RNAlib-2.4.16
model.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_MODEL_H
2 #define VIENNA_RNA_PACKAGE_MODEL_H
3 
17 #ifndef NBASES
18 #define NBASES 8
19 #endif
20 
22 typedef struct vrna_md_s vrna_md_t;
23 
30 #define VRNA_MODEL_DEFAULT_TEMPERATURE 37.0
31 
36 #define VRNA_MODEL_DEFAULT_PF_SCALE -1
37 
42 #define VRNA_MODEL_DEFAULT_BETA_SCALE 1.
43 
47 #define VRNA_MODEL_DEFAULT_DANGLES 2
48 
53 #define VRNA_MODEL_DEFAULT_SPECIAL_HP 1
54 
59 #define VRNA_MODEL_DEFAULT_NO_LP 0
60 
65 #define VRNA_MODEL_DEFAULT_NO_GU 0
66 
71 #define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE 0
72 
77 #define VRNA_MODEL_DEFAULT_CIRC 0
78 
83 #define VRNA_MODEL_DEFAULT_GQUAD 0
84 
89 #define VRNA_MODEL_DEFAULT_UNIQ_ML 0
90 
95 #define VRNA_MODEL_DEFAULT_ENERGY_SET 0
96 
101 #define VRNA_MODEL_DEFAULT_BACKTRACK 1
102 
107 #define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE 'F'
108 
113 #define VRNA_MODEL_DEFAULT_COMPUTE_BPP 1
114 
119 #define VRNA_MODEL_DEFAULT_MAX_BP_SPAN -1
120 
125 #define VRNA_MODEL_DEFAULT_WINDOW_SIZE -1
126 
131 #define VRNA_MODEL_DEFAULT_LOG_ML 0
132 
137 #define VRNA_MODEL_DEFAULT_ALI_OLD_EN 0
138 
143 #define VRNA_MODEL_DEFAULT_ALI_RIBO 0
144 
149 #define VRNA_MODEL_DEFAULT_ALI_CV_FACT 1.
150 
154 #define VRNA_MODEL_DEFAULT_ALI_NC_FACT 1.
155 
156 
157 #define VRNA_MODEL_DEFAULT_PF_SMOOTH 1
158 
159 
160 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
161 
162 #ifndef MAXALPHA
163 
166 #define MAXALPHA 20
167 #endif
168 
169 #endif
170 
180 struct vrna_md_s {
181  double temperature;
182  double betaScale;
183  int pf_smooth;
184  int dangles;
209  int noLP;
210  int noGU;
212  int logML;
213  int circ;
214  int gquad;
215  int uniq_ML;
217  int backtrack;
220  char nonstandards[64];
228  int oldAliEn;
229  int ribo;
230  double cv_fact;
231  double nc_fact;
232  double sfact;
233  int rtype[8];
234  short alias[MAXALPHA + 1];
235  int pair[MAXALPHA + 1][MAXALPHA + 1];
236 };
237 
238 
247 void
249 
250 
263 void
265 
266 
277 vrna_md_t *
279  const vrna_md_t *md_from);
280 
281 
287 char *
289 
290 
291 void
292 vrna_md_set_nonstandards(vrna_md_t *md,
293  const char *ns_bases);
294 
295 
313 void
315 
316 
322 void
324 
325 
331 double
333 
334 
342 void
344 
345 
352 double
354 
355 
356 void
357 vrna_md_defaults_pf_smooth(int s);
358 
359 
360 int
361 vrna_md_defaults_pf_smooth_get(void);
362 
363 
369 void
371 
372 
378 int
380 
381 
387 void
389 
390 
396 int
398 
399 
405 void
407 
408 
414 int
416 
417 
423 void
425 
426 
432 int
434 
435 
441 void
443 
444 
450 int
452 
453 
459 void
461 
462 
468 int
470 
471 
477 void
479 
480 
486 int
488 
489 
495 void
497 
498 
504 int
506 
507 
514 void
516 
517 
523 int
525 
526 
532 void
534 
535 
541 int
543 
544 
550 void
552 
553 
559 int
561 
562 
568 void
570 
571 
577 char
579 
580 
586 void
588 
589 
595 int
597 
598 
604 void
606 
607 
613 int
615 
616 
622 void
624 
625 
631 int
633 
634 
640 void
642 
643 
649 int
651 
652 
660 void
662 
663 
669 int
671 
672 
678 void
680 
681 
687 int
689 
690 
696 void
698 
699 
705 double
707 
708 
714 void
716 
717 
723 double
725 
726 
732 void
733 vrna_md_defaults_sfact(double factor);
734 
735 
741 double
743 
744 
745 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
746 
747 #define model_detailsT vrna_md_t /* restore compatibility of struct rename */
748 
749 /* BEGIN deprecated global variables: */
750 
760 extern double temperature;
761 
773 extern double pf_scale;
774 
796 extern int dangles;
797 
803 extern int tetra_loop;
804 
812 extern int noLonelyPairs;
813 
817 extern int noGU;
818 
822 extern int no_closingGU;
823 
827 extern int circ;
828 
832 extern int gquad;
833 
837 extern int uniq_ML;
838 
846 extern int energy_set;
847 
