struct TwoDfold_vars

#include <ViennaRNA/2Dfold.h>

Overview

Variables compound for 2Dfold MFE folding. More…

// fields

vrna_param_t* P
int do_backtrack
char* ptype
char* sequence
short* S
short* S1
unsigned int maxD1
unsigned int maxD2
unsigned int* mm1
unsigned int* mm2
int* my_iindx
double temperature
unsigned int* referenceBPs1
unsigned int* referenceBPs2
unsigned int* bpdist
short* reference_pt1
short* reference_pt2
int circ
int dangles
unsigned int seq_length
int*** E_F5
int*** E_F3
int*** E_C
int*** E_M
int*** E_M1
int*** E_M2
int** E_Fc
int** E_FcH
int** E_FcI
int** E_FcM
int** l_min_values
int** l_max_values
int* k_min_values
int* k_max_values
int** l_min_values_m
int** l_max_values_m
int* k_min_values_m
int* k_max_values_m
int** l_min_values_m1
int** l_max_values_m1
int* k_min_values_m1
int* k_max_values_m1
int** l_min_values_f
int** l_max_values_f
int* k_min_values_f
int* k_max_values_f
int** l_min_values_f3
int** l_max_values_f3
int* k_min_values_f3
int* k_max_values_f3
int** l_min_values_m2
int** l_max_values_m2
int* k_min_values_m2
int* k_max_values_m2
int* l_min_values_fc
int* l_max_values_fc
int k_min_values_fc
int k_max_values_fc
int* l_min_values_fcH
int* l_max_values_fcH
int k_min_values_fcH
int k_max_values_fcH
int* l_min_values_fcI
int* l_max_values_fcI
int k_min_values_fcI
int k_max_values_fcI
int* l_min_values_fcM
int* l_max_values_fcM
int k_min_values_fcM
int k_max_values_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
vrna_fold_compound_t* compatibility

Detailed Documentation

Variables compound for 2Dfold MFE folding.
Deprecated This data structure will be removed from the library soon! Use vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD() , vrna_mfe_TwoD() , and vrna_fold_compound_free() instead!

Fields

vrna_param_t* P
Precomputed energy parameters and model details.
int do_backtrack
Flag whether to do backtracing of the structure(s) or not.
char* ptype
Precomputed array of pair types.
char* sequence
The input sequence.
short* S1
The input sequences in numeric form.
unsigned int maxD1
Maximum allowed base pair distance to first reference.
unsigned int maxD2
Maximum allowed base pair distance to second reference.
unsigned int* mm1
Maximum matching matrix, reference struct 1 disallowed.
unsigned int* mm2
Maximum matching matrix, reference struct 2 disallowed.
int* my_iindx
Index for moving in quadratic distancy dimensions.
unsigned int* referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
unsigned int* referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
unsigned int* bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].