Go to the documentation of this file. 1 #ifndef VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H
2 #define VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H
76 #define VRNA_STATUS_MFE_PRE (unsigned char)1
84 #define VRNA_STATUS_MFE_POST (unsigned char)2
91 #define VRNA_STATUS_PF_PRE (unsigned char)3
98 #define VRNA_STATUS_PF_POST (unsigned char)4
112 #include <ViennaRNA/zscore.h>
159 unsigned int strands;
213 #ifndef VRNA_DISABLE_C11_FEATURES
230 short *sequence_encoding2;
253 #ifndef VRNA_DISABLE_C11_FEATURES
305 #ifndef VRNA_DISABLE_C11_FEATURES
341 vrna_zsc_dat_t zscore_data;
355 #define VRNA_OPTION_DEFAULT 0U
363 #define VRNA_OPTION_MFE 1U
371 #define VRNA_OPTION_PF 2U
376 #define VRNA_OPTION_HYBRID 4U
387 #define VRNA_OPTION_EVAL_ONLY 8U
392 #define VRNA_OPTION_WINDOW 16U
434 unsigned int options);
477 unsigned int options);
481 vrna_fold_compound_comparative2(
const char **sequences,
483 const unsigned char *orientation,
484 const unsigned long long *start,
485 const unsigned long long *genome_size,
487 unsigned int options);
491 vrna_fold_compound_TwoD(
const char *sequence,
495 unsigned int options);
500 unsigned int options);
short * reference_pt2
A pairtable of the second reference structure.
Definition: fold_compound.h:319
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: fold_compound.h:165
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.
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors
Definition: fold_compound.h:169
short ** S
Numerical encoding of the sequences in the alignment.
Definition: fold_compound.h:276
Definition: sequence.h:52
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: fold_compound.h:245
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: fold_compound.h:316
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: fold_compound.h:317
unsigned int * strand_end
The end (last) position of a particular strand within the current concatenated sequence.
Definition: fold_compound.h:157
The model details data structure and its corresponding modifiers.
Functions and data structures for handling of secondary structure hard constraints.
int window_size
window size for local folding sliding window approach
Definition: fold_compound.h:338
The hard constraints data structure.
Definition: hard.h:367
char * ptype
Pair type array.
Definition: fold_compound.h:231
short * reference_pt1
A pairtable of the first reference structure.
Definition: fold_compound.h:318
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition: dp_matrices.h:46
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: fold_compound.h:321
short * sequence_encoding
Numerical encoding of the input sequence.
Definition: fold_compound.h:226
short * S_cons
Numerical encoding of the consensus sequence.
Definition: fold_compound.h:273
Implementations for the RNA folding grammar.
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,...
Definition: fold_compound.h:323
void vrna_fold_compound_free(vrna_fold_compound_t *fc)
Free memory occupied by a vrna_fold_compound_t.
vrna_mx_pf_t * exp_matrices
The PF DP matrices
Definition: fold_compound.h:166
char ** sequences
The aligned sequences.
Definition: fold_compound.h:263
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: fold_compound.h:270
Data structure representing a nucleotide sequence.
Definition: sequence.h:41
int * jindx
DP matrix accessor
Definition: fold_compound.h:172
short ** S3
Sl[s][i] holds next base 3' of i in sequence s.
Definition: fold_compound.h:282
@ VRNA_FC_TYPE_COMPARATIVE
Definition: fold_compound.h:121
Functions to deal with standard dynamic programming (DP) matrices.
vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition: fold_compound.h:297
vrna_sd_t * domains_struc
Additional structured domains.
Definition: fold_compound.h:201
Functions and data structures related to sequence representations ,.
The soft constraints data structure.
Definition: soft.h:171
void vrna_fold_compound_add_callback(vrna_fold_compound_t *fc, vrna_callback_recursion_status *f)
Add a recursion status callback to the vrna_fold_compound_t.
void * auxdata
A pointer to auxiliary, user-defined data.
Definition: fold_compound.h:185
This module provides interfaces that deal with additional structured domains in the folding grammar.
Functions and data structures for secondary structure soft constraints.
unsigned int * strand_number
The strand number a particular nucleotide is associated with.
Definition: fold_compound.h:154
void vrna_fold_compound_add_auxdata(vrna_fold_compound_t *fc, void *data, vrna_callback_free_auxdata *f)
Add auxiliary data to the vrna_fold_compound_t.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition: basic.h:103
short ** S5
S5[s][i] holds next base 5' of i in sequence s.
Definition: fold_compound.h:279
int ** pscore_local
Precomputed array of pair types expressed as pairing scores.
Definition: fold_compound.h:290
unsigned int * strand_order
The strand order, i.e. permutation of current concatenated sequence.
Definition: fold_compound.h:155
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: fold_compound.h:163
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: fold_compound.h:326
vrna_ud_t * domains_up
Additional unstructured domains.
Definition: fold_compound.h:204
char * ptype_pf_compat
ptype array indexed via iindx
Definition: fold_compound.h:240
short * pscore_pf_compat
Precomputed array of pair types expressed as pairing scores indexed via iindx.
Definition: fold_compound.h:293
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition: dp_matrices.h:204
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint,...
Definition: fold_compound.h:150
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:180
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:137
unsigned int * strand_start
The start position of a particular strand within the current concatenated sequence.
Definition: fold_compound.h:156
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: fold_compound.h:287
@ VRNA_FC_TYPE_SINGLE
Definition: fold_compound.h:120
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: fold_compound.h:322
unsigned int length
The length of the sequence (or sequence alignment)
Definition: fold_compound.h:149
vrna_callback_free_auxdata * free_auxdata
A callback to free auxiliary user data whenever the fold_compound itself is free'd.
Definition: fold_compound.h:189
void() vrna_callback_recursion_status(unsigned char status, void *data)
Callback to perform specific user-defined actions before, or after recursive computations.
Definition: fold_compound.h:67
Data structure to store all functionality for ligand binding.
Definition: unstructured_domains.h:228
unsigned int n_seq
The number of sequences in the alignment.
Definition: fold_compound.h:267
vrna_fc_type_e
An enumerator that is used to specify the type of a vrna_fold_compound_t.
Definition: fold_compound.h:119
void() vrna_callback_free_auxdata(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: fold_compound.h:46
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: fold_compound.h:168
Definition: structured_domains.h:26
vrna_fold_compound_t * vrna_fold_compound(const char *sequence, const vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound_t data structure for single sequences and hybridizing sequences.
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: fold_compound.h:325
char ** ptype_local
Pair type array (for local folding)
Definition: fold_compound.h:339
char * sequence
The input sequence string.
Definition: fold_compound.h:223
vrna_callback_recursion_status * stat_cb
Recursion status callback (usually called just before, and after recursive computations in the librar...
Definition: fold_compound.h:180
const vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: fold_compound.h:142
int * iindx
DP matrix accessor
Definition: fold_compound.h:171
Functions to deal with sets of energy parameters.