double Gikjl
full free energy for interaction between [k,i] k
Definition: data_structures.h:240
Definition: data_structures.h:344
double * Gi
free energies of interaction
Definition: data_structures.h:239
void vrna_free_mfe_matrices(vrna_fold_compound *vc)
Free memory occupied by the Minimum Free Energy (MFE) Dynamic Programming (DP) matrices.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:437
Solution element from subopt.c.
Definition: data_structures.h:115
constraints for cofolding
Definition: data_structures.h:264
Definition: data_structures.h:278
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: data_structures.h:258
double * Pi
probabilities of interaction
Definition: data_structures.h:238
A base pair info structure.
Definition: data_structures.h:172
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:46
void vrna_free_fold_compound(vrna_fold_compound *vc)
Free memory occupied by a vrna_fold_compound.
vrna_fold_compound * vrna_get_fold_compound(const char *sequence, vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound data structure for single sequences and hybridizing sequences...
void vrna_free_pf_matrices(vrna_fold_compound *vc)
Free memory occupied by the Partition Function (PF) Dynamic Programming (DP) matrices.
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition: data_structures.h:410
double F0AB
Null model without DuplexInit.
Definition: data_structures.h:131
int k
k
Definition: data_structures.h:244
double A0
start concentration A
Definition: data_structures.h:142
Sequence interval stack element used in subopt.c.
Definition: data_structures.h:106
Definition: data_structures.h:237
int l
j
Definition: data_structures.h:246
double ABc
End concentration AB.
Definition: data_structures.h:144
Base pair.
Definition: data_structures.h:74
Stack of partial structures for backtracking.
Definition: data_structures.h:65
int len
sequence length
Definition: data_structures.h:254
double ** E
exterior loop
Definition: data_structures.h:229
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:41
The soft constraints data structure.
Definition: constraints.h:346
double ** I
interior loops
Definition: data_structures.h:227
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:63
this datastructure is used as input parameter in functions of PS_dot.c
Definition: data_structures.h:56
int i
k
Definition: data_structures.h:243
Definition: data_structures.h:211
int length
length of the input sequence
Definition: data_structures.h:230
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: data_structures.h:242
int j
j
Definition: data_structures.h:245
vrna_fold_compound * vrna_get_fold_compound_ali(const char **sequences, vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound data structure for sequence alignments.
Base pair data structure used in subopt.c.
Definition: data_structures.h:98
double ** M
multi loops
Definition: data_structures.h:228
contributions to p_u
Definition: data_structures.h:225
Definition: data_structures.h:154
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:86
int * iindx
index array to move through pr.
double B0
start concentration B
Definition: data_structures.h:143
Definition: data_structures.h:141
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition: data_structures.h:390
int u_vals
number of different -u values
Definition: data_structures.h:255
double FA
monomer A
Definition: data_structures.h:134