struct vrna_mx_mfe_s

#include <ViennaRNA/dp_matrices.h>

Overview

Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_fold_compound_t . More…

// fields

vrna_mx_type_e type
unsigned int length
int* c
int* f5
int* f3
int* fc
int* fML
int* fM1
int* fM2
int* ggg
int Fc
int FcH
int FcI
int FcM
int** c_local
int* f3_local
int** fML_local
int** ggg_local
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

Detailed Documentation

Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_fold_compound_t .

Fields

unsigned int length
Length of the sequence, therefore an indicator of the size of the 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** c_local
Energy array, given that i-j pair.
int* f3_local
Energy of 5’ end.
int** fML_local
Multi-loop auxiliary energy array.
int** ggg_local
Energies of g-quadruplexes.