854 extern int do_backtrack;
855 
863 extern char backtrack_type;
864 
872 extern char *nonstandards;
873 
879 extern int max_bp_span;
880 
884 extern int oldAliEn;
885 
889 extern int ribo;
890 
891 extern double cv_fact;
892 
893 extern double nc_fact;
894 
896 extern int logML;
897 
898 /* END deprecated global variables: */
899 
913 void
915 
916 
917 char *
918 option_string(void);
919 
920 
921 #endif
922 
926 #endif
oldAliEn
int oldAliEn
use old alifold energies (with gaps)
vrna_md_defaults_betaScale_get
double vrna_md_defaults_betaScale_get(void)
Get default scaling factor of thermodynamic temperature in Boltzmann factors.
vrna_md_defaults_uniq_ML
void vrna_md_defaults_uniq_ML(int flag)
Set default behavior for creating additional matrix for unique multi-branch loop prediction.
vrna_md_s::ribo
int ribo
Use ribosum scoring table in alifold energy model.
Definition: model.h:229
cv_fact
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
pf_scale
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
vrna_md_s::pair
int pair[MAXALPHA+1][MAXALPHA+1]
Integer representation of a base pair.
Definition: model.h:235
vrna_md_defaults_window_size
void vrna_md_defaults_window_size(int size)
Set default window size for sliding window structure prediction approaches.
vrna_md_s::rtype
int rtype[8]
Reverse base pair type array.
Definition: model.h:233
no_closingGU
int no_closingGU
GU allowed only inside stacks if set to 1.
vrna_md_defaults_cv_fact_get
double vrna_md_defaults_cv_fact_get(void)
Get the default co-variance scaling factor used in comparative structure prediction.
vrna_md_s::gquad
int gquad
Include G-quadruplexes in structure prediction.
Definition: model.h:214
vrna_md_defaults_energy_set_get
int vrna_md_defaults_energy_set_get(void)
Get default energy set.
vrna_md_defaults_compute_bpp
void vrna_md_defaults_compute_bpp(int flag)
Set the default behavior for whether to compute base pair probabilities after partition function comp...
vrna_md_defaults_cv_fact
void vrna_md_defaults_cv_fact(double factor)
Set the default co-variance scaling factor used in comparative structure prediction.
vrna_md_s::backtrack_type
char backtrack_type
Specifies in which matrix to backtrack.
Definition: model.h:218
vrna_md_defaults_oldAliEn
void vrna_md_defaults_oldAliEn(int flag)
Set default behavior for whether to use old energy model for comparative structure prediction.
vrna_md_defaults_special_hp_get
int vrna_md_defaults_special_hp_get(void)
Get default behavior for lookup of tabulated free energies for special hairpin loops,...
MAXALPHA
#define MAXALPHA
Maximal length of alphabet.
Definition: model.h:166
vrna_md_defaults_ribo
void vrna_md_defaults_ribo(int flag)
Set default behavior for whether to use Ribosum Scoring in comparative structure prediction.
vrna_md_defaults_backtrack_type
void vrna_md_defaults_backtrack_type(char t)
Set default backtrack type, i.e. which DP matrix is used.
noLonelyPairs
int noLonelyPairs
Global switch to avoid/allow helices of length 1.
vrna_md_defaults_backtrack_type_get
char vrna_md_defaults_backtrack_type_get(void)
Get default backtrack type, i.e. which DP matrix is used.
vrna_md_defaults_ribo_get
int vrna_md_defaults_ribo_get(void)
Get default behavior for whether to use Ribosum Scoring in comparative structure prediction.
energy_set
int energy_set
0 = BP; 1=any with GC; 2=any with AU-parameter
nonstandards
char * nonstandards
contains allowed non standard base pairs
vrna_md_defaults_circ
void vrna_md_defaults_circ(int flag)
Set default behavior whether input sequences are circularized.
vrna_md_s::dangles
int dangles
Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
Definition: model.h:184
vrna_md_s::circ
int circ
Assume RNA to be circular instead of linear.
