RNAlib-2.2.10
model.h
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1 #ifndef VIENNA_RNA_PACKAGE_MODEL_H
2 #define VIENNA_RNA_PACKAGE_MODEL_H
3 
4 #ifdef DEPRECATION_WARNINGS
5 # ifdef __GNUC__
6 # define DEPRECATED(func) func __attribute__ ((deprecated))
7 # else
8 # define DEPRECATED(func) func
9 # endif
10 #else
11 # define DEPRECATED(func) func
12 #endif
13 
14 
15 /* make this interface backward compatible with RNAlib < 2.2.0 */
16 #define VRNA_BACKWARD_COMPAT
17 
26 #ifndef NBASES
27 #define NBASES 8
28 #endif
29 
31 typedef struct vrna_md_s vrna_md_t;
32 
39 #define VRNA_MODEL_DEFAULT_TEMPERATURE 37.0
40 
45 #define VRNA_MODEL_DEFAULT_PF_SCALE -1
46 
51 #define VRNA_MODEL_DEFAULT_BETA_SCALE 1.
52 
56 #define VRNA_MODEL_DEFAULT_DANGLES 2
57 
62 #define VRNA_MODEL_DEFAULT_SPECIAL_HP 1
63 
68 #define VRNA_MODEL_DEFAULT_NO_LP 0
69 
74 #define VRNA_MODEL_DEFAULT_NO_GU 0
75 
80 #define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE 0
81 
86 #define VRNA_MODEL_DEFAULT_CIRC 0
87 
92 #define VRNA_MODEL_DEFAULT_GQUAD 0
93 
94 #define VRNA_MODEL_DEFAULT_CANONICAL_BP 0
95 
100 #define VRNA_MODEL_DEFAULT_UNIQ_ML 0
101 
106 #define VRNA_MODEL_DEFAULT_ENERGY_SET 0
107 
112 #define VRNA_MODEL_DEFAULT_BACKTRACK 1
113 
118 #define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE 'F'
119 
124 #define VRNA_MODEL_DEFAULT_COMPUTE_BPP 1
125 
130 #define VRNA_MODEL_DEFAULT_MAX_BP_SPAN -1
131 
136 #define VRNA_MODEL_DEFAULT_WINDOW_SIZE -1
137 
142 #define VRNA_MODEL_DEFAULT_LOG_ML 0
143 
148 #define VRNA_MODEL_DEFAULT_ALI_OLD_EN 0
149 
154 #define VRNA_MODEL_DEFAULT_ALI_RIBO 0
155 
160 #define VRNA_MODEL_DEFAULT_ALI_CV_FACT 1.
161 
165 #define VRNA_MODEL_DEFAULT_ALI_NC_FACT 1.
166 
167 
168 #ifdef VRNA_BACKWARD_COMPAT
169 
170 #ifndef MAXALPHA
171 
174 #define MAXALPHA 20
175 #endif
176 
177 #endif
178 
188 struct vrna_md_s {
189  double temperature;
190  double betaScale;
191  int dangles;
216  int noLP;
217  int noGU;
219  int logML;
220  int circ;
221  int gquad;
223  int uniq_ML;
225  int backtrack;
228  char nonstandards[64];
236  int oldAliEn;
237  int ribo;
238  double cv_fact;
239  double nc_fact;
240  double sfact;
241  int rtype[8];
242  short alias[MAXALPHA+1];
243  int pair[MAXALPHA+1][MAXALPHA+1];
244 };
245 
246 
255 void
257 
270 void
272 
278 char *
280 
281 void
282 vrna_md_set_nonstandards(vrna_md_t *md, const char *ns_bases);
283 
301 void
303 
309 void
311 
317 double
319 
327 void
329 
336 double
338 
344 void
346 
352 int
354 
360 void
362 
368 int
370 
376 void
377 vrna_md_defaults_noLP(int flag);
378 
384 int
386 
392 void
393 vrna_md_defaults_noGU(int flag);
394 
400 int
402 
408 void
410 
416 int
418 
424 void
425 vrna_md_defaults_logML(int flag);
426 
432 int
434 
440 void
441 vrna_md_defaults_circ(int flag);
442 
448 int
450 
456 void
457 vrna_md_defaults_gquad(int flag);
458 
464 int
466 
473 void
474 vrna_md_defaults_uniq_ML(int flag);
475 
481 int
483 
489 void
491 
497 int
499 
505 void
507 
513 int
515 
521 void
523 
529 char
531 
537 void
539 
545 int
547 
553 void
555 
561 int
563 
569 void
571 
577 int
579 
585 void
587 
593 int
595 
603 void
604 vrna_md_defaults_oldAliEn(int flag);
605 
611 int
613 
619 void
620 vrna_md_defaults_ribo(int flag);
621 
627 int
629 
635 void
636 vrna_md_defaults_cv_fact(double factor);
637 
643 double
645 
651 void
652 vrna_md_defaults_nc_fact(double factor);
653 
659 double
661 
667 void
668 vrna_md_defaults_sfact(double factor);
669 
675 double
677 
678 #ifdef VRNA_BACKWARD_COMPAT
679 
680 #define model_detailsT vrna_md_t /* restore compatibility of struct rename */
681 
682 /* BEGIN deprecated global variables: */
683 
693 extern double temperature;
694 
706 extern double pf_scale;
707 
729 extern int dangles;
730 
736 extern int tetra_loop;
737 
745 extern int noLonelyPairs;
746 
750 extern int noGU;
751 
755 extern int no_closingGU;
756 
760 extern int circ;
761 
765 extern int gquad;
766 
770 extern int canonicalBPonly;
771 
