1 #ifndef VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 2 #define VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 80 #define VRNA_STATUS_MFE_PRE (unsigned char)1 89 #define VRNA_STATUS_MFE_POST (unsigned char)2 97 #define VRNA_STATUS_PF_PRE (unsigned char)3 105 #define VRNA_STATUS_PF_POST (unsigned char)4 108 #define VRNA_PLIST_TYPE_BASEPAIR 0 109 #define VRNA_PLIST_TYPE_GQUAD 1 110 #define VRNA_PLIST_TYPE_H_MOTIF 2 111 #define VRNA_PLIST_TYPE_I_MOTIF 3 112 #define VRNA_PLIST_TYPE_UD_MOTIF 4 116 #define VRNA_BACKWARD_COMPAT 119 #ifdef VRNA_BACKWARD_COMPAT 204 unsigned int position;
296 double energy_backtrack;
297 double opening_backtrack_x;
298 double opening_backtrack_y;
343 float fullStemEnergy;
405 #ifndef VRNA_DISABLE_C11_FEATURES 522 #ifndef VRNA_DISABLE_C11_FEATURES 539 short *sequence_encoding2;
562 #ifndef VRNA_DISABLE_C11_FEATURES 595 unsigned short **a2s;
611 #ifndef VRNA_DISABLE_C11_FEATURES 658 #define VRNA_OPTION_DEFAULT 0U 666 #define VRNA_OPTION_MFE 1U 674 #define VRNA_OPTION_PF 2U 679 #define VRNA_OPTION_HYBRID 4U 690 #define VRNA_OPTION_EVAL_ONLY 8U 695 #define VRNA_OPTION_WINDOW 16U 739 unsigned int options);
781 unsigned int options);
784 vrna_fold_compound_TwoD(
const char *sequence,
788 unsigned int options);
792 unsigned int options);
short ** S3
Sl[s][i] holds next base 3' of i in sequence s.
Definition: data_structures.h:591
short ** S
Numerical encoding of the sequences in the alignment.
Definition: data_structures.h:585
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:258
double ** M
multi loops
Definition: data_structures.h:240
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: data_structures.h:631
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:582
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:540
Functions to deal with standard dynamic programming (DP) matrices.
short * sequence_encoding
Numerical encoding of the input sequence.
Definition: data_structures.h:535
double ** H
hairpin loops
Definition: data_structures.h:238
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors.
Definition: data_structures.h:478
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:267
Data structure used in RNApkplex.
Definition: data_structures.h:356
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: data_structures.h:629
short * reference_pt1
A pairtable of the first reference structure.
Definition: data_structures.h:624
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: data_structures.h:554
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:454
char ** sequences
The aligned sequences.
Definition: data_structures.h:572
int j
j<l in shorter seq
Definition: data_structures.h:257
Data structure for RNAsnoop (fold energy list)
Definition: data_structures.h:318
contributions to p_u
Definition: data_structures.h:237
int contribs
[-c "SHIME"]
Definition: data_structures.h:268
The model details data structure and its corresponding modifiers.
void * auxdata
A pointer to auxiliary, user-defined data.
Definition: data_structures.h:494
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:599
vrna_sd_t * domains_struc
Additional structured domains.
Definition: data_structures.h:510
int i
k<i in longer seq
Definition: data_structures.h:255
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:513
Data structure for RNAsnoop.
Definition: data_structures.h:327
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: data_structures.h:270
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: data_structures.h:579
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: data_structures.h:472
char * ptype_pf_compat
ptype array indexed via iindx
Definition: data_structures.h:549
Stack of partial structures for backtracking.
Definition: data_structures.h:213
this datastructure is used as input parameter in functions of PS_dot.c
Definition: data_structures.h:192
int * jindx
DP matrix accessor.
Definition: data_structures.h:481
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:436
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:174
The soft constraints data structure.
Definition: constraints_soft.h:101
int w
longest unpaired region
Definition: data_structures.h:243
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:588
Definition: data_structures.h:203
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:603
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:256
The hard constraints data structure.
Definition: constraints_hard.h:305
Definition: data_structures.h:438
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches...
interaction data structure for RNAup
Definition: data_structures.h:249
double * Pi
probabilities of interaction
Definition: data_structures.h:250
int oldAliEn
use old alifold energies (with gaps)
constraints for cofolding
Definition: data_structures.h:276
double ** I
interior loops
Definition: data_structures.h:239
struct node folden
Data structure for RNAsnoop (fold energy list)
int len
sequence length
Definition: data_structures.h:266
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:242
char ** header
header line
Definition: data_structures.h:269
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:182
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: data_structures.h:477
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: data_structures.h:596
unsigned int n_seq
The number of sequences in the alignment.
Definition: data_structures.h:576
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: data_structures.h:628
int length
length of longer sequence
Definition: data_structures.h:259
char * sequence
The input sequence string.
Definition: data_structures.h:532
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: data_structures.h:474
Definition: data_structures.h:437
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:489
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint...
Definition: data_structures.h:468
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:498
Collection of all free_energy of beeing unpaired values for output.
Definition: data_structures.h:265
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:252
unsigned int length
The length of the sequence (or sequence alignment)
Definition: data_structures.h:467
Base pair stack element.
Definition: data_structures.h:222
Functions and data structures for constraining secondary structure predictions and evaluation...
double * Gi
free energies of interaction
Definition: data_structures.h:251
Definition: data_structures.h:197
short * reference_pt2
A pairtable of the second reference structure.
Definition: data_structures.h:625
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:622
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: data_structures.h:632
Data structure for RNAduplex.
Definition: data_structures.h:290
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: data_structures.h:627
Implementations for the RNA folding grammar.
vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: data_structures.h:460
int window_size
window size for local folding sliding window approach
Definition: data_structures.h:644
char ** ptype_local
Pair type array (for local folding)
Definition: data_structures.h:645
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: data_structures.h:254
int * iindx
DP matrix accessor.
Definition: data_structures.h:480
double ** E
exterior loop
Definition: data_structures.h:241
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:623
vrna_mx_pf_t * exp_matrices
The PF DP matrices.
Definition: data_structures.h:475