RNAlib-2.2.5
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 
29 #ifndef NBASES
30 #define NBASES 8
31 #endif
32 
34 typedef struct vrna_md_s vrna_md_t;
35 
42 #define VRNA_MODEL_DEFAULT_TEMPERATURE 37.0
43 
48 #define VRNA_MODEL_DEFAULT_PF_SCALE -1
49 
54 #define VRNA_MODEL_DEFAULT_BETA_SCALE 1.
55 
59 #define VRNA_MODEL_DEFAULT_DANGLES 2
60 
65 #define VRNA_MODEL_DEFAULT_SPECIAL_HP 1
66 
71 #define VRNA_MODEL_DEFAULT_NO_LP 0
72 
77 #define VRNA_MODEL_DEFAULT_NO_GU 0
78 
83 #define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE 0
84 
89 #define VRNA_MODEL_DEFAULT_CIRC 0
90 
95 #define VRNA_MODEL_DEFAULT_GQUAD 0
96 
97 #define VRNA_MODEL_DEFAULT_CANONICAL_BP 0
98 
103 #define VRNA_MODEL_DEFAULT_UNIQ_ML 0
104 
109 #define VRNA_MODEL_DEFAULT_ENERGY_SET 0
110 
115 #define VRNA_MODEL_DEFAULT_BACKTRACK 1
116 
121 #define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE 'F'
122 
127 #define VRNA_MODEL_DEFAULT_COMPUTE_BPP 1
128 
133 #define VRNA_MODEL_DEFAULT_MAX_BP_SPAN -1
134 
139 #define VRNA_MODEL_DEFAULT_WINDOW_SIZE -1
140 
145 #define VRNA_MODEL_DEFAULT_LOG_ML 0
146 
151 #define VRNA_MODEL_DEFAULT_ALI_OLD_EN 0
152 
157 #define VRNA_MODEL_DEFAULT_ALI_RIBO 0
158 
163 #define VRNA_MODEL_DEFAULT_ALI_CV_FACT 1.
164 
168 #define VRNA_MODEL_DEFAULT_ALI_NC_FACT 1.
169 
170 
171 #ifdef VRNA_BACKWARD_COMPAT
172 
173 #ifndef MAXALPHA
174 
177 #define MAXALPHA 20
178 #endif
179 
180 #endif
181 
190 struct vrna_md_s {
191  double temperature;
192  double betaScale;
193  int dangles;
218  int noLP;
219  int noGU;
221  int logML;
222  int circ;
223  int gquad;
225  int uniq_ML;
227  int backtrack;
230  char nonstandards[33];
238  int oldAliEn;
239  int ribo;
240  double cv_fact;
241  double nc_fact;
242  double sfact;
243  int rtype[8];
244  short alias[MAXALPHA+1];
245  int pair[MAXALPHA+1][MAXALPHA+1];
246 };
247 
248 
257 void
259 
272 void
274 
280 char *
282 
283 void
284 vrna_md_set_nonstandards(vrna_md_t *md, const char *ns);
285 
303 void
305 
311 void
313 
319 double
321 
329 void
331 
338 double
340 
346 void
348 
354 int
356 
362 void
364 
370 int
372 
378 void
379 vrna_md_defaults_noLP(int flag);
380 
386 int
388 
394 void
395 vrna_md_defaults_noGU(int flag);
396 
402 int
404 
410 void
412 
418 int
420 
426 void
427 vrna_md_defaults_logML(int flag);
428 
434 int
436 
442 void
443 vrna_md_defaults_circ(int flag);
444 
450 int
452 
458 void
459 vrna_md_defaults_gquad(int flag);
460 
466 int
468 
475 void
476 vrna_md_defaults_uniq_ML(int flag);
477 
483 int
485 
491 void
493 
499 int
501 
507 void
509 
515 int
517 
523 void
525 
531 char
533 
539 void
541 
547 int
549 
555 void
557 
563 int
565 
571 void
573 
579 int
581 
587 void
589 
595 int
597 
605 void
606 vrna_md_defaults_oldAliEn(int flag);
607 
613 int
615 
621 void
622 vrna_md_defaults_ribo(int flag);
623 
629 int
631 
637 void
638 vrna_md_defaults_cv_fact(double factor);
639 
645 double
647 
653 void
654 vrna_md_defaults_nc_fact(double factor);
655 
661 double
663 
669 void
670 vrna_md_defaults_sfact(double factor);
671 
677 double
679 
680 #ifdef VRNA_BACKWARD_COMPAT
681 
682 #define model_detailsT vrna_md_t /* restore compatibility of struct rename */
683 
684 /* BEGIN deprecated global variables: */
685 
695 extern double temperature;
696 
708 extern double pf_scale;
709 
731 extern int dangles;
732 
738 extern int tetra_loop;
739 
747 extern int noLonelyPairs;
748 
752 extern int noGU;
753 
757 extern int no_closingGU;
758 
762 extern int circ;
763 
767 extern int gquad;
768 
772 extern int canonicalBPonly;
773 
777 extern int uniq_ML;
778 
786 extern int energy_set;
787 
794 extern int do_backtrack;
795 
803 extern char backtrack_type;
804 
812 extern char *nonstandards;
813 
819 extern int max_bp_span;
820 
824 extern int oldAliEn;
825 
829 extern int ribo;
830 
831 extern double cv_fact;
832 
833 extern double nc_fact;
834 
836 extern int logML;
837 
838 /* END deprecated global variables: */
839 
853 void
855 
856 char *
857 option_string(void);
858 
859 #endif
860 
864 #endif
int energy_set
0 = BP; 1=any mit GC; 2=any mit AU-parameter
void vrna_md_defaults_sfact(double factor)
Set the default scaling factor used to avoid under-/overflows in partition function computation...