775 extern int uniq_ML;
776 
784 extern int energy_set;
785 
792 extern int do_backtrack;
793 
801 extern char backtrack_type;
802 
810 extern char *nonstandards;
811 
817 extern int max_bp_span;
818 
822 extern int oldAliEn;
823 
827 extern int ribo;
828 
829 extern double cv_fact;
830 
831 extern double nc_fact;
832 
834 extern int logML;
835 
836 /* END deprecated global variables: */
837 
851 void
853 
854 char *
855 option_string(void);
856 
857 #endif
858 
862 #endif
void vrna_md_defaults_sfact(double factor)
Set the default scaling factor used to avoid under-/overflows in partition function computation...
int backtrack
Specifies whether or not secondary structures should be backtraced.
Definition: model.h:225
void vrna_md_update(vrna_md_t *md)
Update the model details data structure.
int vrna_md_defaults_noLP_get(void)
Get default behavior for prediction of canonical secondary structures.
int vrna_md_defaults_min_loop_size_get(void)
Get default minimal loop size.
void vrna_md_set_default(vrna_md_t *md)
Apply default model details to a provided vrna_md_t data structure.
double vrna_md_defaults_sfact_get(void)
Get the default scaling factor used to avoid under-/overflows in partition function computation...
int vrna_md_defaults_max_bp_span_get(void)
Get default maximal base pair span.
char vrna_md_defaults_backtrack_type_get(void)
Get default backtrack type, i.e. which DP matrix is used.
int tetra_loop
Include special stabilizing energies for some tri-, tetra- and hexa-loops;.
short alias[MAXALPHA+1]
alias of an integer nucleotide representation
Definition: model.h:242
int vrna_md_defaults_backtrack_get(void)
Get default behavior for whether to backtrack secondary structures.
int special_hp
Include special hairpin contributions for tri, tetra and hexaloops.
Definition: model.h:215
int compute_bpp
Specifies whether or not backward recursions for base pair probability (bpp) computation will be perf...
Definition: model.h:227
void vrna_md_defaults_circ(int flag)
Set default behavior whether input sequences are circularized.
double vrna_md_defaults_temperature_get(void)
Get default temperature for energy evaluation of loops.
int vrna_md_defaults_window_size_get(void)
Get default window size for sliding window structure prediction approaches.
void vrna_md_defaults_noGU(int flag)
Set default behavior for treatment of G-U wobble pairs.
void vrna_md_defaults_betaScale(double b)
Set default scaling factor of thermodynamic temperature in Boltzmann factors.
int do_backtrack
do backtracking, i.e. compute secondary structures or base pair probabilities
int noLP
Only consider canonical structures, i.e. no &#39;lonely&#39; base pairs.
Definition: model.h:216
void vrna_md_defaults_max_bp_span(int span)
Set default maximal base pair span.
void vrna_md_defaults_dangles(int d)
Set default dangle model for structure prediction.
int uniq_ML
Flag to ensure unique multibranch loop decomposition during folding.
Definition: model.h:223
int vrna_md_defaults_oldAliEn_get(void)
Get default behavior for whether to use old energy model for comparative structure prediction...
int noGU
Do not allow GU pairs.
Definition: model.h:217
void vrna_md_defaults_temperature(double T)
Set default temperature for energy evaluation of loops.
double vrna_md_defaults_nc_fact_get(void)
void vrna_md_defaults_special_hp(int flag)
Set default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops.
double cv_fact
Covariance scaling factor for consensus structure prediction.
Definition: model.h:238
int vrna_md_defaults_energy_set_get(void)
Get default energy set.
int oldAliEn
Use old alifold energy model.
Definition: model.h:236
int window_size
Size of the sliding window for locally optimal structure predition.
Definition: model.h:235
int vrna_md_defaults_ribo_get(void)
Get default behavior for whether to use Ribosum Scoring in comparative structure prediction.
double nc_fact
Scaling factor to weight covariance contributions of non-canonical pairs.
