RNAlib-2.5.0alpha2
fold_compound.h
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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 
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_order_uniq;
152  unsigned int *strand_start;
153  unsigned int *strand_end;
155  unsigned int strands;
156  vrna_seq_t *nucleotides;
157  vrna_msa_t *alignment;
158 
167  int *iindx;
168  int *jindx;
181  void *auxdata;
196  /* data structure to adjust additional structural domains, such as G-quadruplexes */
199  /* data structure to adjust additional contributions to unpaired stretches, e.g. due to protein binding */
202  /* auxiliary (user-defined) extension to the folding grammar */
203  vrna_gr_aux_t *aux_grammar;
204 
209 #ifndef VRNA_DISABLE_C11_FEATURES
210  /* C11 support for unnamed unions/structs */
211  union {
212  struct {
213 #endif
214 
219  char *sequence;
226  short *sequence_encoding2;
227  char *ptype;
249 #ifndef VRNA_DISABLE_C11_FEATURES
250  /* C11 support for unnamed unions/structs */
251 };
252 struct {
253 #endif
254 
259  char **sequences;
263  unsigned int n_seq;
266  char *cons_seq;
269  short *S_cons;
272  short **S;
275  short **S5;
278  short **S3;
281  char **Ss;
282  unsigned int **a2s;
283  int *pscore;
286  int **pscore_local;
296  int oldAliEn;
297 
301 #ifndef VRNA_DISABLE_C11_FEATURES
302 };
303 };
304 #endif
305 
312  unsigned int maxD1;
313  unsigned int maxD2;
314  short *reference_pt1;
315  short *reference_pt2;
317  unsigned int *referenceBPs1;
318  unsigned int *referenceBPs2;
319  unsigned int *bpdist;
321  unsigned int *mm1;
322  unsigned int *mm2;
335  char **ptype_local;
339 };
340 
341 
342 /* the definitions below should be used for functions that return/receive/destroy fold compound data structures */
343 
347 #define VRNA_OPTION_DEFAULT 0U
348 
355 #define VRNA_OPTION_MFE 1U
356 
363 #define VRNA_OPTION_PF 2U
364 
368 #define VRNA_OPTION_HYBRID 4U
369 
379 #define VRNA_OPTION_EVAL_ONLY 8U
380 
384 #define VRNA_OPTION_WINDOW 16U
385 
424 vrna_fold_compound(const char *sequence,
425  vrna_md_t *md_p,
426  unsigned int options);
427 
428 
467 vrna_fold_compound_comparative(const char **sequences,
468  vrna_md_t *md_p,
469  unsigned int options);
470 
471 
473 vrna_fold_compound_comparative2(const char **sequences,
474  const char **names,
475  const unsigned char *orientation,
476  const unsigned long long *start,
477  const unsigned long long *genome_size,
478  vrna_md_t *md_p,
479  unsigned int options);
480 
481 
483 vrna_fold_compound_TwoD(const char *sequence,
484  const char *s1,
485  const char *s2,
486  vrna_md_t *md_p,
487  unsigned int options);
488 
489 
490 int
491 vrna_fold_compound_prepare(vrna_fold_compound_t *fc,
492  unsigned int options);
493 
494 
502 void
504 
505 
523 void
525  void *data,
527 
528 
544 void
547 
548 
553 #endif
vrna_fc_s::reference_pt2
short * reference_pt2
A pairtable of the second reference structure.
Definition: fold_compound.h:315
vrna_fc_s::matrices
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: fold_compound.h:161
vrna_fold_compound_comparative
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_fc_s::exp_params
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors
Definition: fold_compound.h:165
vrna_fc_s::S
short ** S
Numerical encoding of the sequences in the alignment.
Definition: fold_compound.h:272
vrna_alignment_s
Definition: sequence.h:52
vrna_fc_s::sc
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: fold_compound.h:241
vrna_fc_s::maxD1
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: fold_compound.h:312
vrna_fc_s::maxD2
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: fold_compound.h:313
vrna_fc_s::strand_end
unsigned int * strand_end
The end (last) position of a particular strand within the current concatenated sequence.
Definition: fold_compound.h:153
model.h
The model details data structure and its corresponding modifiers.
hard.h
Functions and data structures for handling of secondary structure hard constraints.
vrna_fc_s::window_size
int window_size
window size for local folding sliding window approach
Definition: fold_compound.h:334
vrna_hc_s
The hard constraints data structure.
Definition: hard.h:371
vrna_fc_s::ptype
char * ptype
Pair type array.
Definition: fold_compound.h:227
vrna_fc_s::reference_pt1
short * reference_pt1
A pairtable of the first reference structure.
Definition: fold_compound.h:314
vrna_mx_mfe_s
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition: dp_matrices.h:46
vrna_fc_s::referenceBPs1
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: fold_compound.h:317
vrna_fc_s::sequence_encoding
short * sequence_encoding
Numerical encoding of the input sequence.
Definition: fold_compound.h:222
vrna_fc_s::S_cons
short * S_cons
Numerical encoding of the consensus sequence.
Definition: fold_compound.h:269
grammar.h
Implementations for the RNA folding grammar.
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
vrna_fc_s::bpdist
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,...
