1 #ifndef VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 2 #define VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 72 #define VRNA_STATUS_MFE_PRE (unsigned char)1 81 #define VRNA_STATUS_MFE_POST (unsigned char)2 89 #define VRNA_STATUS_PF_PRE (unsigned char)3 97 #define VRNA_STATUS_PF_POST (unsigned char)4 101 #define VRNA_BACKWARD_COMPAT 104 #ifdef VRNA_BACKWARD_COMPAT 266 double energy_backtrack;
267 double opening_backtrack_x;
268 double opening_backtrack_y;
313 float fullStemEnergy;
375 #ifndef VRNA_DISABLE_C11_FEATURES 476 #ifndef VRNA_DISABLE_C11_FEATURES 493 short *sequence_encoding2;
516 #ifndef VRNA_DISABLE_C11_FEATURES 549 unsigned short **a2s;
565 #ifndef VRNA_DISABLE_C11_FEATURES 612 #define VRNA_OPTION_DEFAULT 0U 620 #define VRNA_OPTION_MFE 1U 628 #define VRNA_OPTION_PF 2U 633 #define VRNA_OPTION_HYBRID 4U 644 #define VRNA_OPTION_EVAL_ONLY 8U 649 #define VRNA_OPTION_WINDOW 16U 693 unsigned int options);
735 unsigned int options);
738 vrna_fold_compound_TwoD(
const char *sequence,
742 unsigned int options);
746 unsigned int options);
short ** S3
Sl[s][i] holds next base 3' of i in sequence s.
Definition: data_structures.h:545
short ** S
Numerical encoding of the sequences in the alignment.
Definition: data_structures.h:539
void vrna_fold_compound_add_callback(vrna_fold_compound_t *vc, vrna_callback_recursion_status *f)
Add a recursion status callback to the vrna_fold_compound_t.
int l
j<l in shorter seq
Definition: data_structures.h:228
double ** M
multi loops
Definition: data_structures.h:210
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: data_structures.h:585
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition: dp_matrices.h:39
vrna_fold_compound_t * vrna_fold_compound_comparative(const char **sequences, vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound_t data structure for sequence alignments.
short * S_cons
Numerical encoding of the consensus sequence.
Definition: data_structures.h:536
void vrna_C11_features(void)
Dummy symbol to check whether the library was build using C11/C++11 features.
char * ptype
Pair type array.
Definition: data_structures.h:494
short * sequence_encoding
Numerical encoding of the input sequence.
Definition: data_structures.h:489
double ** H
hairpin loops
Definition: data_structures.h:208
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors.
Definition: data_structures.h:448
struct dupVar dupVar
Data structure used in RNApkplex.
struct constrain constrain
constraints for cofolding
int u_vals
number of different -u values
Definition: data_structures.h:237
Data structure used in RNApkplex.
Definition: data_structures.h:326
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: data_structures.h:583
short * reference_pt1
A pairtable of the first reference structure.
Definition: data_structures.h:578
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: data_structures.h:508
struct pu_contrib pu_contrib
contributions to p_u
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:424
char ** sequences
The aligned sequences.
Definition: data_structures.h:526
int j
j<l in shorter seq
Definition: data_structures.h:227
Data structure for RNAsnoop (fold energy list)
Definition: data_structures.h:288
contributions to p_u
Definition: data_structures.h:207
int contribs
[-c "SHIME"]
Definition: data_structures.h:238
The model details data structure and its corresponding modifiers.
void * auxdata
A pointer to auxiliary, user-defined data.
Definition: data_structures.h:464
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
short * pscore_pf_compat
Precomputed array of pair types expressed as pairing scores indexed via iindx.
Definition: data_structures.h:553
int i
k<i in longer seq
Definition: data_structures.h:225
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.
Data structure for RNAsnoop.
Definition: data_structures.h:297
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: data_structures.h:240
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: data_structures.h:533
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: data_structures.h:442
char * ptype_pf_compat
ptype array indexed via iindx
Definition: data_structures.h:503
Definition: data_structures.h:407
Stack of partial structures for backtracking.
Definition: data_structures.h:183
this datastructure is used as input parameter in functions of PS_dot.c
Definition: data_structures.h:174
int * jindx
DP matrix accessor.
Definition: data_structures.h:451
void vrna_fold_compound_free(vrna_fold_compound_t *vc)
Free memory occupied by a vrna_fold_compound_t.
vrna_fc_type_e
An enumerator that is used to specify the type of a vrna_fold_compound_t.
Definition: data_structures.h:406
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...
Base pair data structure used in subopt.c.
Definition: data_structures.h:156
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:188
The soft constraints data structure.
Definition: constraints_soft.h:111
int w
longest unpaired region
Definition: data_structures.h:213
struct pu_out pu_out
Collection of all free_energy of beeing unpaired values for output.
short ** S5
S5[s][i] holds next base 5' of i in sequence s.
Definition: data_structures.h:542
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition: data_structures.h:557
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<i in longer seq
Definition: data_structures.h:226
The hard constraints data structure.
Definition: constraints_hard.h:305
interaction data structure for RNAup
Definition: data_structures.h:219
double * Pi
probabilities of interaction
Definition: data_structures.h:220
int oldAliEn
use old alifold energies (with gaps)
constraints for cofolding
Definition: data_structures.h:246
double ** I
interior loops
Definition: data_structures.h:209
struct node folden
Data structure for RNAsnoop (fold energy list)
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:447
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: data_structures.h:550
unsigned int n_seq
The number of sequences in the alignment.
Definition: data_structures.h:530
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: data_structures.h:582
int length
length of longer sequence
Definition: data_structures.h:229
char * sequence
The input sequence string.
Definition: data_structures.h:486
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: data_structures.h:444
Definition: data_structures.h:408
struct interact interact
interaction data structure for RNAup
vrna_callback_recursion_status * stat_cb
Recursion status callback (usually called just before, and after recursive computations in the librar...
Definition: data_structures.h:459
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint...
Definition: data_structures.h:438
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:468
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<i in longer seq and [j,l] j<l in shorter seq ...
Definition: data_structures.h:222
unsigned int length
The length of the sequence (or sequence alignment)
Definition: data_structures.h:437
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:579
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: data_structures.h:576
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: data_structures.h:586
Data structure for RNAduplex.
Definition: data_structures.h:260
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: data_structures.h:581
vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: data_structures.h:430
int window_size
window size for local folding sliding window approach
Definition: data_structures.h:598
char ** ptype_local
Pair type array (for local folding)
Definition: data_structures.h:599
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: data_structures.h:224
int * iindx
DP matrix accessor.
Definition: data_structures.h:450
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:577
vrna_mx_pf_t * exp_matrices
The PF DP matrices.
Definition: data_structures.h:445