Definition: model.h:239
int logML
Use logarithmic scaling for multi loops.
Definition: model.h:219
void vrna_md_defaults_uniq_ML(int flag)
Set default behavior for creating additional matrix for unique multibranch loop prediction.
int max_bp_span
maximum allowed base pair span
Definition: model.h:229
char * vrna_md_option_string(vrna_md_t *md)
Get a corresponding commandline parameter string of the options in a vrna_md_t.
int vrna_md_defaults_special_hp_get(void)
Get default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops.
int rtype[8]
Reverse base pair type array.
Definition: model.h:241
int vrna_md_defaults_circ_get(void)
Get default behavior whether input sequences are circularized.
void vrna_md_defaults_reset(vrna_md_t *md_p)
Reset the global default model details to a specific set of parameters, or their initial values...
void set_model_details(vrna_md_t *md)
Set default model details.
void vrna_md_defaults_min_loop_size(int size)
Set default minimal loop size.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:188
void vrna_md_defaults_energy_set(int e)
Set default energy set.
double sfact
Scaling factor for partition function scaling.
Definition: model.h:240
void vrna_md_defaults_cv_fact(double factor)
Set the default covariance scaling factor used in comparative structure prediction.
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
void vrna_md_defaults_logML(int flag)
Set default behavior recomputing free energies of multibranch loops using a logarithmic model...
int gquad
Include G-quadruplexes in structure prediction.
Definition: model.h:221
void vrna_md_defaults_noLP(int flag)
Set default behavior for prediction of canonical secondary structures.
#define MAXALPHA
Maximal length of alphabet.
Definition: model.h:174
void vrna_md_defaults_window_size(int size)
Set default window size for sliding window structure prediction approaches.
void vrna_md_defaults_gquad(int flag)
Set default behavior for treatment of G-Quadruplexes.
void vrna_md_defaults_backtrack_type(char t)
Set default backtrack type, i.e. which DP matrix is used.
void vrna_md_defaults_backtrack(int flag)
Set default behavior for whether to backtrack secondary structures.
int vrna_md_defaults_noGU_get(void)
Get default behavior for treatment of G-U wobble pairs.
char backtrack_type
Specifies in which matrix to backtrack.
Definition: model.h:226
void vrna_md_defaults_oldAliEn(int flag)
Set default behavior for whether to use old energy model for comparative structure prediction...
int vrna_md_defaults_uniq_ML_get(void)
Get default behavior for creating additional matrix for unique multibranch loop prediction.
void vrna_md_defaults_ribo(int flag)
Set default behavior for whether to use Ribosum Scoring in comparative structure prediction.
int ribo
Use ribosum scoring table in alifold energy model.
Definition: model.h:237
int vrna_md_defaults_compute_bpp_get(void)
Get the default behavior for whether to compute base pair probabilities after partition function comp...
int pair[MAXALPHA+1][MAXALPHA+1]
Integer representation of a base pair.
Definition: model.h:243
char nonstandards[64]
contains allowed non standard bases
Definition: model.h:228
double vrna_md_defaults_cv_fact_get(void)
Get the default covariance scaling factor used in comparative structure prediction.
double temperature
The temperature used to scale the thermodynamic parameters.
Definition: model.h:189
int dangles
Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
Definition: model.h:191
int noLonelyPairs
Global switch to avoid/allow helices of length 1.
double vrna_md_defaults_betaScale_get(void)
Get default scaling factor of thermodynamic temperature in Boltzmann factors.
int circ
Assume RNA to be circular instead of linear.
Definition: model.h:220
int vrna_md_defaults_gquad_get(void)
Get default behavior for treatment of G-Quadruplexes.
int canonicalBPonly
remove non-canonical bp&#39;s from constraint structures
Definition: model.h:222
void vrna_md_defaults_compute_bpp(int flag)
Set the default behavior for whether to compute base pair probabilities after partition function comp...
void vrna_md_defaults_nc_fact(double factor)
void vrna_md_defaults_noGUclosure(int flag)
Set default behavior for G-U pairs as closing pair for loops.
int no_closingGU
GU allowed only inside stacks if set to 1.
int vrna_md_defaults_logML_get(void)
Get default behavior recomputing free energies of multibranch loops using a logarithmic model...
int noGUclosure
Do not allow loops to be closed by GU pair.
Definition: model.h:218
int energy_set
Specifies the energy set that defines set of compatible base pairs.
Definition: model.h:224
int min_loop_size
Minimum size of hairpin loops.
Definition: model.h:231
int vrna_md_defaults_dangles_get(void)
Get default dangle model for structure prediction.
int vrna_md_defaults_noGUclosure_get(void)
Get default behavior for G-U pairs as closing pair for loops.
double betaScale
A scaling factor for the thermodynamic temperature of the Boltzmann factors.
Definition: model.h:190