1 #ifndef VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 2 #define VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 104 #define VRNA_STATUS_MFE_PRE (unsigned char)1 113 #define VRNA_STATUS_MFE_POST (unsigned char)2 121 #define VRNA_STATUS_PF_PRE (unsigned char)3 129 #define VRNA_STATUS_PF_POST (unsigned char)4 133 #define VRNA_BACKWARD_COMPAT 136 #ifdef VRNA_BACKWARD_COMPAT 211 unsigned int position;
303 double energy_backtrack;
304 double opening_backtrack_x;
305 double opening_backtrack_y;
350 float fullStemEnergy;
412 #ifndef VRNA_DISABLE_C11_FEATURES 532 #ifndef VRNA_DISABLE_C11_FEATURES 549 short *sequence_encoding2;
572 #ifndef VRNA_DISABLE_C11_FEATURES 624 #ifndef VRNA_DISABLE_C11_FEATURES 670 #define VRNA_OPTION_DEFAULT 0U 678 #define VRNA_OPTION_MFE 1U 686 #define VRNA_OPTION_PF 2U 691 #define VRNA_OPTION_HYBRID 4U 702 #define VRNA_OPTION_EVAL_ONLY 8U 707 #define VRNA_OPTION_WINDOW 16U 751 unsigned int options);
794 unsigned int options);
798 vrna_fold_compound_TwoD(
const char *sequence,
802 unsigned int options);
807 unsigned int options);
short ** S3
Sl[s][i] holds next base 3' of i in sequence s.
Definition: data_structures.h:601
short ** S
Numerical encoding of the sequences in the alignment.
Definition: data_structures.h:595
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:265
double ** M
multi loops
Definition: data_structures.h:247
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: data_structures.h:644
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:592
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:550
Functions to deal with standard dynamic programming (DP) matrices.
short * sequence_encoding
Numerical encoding of the input sequence.
Definition: data_structures.h:545
double ** H
hairpin loops
Definition: data_structures.h:245
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors.
Definition: data_structures.h:488
struct dupVar dupVar
Data structure used in RNApkplex.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structure_utils.h:69
struct constrain constrain
constraints for cofolding
Data structure to store all functionality for ligand binding.
Definition: unstructured_domains.h:197
int u_vals
number of different -u values
Definition: data_structures.h:274
Data structure used in RNApkplex.
Definition: data_structures.h:363
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: data_structures.h:642
short * reference_pt1
A pairtable of the first reference structure.
Definition: data_structures.h:637
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: data_structures.h:564
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:463
char ** sequences
The aligned sequences.
Definition: data_structures.h:582
int j
j<l in shorter seq
Definition: data_structures.h:264
Data structure for RNAsnoop (fold energy list)
Definition: data_structures.h:325
contributions to p_u
Definition: data_structures.h:244
int contribs
[-c "SHIME"]
Definition: data_structures.h:275
The model details data structure and its corresponding modifiers.
void * auxdata
A pointer to auxiliary, user-defined data.
Definition: data_structures.h:504
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:57
short * pscore_pf_compat
Precomputed array of pair types expressed as pairing scores indexed via iindx.
Definition: data_structures.h:612
vrna_sd_t * domains_struc
Additional structured domains.
Definition: data_structures.h:520
int i
k<i in longer seq
Definition: data_structures.h:262
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:523
Data structure for RNAsnoop.
Definition: data_structures.h:334
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: data_structures.h:277
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: data_structures.h:589
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: data_structures.h:482
char * ptype_pf_compat
ptype array indexed via iindx
Definition: data_structures.h:559
Stack of partial structures for backtracking.
Definition: data_structures.h:220
this datastructure is used as input parameter in functions of PS_dot.c
Definition: data_structures.h:199
int * jindx
DP matrix accessor.
Definition: data_structures.h:491
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:445
Energy parameter constants.
Various utility- and helper-functions for secondary structure parsing, converting, etc.
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:191
The soft constraints data structure.
Definition: constraints_soft.h:154
int w
longest unpaired region
Definition: data_structures.h:250
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:598
Definition: data_structures.h:210
Functions to deal with sets of energy parameters.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:101
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:189
vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition: data_structures.h:616
void( vrna_callback_free_auxdata)(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: data_structures.h:71
int k
k<i in longer seq
Definition: data_structures.h:263
The hard constraints data structure.
Definition: constraints_hard.h:341
Definition: data_structures.h:447
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches...
interaction data structure for RNAup
Definition: data_structures.h:256
double * Pi
probabilities of interaction
Definition: data_structures.h:257
int oldAliEn
use old alifold energies (with gaps)
constraints for cofolding
Definition: data_structures.h:283
double ** I
interior loops
Definition: data_structures.h:246
struct node folden
Data structure for RNAsnoop (fold energy list)
int len
sequence length
Definition: data_structures.h:273
unsigned int * strand_number
The strand number a particular nucleotide is associated with.
Definition: data_structures.h:480
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:94
int length
length of the input sequence
Definition: data_structures.h:249
char ** header
header line
Definition: data_structures.h:276
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: data_structures.h:487
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: data_structures.h:606
unsigned int n_seq
The number of sequences in the alignment.
Definition: data_structures.h:586
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: data_structures.h:641
int length
length of longer sequence
Definition: data_structures.h:266
char * sequence
The input sequence string.
Definition: data_structures.h:542
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: data_structures.h:484
Definition: data_structures.h:446
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:499
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint...
Definition: data_structures.h:476
int ** pscore_local
Precomputed array of pair types expressed as pairing scores.
Definition: data_structures.h:609
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:508
Collection of all free_energy of beeing unpaired values for output.
Definition: data_structures.h:272
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:259
unsigned int length
The length of the sequence (or sequence alignment)
Definition: data_structures.h:475
Base pair stack element.
Definition: data_structures.h:229
Functions and data structures for constraining secondary structure predictions and evaluation...
double * Gi
free energies of interaction
Definition: data_structures.h:258
Definition: data_structures.h:204
short * reference_pt2
A pairtable of the second reference structure.
Definition: data_structures.h:638
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:635
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: data_structures.h:645
Data structure for RNAduplex.
Definition: data_structures.h:297
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: data_structures.h:640
Implementations for the RNA folding grammar.
vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: data_structures.h:468
int window_size
window size for local folding sliding window approach
Definition: data_structures.h:657
char ** ptype_local
Pair type array (for local folding)
Definition: data_structures.h:658
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: data_structures.h:261
int * iindx
DP matrix accessor.
Definition: data_structures.h:490
double ** E
exterior loop
Definition: data_structures.h:248
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:636
vrna_mx_pf_t * exp_matrices
The PF DP matrices.
Definition: data_structures.h:485