1 #ifndef VIENNA_RNA_PACKAGE_DP_MATRICES_H
2 #define VIENNA_RNA_PACKAGE_DP_MATRICES_H
49 #if ( __STDC_VERSION__ >= 201112L ) || ( __cplusplus >= 201103L )
75 #if ( __STDC_VERSION__ >= 201112L ) || ( __cplusplus >= 201103L )
92 #if ( __STDC_VERSION__ >= 201112L ) || ( __cplusplus >= 201103L )
177 unsigned long ***N_F5;
178 unsigned long ***N_C;
179 unsigned long ***N_M;
180 unsigned long ***N_M1;
187 #if ( __STDC_VERSION__ >= 201112L ) || ( __cplusplus >= 201103L )
211 #if ( __STDC_VERSION__ >= 201112L ) || ( __cplusplus >= 201103L )
241 #if ( __STDC_VERSION__ >= 201112L ) || ( __cplusplus >= 201103L )
322 #if ( __STDC_VERSION__ >= 201112L ) || ( __cplusplus >= 201103L )
361 unsigned int options);
366 unsigned int options);
371 unsigned int options);
int * fc
Energy from i to cutpoint (and vice versa if i>cut)
Definition: dp_matrices.h:62
int vrna_mx_add(vrna_fold_compound_t *vc, vrna_mx_type_e type, unsigned int options)
Add Dynamic Programming (DP) matrices (allocate memory)
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition: dp_matrices.h:39
int * fM1
Second ML array, only for unique multibrnach loop decomposition.
Definition: dp_matrices.h:64
int * fML
Multi-loop auxiliary energy array.
Definition: dp_matrices.h:63
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
unsigned int length
Length of the sequence, therefore an indicator of the size of the DP matrices.
Definition: dp_matrices.h:44
int * fM2
Energy for a multibranch loop region with exactly two stems, extending to 3' end. ...
Definition: dp_matrices.h:65
void vrna_mx_mfe_free(vrna_fold_compound_t *vc)
Free memory occupied by the Minimum Free Energy (MFE) Dynamic Programming (DP) matrices.
DP matrices suitable for local structure prediction using window approach.
Definition: dp_matrices.h:27
int ** ggg_local
Energies of g-quadruplexes.
Definition: dp_matrices.h:88
void vrna_mx_pf_free(vrna_fold_compound_t *vc)
Free memory occupied by the Partition Function (PF) Dynamic Programming (DP) matrices.
int ** c_local
Energy array, given that i-j pair.
Definition: dp_matrices.h:85
Default DP matrices.
Definition: dp_matrices.h:26
int * f3
Energy of 3' end.
Definition: dp_matrices.h:61
DP matrices suitable for distance class partitioned structure prediction.
Definition: dp_matrices.h:31
int * f5
Energy of 5' end.
Definition: dp_matrices.h:60
int Fc
Minimum Free Energy of entire circular RNA.
Definition: dp_matrices.h:67
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:25
int * c
Energy array, given that i-j pair.
Definition: dp_matrices.h:59
int ** fML_local
Multi-loop auxiliary energy array.
Definition: dp_matrices.h:87
int * f3_local
Energy of 5' end.
Definition: dp_matrices.h:86
int * ggg
Energies of g-quadruplexes.
Definition: dp_matrices.h:66
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition: dp_matrices.h:197