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.
int window_size
Size of the sliding window for locally optimal structure predition.
Definition: model.h:237
double vrna_md_defaults_sfact_get(void)
Get the default scaling factor used to avoid under-/overflows in partition function computation...
short alias[MAXALPHA+1]
alias of an integer nucleotide representation
Definition: model.h:244
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;.
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
int vrna_md_defaults_backtrack_get(void)
Get default behavior for whether to backtrack secondary structures.
char backtrack_type
A backtrack array marker for inverse_fold()
int dangles
Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
Definition: model.h:193
void vrna_md_defaults_circ(int flag)
Set default behavior whether input sequences are circularized.
int backtrack
Specifies whether or not secondary structures should be backtraced.
Definition: model.h:227
double vrna_md_defaults_temperature_get(void)
Get default temperature for energy evaluation of loops.
int logML
if nonzero use logarithmic ML energy in energy_of_struct
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 noGU
Global switch to forbid/allow GU base pairs at all.
int max_bp_span
maximum allowed base pair span
Definition: model.h:231
double temperature
Rescale energy parameters to a temperature in degC.
char * nonstandards
contains allowed non standard base pairs
int ribo
use ribosum matrices
int noGUclosure
Do not allow loops to be closed by GU pair.
Definition: model.h:220
int do_backtrack
do backtracking, i.e. compute secondary structures or base pair probabilities
int energy_set
Specifies the energy set that defines set of compatible base pairs.
Definition: model.h:226
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 vrna_md_defaults_oldAliEn_get(void)
Get default behavior for whether to use old energy model for comparative structure prediction...
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 nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
int vrna_md_defaults_energy_set_get(void)
Get default energy set.
int vrna_md_defaults_ribo_get(void)
Get default behavior for whether to use Ribosum Scoring in comparative structure prediction.
double betaScale
A scaling factor for the thermodynamic temperature of the Boltzmann factors.
Definition: model.h:192
char backtrack_type
Specifies in which matrix to backtrack.
Definition: model.h:228
int noLP
Only consider canonical structures, i.e. no 'lonely' base pairs.
Definition: model.h:218
int ribo
Use ribosum scoring table in alifold energy model.
Definition: model.h:239
int pair[MAXALPHA+1][MAXALPHA+1]
Integer representation of a base pair.
Definition: model.h:245
void vrna_md_defaults_uniq_ML(int flag)
Set default behavior for creating additional matrix for unique multibranch loop prediction.
int gquad
Include G-quadruplexes in structure prediction.
Definition: model.h:223
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 uniq_ML
do ML decomposition uniquely (for subopt)
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.
void vrna_md_defaults_energy_set(int e)
Set default energy set.
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.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:190
void vrna_md_defaults_logML(int flag)
Set default behavior recomputing free energies of multibranch loops using a logarithmic model...
void vrna_md_defaults_noLP(int flag)
Set default behavior for prediction of canonical secondary structures.
int special_hp
Include special hairpin contributions for tri, tetra and hexaloops.
Definition: model.h:217
#define MAXALPHA
Maximal length of alphabet.
Definition: model.h:177
void vrna_md_defaults_window_size(int size)
Set default window size for sliding window structure prediction approaches.
int uniq_ML
Flag to ensure unique multibranch loop decomposition during folding.
Definition: model.h:225
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.
int oldAliEn
use old alifold energies (with gaps)
int oldAliEn
Use old alifold energy model.
Definition: model.h:238
double temperature
The temperature used to scale the thermodynamic parameters.
Definition: model.h:191
int min_loop_size
Minimum size of hairpin loops.
Definition: model.h:233
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.
int canonicalBPonly
int logML
Use logarithmic scaling for multi loops.
Definition: model.h:221
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.
int gquad
Allow G-quadruplex formation.
void vrna_md_defaults_ribo(int flag)
Set default behavior for whether to use Ribosum Scoring in comparative structure prediction.
int vrna_md_defaults_compute_bpp_get(void)
Get the default behavior for whether to compute base pair probabilities after partition function comp...
int canonicalBPonly
remove non-canonical bp's from constraint structures
Definition: model.h:224
double vrna_md_defaults_cv_fact_get(void)
Get the default covariance scaling factor used in comparative structure prediction.
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 vrna_md_defaults_gquad_get(void)
Get default behavior for treatment of G-Quadruplexes.
int max_bp_span
Maximum allowed base pair span.
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)
char nonstandards[33]
contains allowed non standard bases
Definition: model.h:230
int circ
Assume RNA to be circular instead of linear.
Definition: model.h:222
int compute_bpp
Specifies whether or not backward recursions for base pair probability (bpp) computation will be perf...
Definition: model.h:229
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 rtype[8]
Reverse base pair type array.
Definition: model.h:243
double cv_fact
Covariance scaling factor for consensus structure prediction.
Definition: model.h:240
int vrna_md_defaults_logML_get(void)
Get default behavior recomputing free energies of multibranch loops using a logarithmic model...
int circ
backward compatibility variable.. this does not effect anything
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
int noGU
Do not allow GU pairs.
Definition: model.h:219
double sfact
Scaling factor for partition function scaling.
Definition: model.h:242
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.