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
 

Detailed Description

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


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