RNAlib-2.4.18
fold_compound.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H
2 #define VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H
3 
26 typedef struct vrna_fc_s vrna_fold_compound_t;
27 
46 typedef void (vrna_callback_free_auxdata)(void *data);
47 
67 typedef void (vrna_callback_recursion_status)(unsigned char status,
68  void *data);
69 
76 #define VRNA_STATUS_MFE_PRE (unsigned char)1
77 
84 #define VRNA_STATUS_MFE_POST (unsigned char)2
85 
91 #define VRNA_STATUS_PF_PRE (unsigned char)3
92 
98 #define VRNA_STATUS_PF_POST (unsigned char)4
99 
100 
101 #include <ViennaRNA/model.h>
102 #include <ViennaRNA/params/basic.h>
103 #include <ViennaRNA/sequence.h>
104 #include <ViennaRNA/dp_matrices.h>
107 #include <ViennaRNA/grammar.h>
110 
111 #ifdef VRNA_WITH_SVM
112 #include <ViennaRNA/zscore.h>
113 #endif
114 
115 
119 typedef enum {
123 
124 
137 struct vrna_fc_s {
149  unsigned int length;
150  int cutpoint;
154  unsigned int *strand_number;
155  unsigned int *strand_order;
156  unsigned int *strand_start;
157  unsigned int *strand_end;
159  unsigned int strands;
160  vrna_seq_t *nucleotides;
161  vrna_msa_t *alignment;
162 
171  int *iindx;
172  int *jindx;
185  void *auxdata;
200  /* data structure to adjust additional structural domains, such as G-quadruplexes */
203  /* data structure to adjust additional contributions to unpaired stretches, e.g. due to protein binding */
206  /* auxiliary (user-defined) extension to the folding grammar */
207  vrna_gr_aux_t *aux_grammar;
208 
213 #ifndef VRNA_DISABLE_C11_FEATURES
214  /* C11 support for unnamed unions/structs */
215  union {
216  struct {
217 #endif
218 
223  char *sequence;
230  short *sequence_encoding2;
231  char *ptype;
253 #ifndef VRNA_DISABLE_C11_FEATURES
254  /* C11 support for unnamed unions/structs */
255 };
256 struct {
257 #endif
258 
263  char **sequences;
267  unsigned int n_seq;
270  char *cons_seq;
273  short *S_cons;
276  short **S;
279  short **S5;
282  short **S3;
285  char **Ss;
286  unsigned int **a2s;
287  int *pscore;
290  int **pscore_local;
300  int oldAliEn;
301 
305 #ifndef VRNA_DISABLE_C11_FEATURES
306 };
307 };
308 #endif
309 
316  unsigned int maxD1;
317  unsigned int maxD2;
318  short *reference_pt1;
319  short *reference_pt2;
321  unsigned int *referenceBPs1;
322  unsigned int *referenceBPs2;
323  unsigned int *bpdist;
325  unsigned int *mm1;
326  unsigned int *mm2;
339  char **ptype_local;
340 #ifdef VRNA_WITH_SVM
341  vrna_zsc_dat_t zscore_data;
342 #endif
343 
347 };
348 
349 
350 /* the definitions below should be used for functions that return/receive/destroy fold compound data structures */
351 
355 #define VRNA_OPTION_DEFAULT 0U
356 
363 #define VRNA_OPTION_MFE 1U
364 
371 #define VRNA_OPTION_PF 2U
372 
376 #define VRNA_OPTION_HYBRID 4U
377 
387 #define VRNA_OPTION_EVAL_ONLY 8U
388 
392 #define VRNA_OPTION_WINDOW 16U
393 
432 vrna_fold_compound(const char *sequence,
433  const vrna_md_t *md_p,
434  unsigned int options);
435 
436 
475 vrna_fold_compound_comparative(const char **sequences,
476  vrna_md_t *md_p,
477  unsigned int options);
478 
479 
481 vrna_fold_compound_comparative2(const char **sequences,
482  const char **names,
483  const unsigned char *orientation,
484  const unsigned long long *start,
485  const unsigned long long *genome_size,
486  vrna_md_t *md_p,
487  unsigned int options);
488 
489 
491 vrna_fold_compound_TwoD(const char *sequence,
492  const char *s1,
493  const char *s2,
494  vrna_md_t *md_p,
495  unsigned int options);
496 
497 
498 int
499 vrna_fold_compound_prepare(vrna_fold_compound_t *fc,
500  unsigned int options);
501 
502 
510 void
512 
513 
531 void
533  void *data,
535 
536 
552 void
555 
556 
561 #endif
Functions to deal with standard dynamic programming (DP) matrices.
