RNAlib-2.4.4
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.h>
103 #include <ViennaRNA/sequence.h>
104 #include <ViennaRNA/dp_matrices.h>
105 #include <ViennaRNA/constraints.h>
106 #include <ViennaRNA/grammar.h>
109 
113 typedef enum {
117 
118 
131 struct vrna_fc_s {
143  unsigned int length;
144  int cutpoint;
148  unsigned int *strand_number;
149  unsigned int *strand_order;
150  unsigned int *strand_start;
151  unsigned int *strand_end;
152 
153  unsigned int strands;
154  vrna_seq_t *nucleotides;
155 
164  int *iindx;
165  int *jindx;
178  void *auxdata;
193  /* data structure to adjust additional structural domains, such as G-quadruplexes */
196  /* data structure to adjust additional contributions to unpaired stretches, e.g. due to protein binding */
199  /* auxiliary (user-defined) extension to the folding grammar */
200  vrna_gr_aux_t *aux_grammar;
201 
206 #ifndef VRNA_DISABLE_C11_FEATURES
207  /* C11 support for unnamed unions/structs */
208  union {
209  struct {
210 #endif
211 
216  char *sequence;
223  short *sequence_encoding2;
224  char *ptype;
246 #ifndef VRNA_DISABLE_C11_FEATURES
247  /* C11 support for unnamed unions/structs */
248  };
249  struct {
250 #endif
251 
256  char **sequences;
260  unsigned int n_seq;
263  char *cons_seq;
266  short *S_cons;
269  short **S;
272  short **S5;
275  short **S3;
278  char **Ss;
279  unsigned int **a2s;
280  int *pscore;
283  int **pscore_local;
293  int oldAliEn;
294 
298 #ifndef VRNA_DISABLE_C11_FEATURES
299  };
300  };
301 #endif
302 
309  unsigned int maxD1;
310  unsigned int maxD2;
311  short *reference_pt1;
312  short *reference_pt2;
314  unsigned int *referenceBPs1;
315  unsigned int *referenceBPs2;
316  unsigned int *bpdist;
318  unsigned int *mm1;
319  unsigned int *mm2;
332  char **ptype_local;
336 };
337 
338 
339 /* the definitions below should be used for functions that return/receive/destroy fold compound data structures */
340 
344 #define VRNA_OPTION_DEFAULT 0U
345 
352 #define VRNA_OPTION_MFE 1U
353 
360 #define VRNA_OPTION_PF 2U
361 
365 #define VRNA_OPTION_HYBRID 4U
366 
376 #define VRNA_OPTION_EVAL_ONLY 8U
377 
381 #define VRNA_OPTION_WINDOW 16U
382 
423 vrna_fold_compound(const char *sequence,
424  vrna_md_t *md_p,
425  unsigned int options);
426 
427 
467  vrna_md_t *md_p,
468  unsigned int options);
469 
470 
472 vrna_fold_compound_TwoD(const char *sequence,
473  const char *s1,
474  const char *s2,
475  vrna_md_t *md_p,
476  unsigned int options);
477 
478 
479 int
480 vrna_fold_compound_prepare(vrna_fold_compound_t *vc,
481  unsigned int options);
482 
483 
491 void
493 
494 
513  void *data,
515 
516 
534 
535 
540 #endif
short ** S3
Sl[s][i] holds next base 3&#39; of i in sequence s.
Definition: fold_compound.h:275
short ** S
Numerical encoding of the sequences in the alignment.
Definition: fold_compound.h:269
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
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: fold_compound.h:318
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:266
char * ptype
Pair type array.
Definition: fold_compound.h:224
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:219
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors.
Definition: fold_compound.h:162
Data structure to store all functionality for ligand binding.
Definition: unstructured_domains.h:203
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: fold_compound.h:316
short * reference_pt1
A pairtable of the first reference structure.
Definition: fold_compound.h:311
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: fold_compound.h:238
Data structure representing a nucleotide sequence.
Definition: sequence.h:35
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:131
char ** sequences
The aligned sequences.
Definition: fold_compound.h:256
The model details data structure and its corresponding modifiers.
void * auxdata
A pointer to auxiliary, user-defined data.
Definition: fold_compound.h:178
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:56
short * pscore_pf_compat
Precomputed array of pair types expressed as pairing scores indexed via iindx.
Definition: fold_compound.h:286
vrna_sd_t * domains_struc
Additional structured domains.
Definition: fold_compound.h:194
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: fold_compound.h:197
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: fold_compound.h:263
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: fold_compound.h:156
Definition: grammar.h:24
char * ptype_pf_compat
ptype array indexed via iindx
Definition: fold_compound.h:233
int * jindx
DP matrix accessor.
Definition: fold_compound.h:165
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: fold_compound.h:113
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...
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:177
The soft constraints data structure.
Definition: constraints_soft.h:166
short ** S5
S5[s][i] holds next base 5&#39; of i in sequence s.
Definition: fold_compound.h:272
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
vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition: fold_compound.h:290
The hard constraints data structure.
Definition: constraints_hard.h:372
Definition: fold_compound.h:115
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches...
unsigned int * strand_number
The strand number a particular nucleotide is associated with.
Definition: fold_compound.h:148
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: fold_compound.h:161
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: fold_compound.h:280
unsigned int n_seq
The number of sequences in the alignment.
Definition: fold_compound.h:260
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: fold_compound.h:315
char * sequence
The input sequence string.
Definition: fold_compound.h:216
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: fold_compound.h:158
Definition: fold_compound.h:114
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:173
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint...
Definition: fold_compound.h:144
int ** pscore_local
Precomputed array of pair types expressed as pairing scores.
Definition: fold_compound.h:283
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:182
unsigned int length
The length of the sequence (or sequence alignment)
Definition: fold_compound.h:143
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 and data structures for constraining secondary structure predictions and evaluation...
short * reference_pt2
A pairtable of the second reference structure.
Definition: fold_compound.h:312
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:309
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: fold_compound.h:319
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: fold_compound.h:314
Implementations for the RNA folding grammar.
vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: fold_compound.h:136
int window_size
window size for local folding sliding window approach
Definition: fold_compound.h:331
char ** ptype_local
Pair type array (for local folding)
Definition: fold_compound.h:332
int * iindx
DP matrix accessor.
Definition: fold_compound.h:164
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:310
vrna_mx_pf_t * exp_matrices
The PF DP matrices.
Definition: fold_compound.h:159