Definition: fold_compound.h:319
vrna_fold_compound_free
void vrna_fold_compound_free(vrna_fold_compound_t *fc)
Free memory occupied by a vrna_fold_compound_t.
vrna_fc_s::exp_matrices
vrna_mx_pf_t * exp_matrices
The PF DP matrices
Definition: fold_compound.h:162
vrna_fc_s::sequences
char ** sequences
The aligned sequences.
Definition: fold_compound.h:259
vrna_fc_s::cons_seq
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: fold_compound.h:266
vrna_sequence_s
Data structure representing a nucleotide sequence.
Definition: sequence.h:41
vrna_fc_s::jindx
int * jindx
DP matrix accessor
Definition: fold_compound.h:168
vrna_fc_s::S3
short ** S3
Sl[s][i] holds next base 3' of i in sequence s.
Definition: fold_compound.h:278
VRNA_FC_TYPE_COMPARATIVE
@ VRNA_FC_TYPE_COMPARATIVE
Definition: fold_compound.h:116
dp_matrices.h
Functions to deal with standard dynamic programming (DP) matrices.
vrna_fc_s::scs
vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition: fold_compound.h:293
vrna_fc_s::domains_struc
vrna_sd_t * domains_struc
Additional structured domains.
Definition: fold_compound.h:197
sequence.h
Functions and data structures related to sequence representations.
vrna_sc_s
The soft constraints data structure.
Definition: soft.h:171
vrna_fold_compound_add_callback
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.
vrna_fc_s::auxdata
void * auxdata
A pointer to auxiliary, user-defined data.
Definition: fold_compound.h:181
structured_domains.h
This module provides interfaces that deal with additional structured domains in the folding grammar.
soft.h
Functions and data structures for secondary structure soft constraints.
vrna_fc_s::strand_number
unsigned int * strand_number
The strand number a particular nucleotide is associated with.
Definition: fold_compound.h:149
vrna_fold_compound_add_auxdata
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_exp_param_s
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition: basic.h:103
vrna_fc_s::S5
short ** S5
S5[s][i] holds next base 5' of i in sequence s.
Definition: fold_compound.h:275
vrna_fc_s::pscore_local
int ** pscore_local
Precomputed array of pair types expressed as pairing scores.
Definition: fold_compound.h:286
vrna_fc_s::strand_order
unsigned int * strand_order
The strand order, i.e. permutation of current concatenated sequence.
Definition: fold_compound.h:150
vrna_fc_s::hc
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: fold_compound.h:159
vrna_fc_s::mm2
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: fold_compound.h:322
vrna_fc_s::domains_up
vrna_ud_t * domains_up
Additional unstructured domains.
Definition: fold_compound.h:200
vrna_fc_s::strand_order_uniq
unsigned int * strand_order_uniq
The strand order array where identical sequences have the same ID.
Definition: fold_compound.h:151
vrna_fc_s::ptype_pf_compat
char * ptype_pf_compat
ptype array indexed via iindx
Definition: fold_compound.h:236
vrna_fc_s::pscore_pf_compat
short * pscore_pf_compat
Precomputed array of pair types expressed as pairing scores indexed via iindx.
Definition: fold_compound.h:289
vrna_mx_pf_s
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition: dp_matrices.h:204
vrna_fc_s::cutpoint
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint,...
Definition: fold_compound.h:145
vrna_md_s
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:180
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
vrna_fc_s::strand_start
unsigned int * strand_start
The start position of a particular strand within the current concatenated sequence.
Definition: fold_compound.h:152
unstructured_domains.h
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.
vrna_fc_s::pscore
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: fold_compound.h:283
VRNA_FC_TYPE_SINGLE
@ VRNA_FC_TYPE_SINGLE
Definition: fold_compound.h:115
vrna_fc_s::referenceBPs2
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: fold_compound.h:318
vrna_fc_s::length
unsigned int length
The length of the sequence (or sequence alignment)
Definition: fold_compound.h:144
vrna_gr_aux_s
Definition: grammar.h:53
vrna_fc_s::free_auxdata
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:185
vrna_callback_recursion_status
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_unstructured_domain_s
Data structure to store all functionality for ligand binding.
Definition: unstructured_domains.h:228
vrna_fc_s::n_seq
unsigned int n_seq
The number of sequences in the alignment.
Definition: fold_compound.h:263
vrna_fold_compound
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.
vrna_fc_type_e
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_callback_free_auxdata
void() vrna_callback_free_auxdata(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: fold_compound.h:46
vrna_fc_s::params
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: fold_compound.h:164
vrna_structured_domains_s
Definition: structured_domains.h:26
vrna_fc_s::mm1
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: fold_compound.h:321
vrna_fc_s::ptype_local
char ** ptype_local
Pair type array (for local folding)
Definition: fold_compound.h:335
vrna_fc_s::sequence
char * sequence
The input sequence string.
Definition: fold_compound.h:219
vrna_fc_s::stat_cb
vrna_callback_recursion_status * stat_cb
Recursion status callback (usually called just before, and after recursive computations in the librar...
Definition: fold_compound.h:176
vrna_fc_s::type
const vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: fold_compound.h:137
vrna_fc_s::iindx
int * iindx
DP matrix accessor
Definition: fold_compound.h:167
basic.h
Functions to deal with sets of energy parameters.