Implementations for the RNA folding grammar.
Definition: sequence.h:52
Data structure representing a nucleotide sequence.
Definition: sequence.h:41
Data structure to store all functionality for ligand binding.
Definition: unstructured_domains.h:228
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition: dp_matrices.h:46
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition: dp_matrices.h:204
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition: basic.h:103
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: fold_compound.h:325
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: fold_compound.h:287
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: fold_compound.h:322
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: fold_compound.h:168
void * auxdata
A pointer to auxiliary, user-defined data.
Definition: fold_compound.h:185
unsigned int * strand_number
The strand number a particular nucleotide is associated with.
Definition: fold_compound.h:154
char ** ptype_local
Pair type array (for local folding)
Definition: fold_compound.h:339
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: fold_compound.h:317
const vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: fold_compound.h:142
unsigned int * strand_order
The strand order, i.e. permutation of current concatenated sequence.
Definition: fold_compound.h:155
char * ptype
Pair type array.
Definition: fold_compound.h:231
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: fold_compound.h:316
vrna_ud_t * domains_up
Additional unstructured domains.
Definition: fold_compound.h:204
int * jindx
DP matrix accessor
Definition: fold_compound.h:172
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: fold_compound.h:326
unsigned int * strand_start
The start position of a particular strand within the current concatenated sequence.
Definition: fold_compound.h:156
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,...
Definition: fold_compound.h:323
unsigned int n_seq
The number of sequences in the alignment.
Definition: fold_compound.h:267
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: fold_compound.h:321
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors
Definition: fold_compound.h:169
short ** S5
S5[s][i] holds next base 5' of i in sequence s.
Definition: fold_compound.h:279
char * ptype_pf_compat
ptype array indexed via iindx
Definition: fold_compound.h:240
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
char * sequence
The input sequence string.
Definition: fold_compound.h:223
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
short * reference_pt2
A pairtable of the second reference structure.
Definition: fold_compound.h:319
unsigned int length
The length of the sequence (or sequence alignment)
Definition: fold_compound.h:149
char ** sequences
The aligned sequences.
Definition: fold_compound.h:263
short * sequence_encoding
Numerical encoding of the input sequence.
Definition: fold_compound.h:226
short * reference_pt1
A pairtable of the first reference structure.
Definition: fold_compound.h:318
short * S_cons
Numerical encoding of the consensus sequence.
Definition: fold_compound.h:273
unsigned int * strand_end
The end (last) position of a particular strand within the current concatenated sequence.
Definition: fold_compound.h:157
short * pscore_pf_compat
Precomputed array of pair types expressed as pairing scores indexed via iindx.
Definition: fold_compound.h:293
vrna_sd_t * domains_struc
Additional structured domains.
Definition: fold_compound.h:201
vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition: fold_compound.h:297
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: fold_compound.h:270
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: fold_compound.h:245
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: fold_compound.h:165
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: fold_compound.h:163
int ** pscore_local
Precomputed array of pair types expressed as pairing scores.
Definition: fold_compound.h:290
int window_size
window size for local folding sliding window approach
Definition: fold_compound.h:338
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint,...
Definition: fold_compound.h:150
short ** S
Numerical encoding of the sequences in the alignment.
Definition: fold_compound.h:276
short ** S3
Sl[s][i] holds next base 3' of i in sequence s.
Definition: fold_compound.h:282
vrna_mx_pf_t * exp_matrices
The PF DP matrices
Definition: fold_compound.h:166
int * iindx
DP matrix accessor
Definition: fold_compound.h:171
vrna_fc_type_e
An enumerator that is used to specify the type of a vrna_fold_compound_t.
Definition: fold_compound.h:119
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.
void vrna_fold_compound_free(vrna_fold_compound_t *fc)
Free memory occupied by a vrna_fold_compound_t.
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() vrna_callback_free_auxdata(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: fold_compound.h:46
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
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.
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.
@ VRNA_FC_TYPE_SINGLE
Definition: fold_compound.h:120
@ VRNA_FC_TYPE_COMPARATIVE
Definition: fold_compound.h:121
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:137
Definition: grammar.h:53
The hard constraints data structure.
Definition: hard.h:368
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:180
The soft constraints data structure.
Definition: soft.h:171
Functions and data structures for handling of secondary structure hard constraints.
The model details data structure and its corresponding modifiers.
Functions to deal with sets of energy parameters.
Functions and data structures related to sequence representations ,.
Functions and data structures for secondary structure soft constraints.
This module provides interfaces that deal with additional structured domains in the folding grammar.
Definition: structured_domains.h:26
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.