energy evaluation of multibranch loops for MFE and partition function calculations. More...
Include dependency graph for multibranch_loops.h:
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Data Structures | |
| struct | vrna_mx_pf_aux_ml_t |
| Auxiliary helper arrays for fast exterior loop computations. More... | |
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 . More... | |
Energy evaluation of multibranch loops for MFE and partition function calculations.
| 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
.
| vc | The vrna_fold_compound_t filled with all relevant data for backtracking |
| i | 5' position of base pair closing the loop (will be set to 5' position of leftmost decomposed block upon successful backtracking) |
| j | 3' position of base pair closing the loop (will be set to 3' position of rightmost decomposed block upon successful backtracking) |
| k | Split position that delimits leftmost from rightmost block, [i,k] and [k+1, j], respectively. (Will be set upon successful backtracking) |
| en | The energy contribution of the substructure enclosed by |
| component1 | Type of leftmost block (1 = ML, 2 = C) |
| component2 | Type of rightmost block (1 = ML, 2 = C) |