RNAlib-2.4.11
fold_compound.h
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1 #ifndef VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H
2 #define VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H
3 
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 
114 typedef enum {
118 
119 
132 struct vrna_fc_s {
144  unsigned int length;
145  int cutpoint;
149  unsigned int *strand_number;
150  unsigned int *strand_order;
151  unsigned int *strand_start;
152  unsigned int *strand_end;
153 
154  unsigned int strands;
155  vrna_seq_t *nucleotides;
156 
165  int *iindx;
166  int *jindx;
179  void *auxdata;
194  /* data structure to adjust additional structural domains, such as G-quadruplexes */
197  /* data structure to adjust additional contributions to unpaired stretches, e.g. due to protein binding */
200  /* auxiliary (user-defined) extension to the folding grammar */
201  vrna_gr_aux_t *aux_grammar;
202 
207 #ifndef VRNA_DISABLE_C11_FEATURES
208  /* C11 support for unnamed unions/structs */
209  union {
210  struct {
211 #endif
212 
217  char *sequence;
224  short *sequence_encoding2;
225  char *ptype;
247 #ifndef VRNA_DISABLE_C11_FEATURES
248  /* C11 support for unnamed unions/structs */
249  };
250  struct {
251 #endif
252 
257  char **sequences;
261  unsigned int n_seq;
264  char *cons_seq;
267  short *S_cons;
270  short **S;
273  short **S5;
276  short **S3;
279  char **Ss;
280  unsigned int **a2s;
281  int *pscore;
284  int **pscore_local;
294  int oldAliEn;
295 
299 #ifndef VRNA_DISABLE_C11_FEATURES
300  };
301  };
302 #endif
303 
310  unsigned int maxD1;
311  unsigned int maxD2;
312  short *reference_pt1;
313  short *reference_pt2;
315  unsigned int *referenceBPs1;
316  unsigned int *referenceBPs2;
317  unsigned int *bpdist;
319  unsigned int *mm1;
320  unsigned int *mm2;
333  char **ptype_local;
337 };
338 
339 
340 /* the definitions below should be used for functions that return/receive/destroy fold compound data structures */
341 
345 #define VRNA_OPTION_DEFAULT 0U
346 
353 #define VRNA_OPTION_MFE 1U
354 
361 #define VRNA_OPTION_PF 2U
362 
366 #define VRNA_OPTION_HYBRID 4U
367 
377 #define VRNA_OPTION_EVAL_ONLY 8U
378 
382 #define VRNA_OPTION_WINDOW 16U
383 
422 vrna_fold_compound(const char *sequence,
423  vrna_md_t *md_p,
424  unsigned int options);
425 
426 
466  vrna_md_t *md_p,
467  unsigned int options);
468 
469 
471 vrna_fold_compound_TwoD(const char *sequence,
472  const char *s1,
473  const char *s2,
474  vrna_md_t *md_p,
475  unsigned int options);
476 
477 
478 int
479 vrna_fold_compound_prepare(vrna_fold_compound_t *fc,
480  unsigned int options);
481 
482 
490 void
492 
493 
512  void *data,
514 
515 
533 
534 
539 #endif
short ** S3
Sl[s][i] holds next base 3&#39; of i in sequence s.
Definition: fold_compound.h:276
short ** S
Numerical encoding of the sequences in the alignment.
Definition: fold_compound.h:270
Definition: structured_domains.h:26
Functions and data structures for secondary structure soft constraints.
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: fold_compound.h:319
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: fold_compound.h:267
char * ptype
Pair type array.
Definition: fold_compound.h:225
Functions and data structures related to sequence representations ,.
Functions to deal with standard dynamic programming (DP) matrices.
short * sequence_encoding
Numerical encoding of the input sequence.
Definition: fold_compound.h:220
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors.
Definition: fold_compound.h:163
Data structure to store all functionality for ligand binding.
Definition: unstructured_domains.h:227
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: fold_compound.h:317
short * reference_pt1
A pairtable of the first reference structure.
Definition: fold_compound.h:312
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: fold_compound.h:239
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
char ** sequences
The aligned sequences.
Definition: fold_compound.h:257
The model details data structure and its corresponding modifiers.
void * auxdata
A pointer to auxiliary, user-defined data.
Definition: fold_compound.h:179
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:56
short * pscore_pf_compat
Precomputed array of pair types expressed as pairing scores indexed via iindx.
Definition: fold_compound.h:287
vrna_sd_t * domains_struc
Additional structured domains.
Definition: fold_compound.h:195
vrna_ud_t * domains_up
Additional unstructured domains.
Definition: fold_compound.h:198
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: fold_compound.h:264
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: fold_compound.h:157
Definition: grammar.h:53
char * ptype_pf_compat
ptype array indexed via iindx
Definition: fold_compound.h:234
int * jindx
DP matrix accessor.
Definition: fold_compound.h:166
vrna_fc_type_e
An enumerator that is used to specify the type of a vrna_fold_compound_t.
Definition: fold_compound.h:114
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...
void vrna_fold_compound_free(vrna_fold_compound_t *fc)
Free memory occupied by a vrna_fold_compound_t.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:177
The soft constraints data structure.
Definition: soft.h:170
short ** S5
S5[s][i] holds next base 5&#39; of i in sequence s.
Definition: fold_compound.h:273
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:102
vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition: fold_compound.h:291
Functions and data structures for handling of secondary structure hard constraints.
The hard constraints data structure.
Definition: hard.h:371
Definition: fold_compound.h:116
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches...
Data structure representing a nucleotide sequence.
Definition: sequence.h:37
unsigned int * strand_number
The strand number a particular nucleotide is associated with.
Definition: fold_compound.h:149
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: fold_compound.h:162
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: fold_compound.h:281
unsigned int n_seq
The number of sequences in the alignment.
Definition: fold_compound.h:261
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: fold_compound.h:316
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.
char * sequence
The input sequence string.
Definition: fold_compound.h:217
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: fold_compound.h:159
Definition: fold_compound.h:115
void() vrna_callback_free_auxdata(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: fold_compound.h:46
vrna_callback_recursion_status * stat_cb
Recursion status callback (usually called just before, and after recursive computations in the librar...
Definition: fold_compound.h:174
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint...
Definition: fold_compound.h:145
int ** pscore_local
Precomputed array of pair types expressed as pairing scores.
Definition: fold_compound.h:284
vrna_callback_free_auxdata * free_auxdata
A callback to free auxiliary user data whenever the fold_compound itself is free&#39;d.
Definition: fold_compound.h:183
unsigned int length
The length of the sequence (or sequence alignment)
Definition: fold_compound.h:144
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
Functions to deal with sets of energy parameters.
short * reference_pt2
A pairtable of the second reference structure.
Definition: fold_compound.h:313
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: fold_compound.h:310
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: fold_compound.h:320
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: fold_compound.h:315
Implementations for the RNA folding grammar.
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.
int window_size
window size for local folding sliding window approach
Definition: fold_compound.h:332
char ** ptype_local
Pair type array (for local folding)
Definition: fold_compound.h:333
const vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: fold_compound.h:137
int * iindx
DP matrix accessor.
Definition: fold_compound.h:165
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: fold_compound.h:311
vrna_mx_pf_t * exp_matrices
The PF DP matrices.
Definition: fold_compound.h:160