1 #ifndef VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 2 #define VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 81 #define VRNA_STATUS_MFE_PRE (unsigned char)1 90 #define VRNA_STATUS_MFE_POST (unsigned char)2 98 #define VRNA_STATUS_PF_PRE (unsigned char)3 106 #define VRNA_STATUS_PF_POST (unsigned char)4 109 #define VRNA_PLIST_TYPE_BASEPAIR 0 110 #define VRNA_PLIST_TYPE_GQUAD 1 111 #define VRNA_PLIST_TYPE_H_MOTIF 2 112 #define VRNA_PLIST_TYPE_I_MOTIF 3 113 #define VRNA_PLIST_TYPE_UD_MOTIF 4 117 #define VRNA_BACKWARD_COMPAT 120 #ifdef VRNA_BACKWARD_COMPAT 205 unsigned int position;
297 double energy_backtrack;
298 double opening_backtrack_x;
299 double opening_backtrack_y;
344 float fullStemEnergy;
406 #ifndef VRNA_DISABLE_C11_FEATURES 526 #ifndef VRNA_DISABLE_C11_FEATURES 543 short *sequence_encoding2;
566 #ifndef VRNA_DISABLE_C11_FEATURES 599 unsigned short **a2s;
618 #ifndef VRNA_DISABLE_C11_FEATURES 664 #define VRNA_OPTION_DEFAULT 0U 672 #define VRNA_OPTION_MFE 1U 680 #define VRNA_OPTION_PF 2U 685 #define VRNA_OPTION_HYBRID 4U 696 #define VRNA_OPTION_EVAL_ONLY 8U 701 #define VRNA_OPTION_WINDOW 16U 745 unsigned int options);
788 unsigned int options);
792 vrna_fold_compound_TwoD(
const char *sequence,
796 unsigned int options);
801 unsigned int options);
short ** S3
Sl[s][i] holds next base 3' of i in sequence s.
Definition: data_structures.h:595
short ** S
Numerical encoding of the sequences in the alignment.
Definition: data_structures.h:589
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.
Definition: structured_domains.h:26
int l
j<l in shorter seq
Definition: data_structures.h:259
double ** M
multi loops
Definition: data_structures.h:241
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: data_structures.h:638
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition: dp_matrices.h:45
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:586
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:544
Functions to deal with standard dynamic programming (DP) matrices.
short * sequence_encoding
Numerical encoding of the input sequence.
Definition: data_structures.h:539
double ** H
hairpin loops
Definition: data_structures.h:239
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors.
Definition: data_structures.h:482
struct dupVar dupVar
Data structure used in RNApkplex.
struct constrain constrain
constraints for cofolding
Data structure to store all functionality for ligand binding.
Definition: unstructured_domains.h:147
int u_vals
number of different -u values
Definition: data_structures.h:268
Data structure used in RNApkplex.
Definition: data_structures.h:357
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: data_structures.h:636
short * reference_pt1
A pairtable of the first reference structure.
Definition: data_structures.h:631
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: data_structures.h:558
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:48
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:457
char ** sequences
The aligned sequences.
Definition: data_structures.h:576
int j
j<l in shorter seq
Definition: data_structures.h:258
Data structure for RNAsnoop (fold energy list)
Definition: data_structures.h:319
contributions to p_u
Definition: data_structures.h:238
int contribs
[-c "SHIME"]
Definition: data_structures.h:269
The model details data structure and its corresponding modifiers.
void * auxdata
A pointer to auxiliary, user-defined data.
Definition: data_structures.h:498
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:55
short * pscore_pf_compat
Precomputed array of pair types expressed as pairing scores indexed via iindx.
Definition: data_structures.h:606
vrna_sd_t * domains_struc
Additional structured domains.
Definition: data_structures.h:514
int i
k<i in longer seq
Definition: data_structures.h:256
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_ud_t * domains_up
Additional unstructured domains.
Definition: data_structures.h:517
Data structure for RNAsnoop.
Definition: data_structures.h:328
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: data_structures.h:271
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: data_structures.h:583
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: data_structures.h:476
char * ptype_pf_compat
ptype array indexed via iindx
Definition: data_structures.h:553
Stack of partial structures for backtracking.
Definition: data_structures.h:214
this datastructure is used as input parameter in functions of PS_dot.c
Definition: data_structures.h:193
int * jindx
DP matrix accessor.
Definition: data_structures.h:485
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:439
Energy parameter constants.
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:175
The soft constraints data structure.
Definition: constraints_soft.h:101
int w
longest unpaired region
Definition: data_structures.h:244
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:592
Definition: data_structures.h:204
Functions to deal with sets of energy parameters.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:99
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:191
vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition: data_structures.h:610
void( vrna_callback_free_auxdata)(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: data_structures.h:60
int k
k<i in longer seq
Definition: data_structures.h:257
The hard constraints data structure.
Definition: constraints_hard.h:305
Definition: data_structures.h:441
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches...
interaction data structure for RNAup
Definition: data_structures.h:250
double * Pi
probabilities of interaction
Definition: data_structures.h:251
int oldAliEn
use old alifold energies (with gaps)
constraints for cofolding
Definition: data_structures.h:277
double ** I
interior loops
Definition: data_structures.h:240
struct node folden
Data structure for RNAsnoop (fold energy list)
int len
sequence length
Definition: data_structures.h:267
unsigned int * strand_number
The strand number a particular nucleotide is associated with.
Definition: data_structures.h:474
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:71
int length
length of the input sequence
Definition: data_structures.h:243
char ** header
header line
Definition: data_structures.h:270
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:183
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: data_structures.h:481
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: data_structures.h:600
unsigned int n_seq
The number of sequences in the alignment.
Definition: data_structures.h:580
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: data_structures.h:635
int length
length of longer sequence
Definition: data_structures.h:260
char * sequence
The input sequence string.
Definition: data_structures.h:536
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: data_structures.h:478
Definition: data_structures.h:440
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:493
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint...
Definition: data_structures.h:470
int ** pscore_local
Precomputed array of pair types expressed as pairing scores.
Definition: data_structures.h:603
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:502
Collection of all free_energy of beeing unpaired values for output.
Definition: data_structures.h:266
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:253
unsigned int length
The length of the sequence (or sequence alignment)
Definition: data_structures.h:469
Base pair stack element.
Definition: data_structures.h:223
Functions and data structures for constraining secondary structure predictions and evaluation...
double * Gi
free energies of interaction
Definition: data_structures.h:252
Definition: data_structures.h:198
short * reference_pt2
A pairtable of the second reference structure.
Definition: data_structures.h:632
This module provides interfaces that deal with additional structured domains in the folding grammar...
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: data_structures.h:629
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: data_structures.h:639
Data structure for RNAduplex.
Definition: data_structures.h:291
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: data_structures.h:634
Implementations for the RNA folding grammar.
vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: data_structures.h:462
int window_size
window size for local folding sliding window approach
Definition: data_structures.h:651
char ** ptype_local
Pair type array (for local folding)
Definition: data_structures.h:652
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: data_structures.h:255
int * iindx
DP matrix accessor.
Definition: data_structures.h:484
double ** E
exterior loop
Definition: data_structures.h:242
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition: dp_matrices.h:203
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: data_structures.h:630
vrna_mx_pf_t * exp_matrices
The PF DP matrices.
Definition: data_structures.h:479