struct TwoDpfold_vars

#include <ViennaRNA/2Dpfold.h>

Overview

Variables compound for 2Dfold partition function folding. More…

// fields

unsigned int alloc
char* ptype
char* sequence
short* S
short* S1
unsigned int maxD1
unsigned int maxD2
double temperature
double init_temp
FLT_OR_DBL* scale
FLT_OR_DBL pf_scale
vrna_exp_param_t* pf_params
int* my_iindx
int* jindx
short* reference_pt1
short* reference_pt2
unsigned int* referenceBPs1
unsigned int* referenceBPs2
unsigned int* bpdist
unsigned int* mm1
unsigned int* mm2
int circ
int dangles
unsigned int seq_length
FLT_OR_DBL*** Q
FLT_OR_DBL*** Q_B
FLT_OR_DBL*** Q_M
FLT_OR_DBL*** Q_M1
FLT_OR_DBL*** Q_M2
FLT_OR_DBL** Q_c
FLT_OR_DBL** Q_cH
FLT_OR_DBL** Q_cI
FLT_OR_DBL** Q_cM
int** l_min_values
int** l_max_values
int* k_min_values
int* k_max_values
int** l_min_values_b
int** l_max_values_b
int* k_min_values_b
int* k_max_values_b
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_m2
int** l_max_values_m2
int* k_min_values_m2
int* k_max_values_m2
int* l_min_values_qc
int* l_max_values_qc
int k_min_values_qc
int k_max_values_qc
int* l_min_values_qcH
int* l_max_values_qcH
int k_min_values_qcH
int k_max_values_qcH
int* l_min_values_qcI
int* l_max_values_qcI
int k_min_values_qcI
int k_max_values_qcI
int* l_min_values_qcM
int* l_max_values_qcM
int k_min_values_qcM
int k_max_values_qcM
FLT_OR_DBL* Q_rem
FLT_OR_DBL* Q_B_rem
FLT_OR_DBL* Q_M_rem
FLT_OR_DBL* Q_M1_rem
FLT_OR_DBL* Q_M2_rem
FLT_OR_DBL Q_c_rem
FLT_OR_DBL Q_cH_rem
FLT_OR_DBL Q_cI_rem
FLT_OR_DBL Q_cM_rem
vrna_fold_compound_t* compatibility

Detailed Documentation

Variables compound for 2Dfold partition function 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_pf_TwoD() , and vrna_fold_compound_free() instead!

Fields

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.
int* my_iindx
Index for moving in quadratic distancy dimensions.
int* jindx
Index for moving in the triangular matrix qm1.
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].
unsigned int* mm1
Maximum matching matrix, reference struct 1 disallowed.
unsigned int* mm2
Maximum matching matrix, reference struct 2 disallowed.