void vrna_fold_compound_add_auxdata(vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *f)
Add auxiliary data to the vrna_fold_compound_t.
vrna_fold_compound_t * vrna_fold_compound(const char *sequence, vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound_t data structure for single sequences and hybridizing sequences...
void( vrna_callback_free_auxdata)(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: data_structures.h:51
int k
k
Definition: data_structures.h:226
The hard constraints data structure.
Definition: constraints_hard.h:300
Definition: data_structures.h:219
double * Pi
probabilities of interaction
Definition: data_structures.h:220
constraints for cofolding
Definition: data_structures.h:246
double ** I
interior loops
Definition: data_structures.h:209
int len
sequence length
Definition: data_structures.h:236
void( vrna_callback_recursion_status)(unsigned char status, void *data)
Callback to perform specific user-defined actions before, or after recursive computations.
Definition: data_structures.h:62
int length
length of the input sequence
Definition: data_structures.h:212
char ** header
header line
Definition: data_structures.h:239
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: data_structures.h:413
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: data_structures.h:516
unsigned int n_seq
The number of sequences in the alignment.
Definition: data_structures.h:496
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: data_structures.h:548
int length
length of longer sequence
Definition: data_structures.h:229
char * sequence
The input sequence string.
Definition: data_structures.h:452
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: data_structures.h:410
Definition: data_structures.h:374
vrna_callback_recursion_status * stat_cb
Recursion status callback (usually called just before, and after recursive computations in the librar...
Definition: data_structures.h:425
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint...
Definition: data_structures.h:404
vrna_callback_free_auxdata * free_auxdata
A callback to free auxiliary user data whenever the fold_compound itself is free'd.
Definition: data_structures.h:434
Collection of all free_energy of beeing unpaired values for output.
Definition: data_structures.h:235
double Gikjl
full free energy for interaction between [k,i] k
Definition: data_structures.h:222
unsigned int length
The length of the sequence (or sequence alignment)
Definition: data_structures.h:403
Base pair stack element.
Definition: data_structures.h:192
Functions and data structures for constraining secondary structure predictions and evaluation...
double * Gi
free energies of interaction
Definition: data_structures.h:221
short * reference_pt2
A pairtable of the second reference structure.
Definition: data_structures.h:545
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: data_structures.h:542
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: data_structures.h:552
Definition: data_structures.h:260
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: data_structures.h:547
vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: data_structures.h:396
int window_size
window size for local folding sliding window approach
Definition: data_structures.h:564
char ** ptype_local
Pair type array (for local folding)
Definition: data_structures.h:565
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: data_structures.h:224
int * iindx
DP matrix accessor.
Definition: data_structures.h:416
double ** E
exterior loop
Definition: data_structures.h:211
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition: dp_matrices.h:197
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: data_structures.h:543
vrna_mx_pf_t * exp_matrices
The PF DP matrices.
Definition: data_structures.h:411