Definition: model.h:213
gquad
int gquad
Allow G-quadruplex formation.
vrna_md_s::pf_smooth
int pf_smooth
A flat specifying whether energies in Boltzmann factors need to be smoothed.
Definition: model.h:183
vrna_md_s::min_loop_size
int min_loop_size
Minimum size of hairpin loops.
Definition: model.h:223
vrna_md_defaults_uniq_ML_get
int vrna_md_defaults_uniq_ML_get(void)
Get default behavior for creating additional matrix for unique multi-branch loop prediction.
vrna_md_s::nonstandards
char nonstandards[64]
contains allowed non standard bases
Definition: model.h:220
vrna_md_s::temperature
double temperature
The temperature used to scale the thermodynamic parameters.
Definition: model.h:181
backtrack_type
char backtrack_type
A backtrack array marker for inverse_fold()
uniq_ML
int uniq_ML
do ML decomposition uniquely (for subopt)
vrna_md_defaults_betaScale
void vrna_md_defaults_betaScale(double b)
Set default scaling factor of thermodynamic temperature in Boltzmann factors.
vrna_md_s::backtrack
int backtrack
Specifies whether or not secondary structures should be backtraced.
Definition: model.h:217
vrna_md_s::noGUclosure
int noGUclosure
Do not allow loops to be closed by GU pair.
Definition: model.h:211
set_model_details
void set_model_details(vrna_md_t *md)
Set default model details.
vrna_md_s::energy_set
int energy_set
Specifies the energy set that defines set of compatible base pairs.
Definition: model.h:216
vrna_md_s::betaScale
double betaScale
A scaling factor for the thermodynamic temperature of the Boltzmann factors.
Definition: model.h:182
dangles
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
max_bp_span
int max_bp_span
Maximum allowed base pair span.
vrna_md_update
void vrna_md_update(vrna_md_t *md)
Update the model details data structure.
vrna_md_defaults_backtrack_get
int vrna_md_defaults_backtrack_get(void)
Get default behavior for whether to backtrack secondary structures.
do_backtrack
int do_backtrack
do backtracking, i.e. compute secondary structures or base pair probabilities
vrna_md_defaults_noGU_get
int vrna_md_defaults_noGU_get(void)
Get default behavior for treatment of G-U wobble pairs.
vrna_md_defaults_max_bp_span
void vrna_md_defaults_max_bp_span(int span)
Set default maximal base pair span.
vrna_md_defaults_dangles
void vrna_md_defaults_dangles(int d)
Set default dangle model for structure prediction.
vrna_md_copy
vrna_md_t * vrna_md_copy(vrna_md_t *md_to, const vrna_md_t *md_from)
Copy/Clone a vrna_md_t model.
vrna_md_defaults_window_size_get
int vrna_md_defaults_window_size_get(void)
Get default window size for sliding window structure prediction approaches.
vrna_md_defaults_temperature
void vrna_md_defaults_temperature(double T)
Set default temperature for energy evaluation of loops.
vrna_md_defaults_noGU
void vrna_md_defaults_noGU(int flag)
Set default behavior for treatment of G-U wobble pairs.
vrna_md_s::compute_bpp
int compute_bpp
Specifies whether or not backward recursions for base pair probability (bpp) computation will be perf...
Definition: model.h:219
vrna_md_defaults_nc_fact_get
double vrna_md_defaults_nc_fact_get(void)
vrna_md_defaults_gquad_get
int vrna_md_defaults_gquad_get(void)
Get default behavior for treatment of G-Quadruplexes.
vrna_md_defaults_backtrack
void vrna_md_defaults_backtrack(int flag)
Set default behavior for whether to backtrack secondary structures.
vrna_md_set_default
void vrna_md_set_default(vrna_md_t *md)
Apply default model details to a provided vrna_md_t data structure.
vrna_md_defaults_nc_fact
void vrna_md_defaults_nc_fact(double factor)
vrna_md_s::noLP
int noLP
Only consider canonical structures, i.e. no 'lonely' base pairs.
Definition: model.h:209
vrna_md_s::special_hp
int special_hp
Include special hairpin contributions for tri, tetra and hexaloops.
