1#ifndef VIENNA_RNA_PACKAGE_DP_MATRICES_H
2#define VIENNA_RNA_PACKAGE_DP_MATRICES_H
57#ifndef VRNA_DISABLE_C11_FEATURES
84#ifndef VRNA_DISABLE_C11_FEATURES
101#ifndef VRNA_DISABLE_C11_FEATURES
186 unsigned long ***N_F5;
187 unsigned long ***N_C;
188 unsigned long ***N_M;
189 unsigned long ***N_M1;
196#ifndef VRNA_DISABLE_C11_FEATURES
219#ifndef VRNA_DISABLE_C11_FEATURES
249#ifndef VRNA_DISABLE_C11_FEATURES
273#ifndef VRNA_DISABLE_C11_FEATURES
354#ifndef VRNA_DISABLE_C11_FEATURES
393 unsigned int options);
399 unsigned int options);
405 unsigned int options);
410 unsigned int options);
Various data structures and pre-processor macros.
The Basic Fold Compound API.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
int * ggg
Energies of g-quadruplexes.
Definition: dp_matrices.h:75
int * fML
Multi-loop auxiliary energy array.
Definition: dp_matrices.h:72
int ** c_local
Energy array, given that i-j pair.
Definition: dp_matrices.h:94
FLT_OR_DBL * scale
Definition: dp_matrices.h:212
int FcH
Minimum Free Energy of hairpin loop cases in circular RNA.
Definition: dp_matrices.h:77
unsigned int length
Length of the sequence, therefore an indicator of the size of the DP matrices.
Definition: dp_matrices.h:51
int * f3
Energy of 3' end.
Definition: dp_matrices.h:69
int * c
Energy array, given that i-j pair.
Definition: dp_matrices.h:67
int * f3_local
Energy of 5' end.
Definition: dp_matrices.h:95
unsigned int length
Definition: dp_matrices.h:211
unsigned int strands
Definition: dp_matrices.h:52
const vrna_mx_type_e type
Definition: dp_matrices.h:50
int FcI
Minimum Free Energy of internal loop cases in circular RNA.
Definition: dp_matrices.h:78
int FcM
Minimum Free Energy of multibranch loop cases in circular RNA.
Definition: dp_matrices.h:79
int * f5
Energy of 5' end.
Definition: dp_matrices.h:68
int ** fms3
nergy for connected interstrand configurations
Definition: dp_matrices.h:71
int Fc
Minimum Free Energy of entire circular RNA.
Definition: dp_matrices.h:76
int * fM2
Energy for a multibranch loop region with exactly two stems, extending to 3' end.
Definition: dp_matrices.h:74
int ** fML_local
Multi-loop auxiliary energy array.
Definition: dp_matrices.h:96
FLT_OR_DBL * expMLbase
Definition: dp_matrices.h:213
int * fM1
Second ML array, only for unique multibrnach loop decomposition.
Definition: dp_matrices.h:73
int ** fms5
Energy for connected interstrand configurations.
Definition: dp_matrices.h:70
const vrna_mx_type_e type
Definition: dp_matrices.h:210
int ** ggg_local
Energies of g-quadruplexes.
Definition: dp_matrices.h:97
int vrna_mx_add(vrna_fold_compound_t *vc, vrna_mx_type_e type, unsigned int options)
Add Dynamic Programming (DP) matrices (allocate memory)
void vrna_mx_pf_free(vrna_fold_compound_t *vc)
Free memory occupied by the Partition Function (PF) Dynamic Programming (DP) matrices.
vrna_mx_type_e
An enumerator that is used to specify the type of a polymorphic Dynamic Programming (DP) matrix data ...
Definition: dp_matrices.h:32
void vrna_mx_mfe_free(vrna_fold_compound_t *vc)
Free memory occupied by the Minimum Free Energy (MFE) Dynamic Programming (DP) matrices.
@ VRNA_MX_WINDOW
DP matrices suitable for local structure prediction using window approach.
Definition: dp_matrices.h:34
@ VRNA_MX_DEFAULT
Default DP matrices.
Definition: dp_matrices.h:33
@ VRNA_MX_2DFOLD
DP matrices suitable for distance class partitioned structure prediction.
Definition: dp_matrices.h:38
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition: dp_matrices.h:46
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition: dp_matrices.h:206
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148