RNAlib-2.2.0-RC2
|
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_fold_compound. More...
Data Fields | |
Common fields for MFE matrices | |
vrna_mx_t | type |
unsigned int | length |
Length of the sequence, therefore an indicator of the size of the DP matrices. | |
Default DP matrices | |
int * | c |
Energy array, given that i-j pair. | |
int * | f5 |
Energy of 5' end. | |
int * | f3 |
Energy of 3' end. | |
int * | fc |
Energy from i to cutpoint (and vice versa if i>cut) | |
int * | fML |
Multi-loop auxiliary energy array. | |
int * | fM1 |
Second ML array, only for unique multibrnach loop decomposition. | |
int * | fM2 |
Energy for a multibranch loop region with exactly two stems, extending to 3' end. | |
int * | ggg |
Energies of g-quadruplexes. | |
int | Fc |
Minimum Free Energy of entire circular RNA. | |
int | FcH |
int | FcI |
int | FcM |
Distance Class DP matrices | |
int *** | E_F5 |
int ** | l_min_F5 |
int ** | l_max_F5 |
int * | k_min_F5 |
int * | k_max_F5 |
int *** | E_F3 |
int ** | l_min_F3 |
int ** | l_max_F3 |
int * | k_min_F3 |
int * | k_max_F3 |
int *** | E_C |
int ** | l_min_C |
int ** | l_max_C |
int * | k_min_C |
int * | k_max_C |
int *** | E_M |
int ** | l_min_M |
int ** | l_max_M |
int * | k_min_M |
int * | k_max_M |
int *** | E_M1 |
int ** | l_min_M1 |
int ** | l_max_M1 |
int * | k_min_M1 |
int * | k_max_M1 |
int *** | E_M2 |
int ** | l_min_M2 |
int ** | l_max_M2 |
int * | k_min_M2 |
int * | k_max_M2 |
int ** | E_Fc |
int * | l_min_Fc |
int * | l_max_Fc |
int | k_min_Fc |
int | k_max_Fc |
int ** | E_FcH |
int * | l_min_FcH |
int * | l_max_FcH |
int | k_min_FcH |
int | k_max_FcH |
int ** | E_FcI |
int * | l_min_FcI |
int * | l_max_FcI |
int | k_min_FcI |
int | k_max_FcI |
int ** | E_FcM |
int * | l_min_FcM |
int * | l_max_FcM |
int | k_min_FcM |
int | k_max_FcM |
int * | E_F5_rem |
int * | E_F3_rem |
int * | E_C_rem |
int * | E_M_rem |
int * | E_M1_rem |
int * | E_M2_rem |
int | E_Fc_rem |
int | E_FcH_rem |
int | E_FcI_rem |
int | E_FcM_rem |
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_fold_compound.