Definition: model.h:208
vrna_md_defaults_reset
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.
vrna_md_defaults_temperature_get
double vrna_md_defaults_temperature_get(void)
Get default temperature for energy evaluation of loops.
vrna_md_defaults_min_loop_size
void vrna_md_defaults_min_loop_size(int size)
Set default minimal loop size.
vrna_md_s
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:180
vrna_md_defaults_logML_get
int vrna_md_defaults_logML_get(void)
Get default behavior recomputing free energies of multi-branch loops using a logarithmic model.
logML
int logML
if nonzero use logarithmic ML energy in energy_of_struct
vrna_md_s::noGU
int noGU
Do not allow GU pairs.
Definition: model.h:210
vrna_md_defaults_sfact
void vrna_md_defaults_sfact(double factor)
Set the default scaling factor used to avoid under-/overflows in partition function computation.
circ
int circ
backward compatibility variable.. this does not effect anything
vrna_md_defaults_noLP_get
int vrna_md_defaults_noLP_get(void)
Get default behavior for prediction of canonical secondary structures.
vrna_md_defaults_energy_set
void vrna_md_defaults_energy_set(int e)
Set default energy set.
vrna_md_s::alias
short alias[MAXALPHA+1]
alias of an integer nucleotide representation
Definition: model.h:234
nc_fact
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
vrna_md_s::uniq_ML
int uniq_ML
Flag to ensure unique multi-branch loop decomposition during folding.
Definition: model.h:215
vrna_md_defaults_dangles_get
int vrna_md_defaults_dangles_get(void)
Get default dangle model for structure prediction.
tetra_loop
int tetra_loop
Include special stabilizing energies for some tri-, tetra- and hexa-loops;.
vrna_md_defaults_max_bp_span_get
int vrna_md_defaults_max_bp_span_get(void)
Get default maximal base pair span.
vrna_md_defaults_special_hp
void vrna_md_defaults_special_hp(int flag)
Set default behavior for lookup of tabulated free energies for special hairpin loops,...
vrna_md_s::oldAliEn
int oldAliEn
Use old alifold energy model.
Definition: model.h:228
vrna_md_s::max_bp_span
int max_bp_span
maximum allowed base pair span
Definition: model.h:221
vrna_md_defaults_sfact_get
double vrna_md_defaults_sfact_get(void)
Get the default scaling factor used to avoid under-/overflows in partition function computation.
vrna_md_defaults_logML
void vrna_md_defaults_logML(int flag)
Set default behavior recomputing free energies of multi-branch loops using a logarithmic model.
vrna_md_s::nc_fact
double nc_fact
Scaling factor to weight co-variance contributions of non-canonical pairs.
Definition: model.h:231
temperature
double temperature
Rescale energy parameters to a temperature in degC.
vrna_md_s::window_size
int window_size
Size of the sliding window for locally optimal structure prediction.
Definition: model.h:227
vrna_md_option_string
char * vrna_md_option_string(vrna_md_t *md)
Get a corresponding commandline parameter string of the options in a vrna_md_t.
vrna_md_defaults_noLP
void vrna_md_defaults_noLP(int flag)
Set default behavior for prediction of canonical secondary structures.
vrna_md_defaults_min_loop_size_get
int vrna_md_defaults_min_loop_size_get(void)
Get default minimal loop size.
vrna_md_defaults_noGUclosure
void vrna_md_defaults_noGUclosure(int flag)
Set default behavior for G-U pairs as closing pair for loops.
vrna_md_defaults_gquad
void vrna_md_defaults_gquad(int flag)
Set default behavior for treatment of G-Quadruplexes.
vrna_md_s::sfact
double sfact
Scaling factor for partition function scaling.
Definition: model.h:232
vrna_md_s::logML
int logML
Use logarithmic scaling for multiloops.
Definition: model.h:212
vrna_md_defaults_noGUclosure_get
int vrna_md_defaults_noGUclosure_get(void)
Get default behavior for G-U pairs as closing pair for loops.
vrna_md_defaults_oldAliEn_get
int vrna_md_defaults_oldAliEn_get(void)
Get default behavior for whether to use old energy model for comparative structure prediction.
vrna_md_defaults_compute_bpp_get
int vrna_md_defaults_compute_bpp_get(void)
Get the default behavior for whether to compute base pair probabilities after partition function comp...
vrna_md_s::cv_fact
double cv_fact
Co-variance scaling factor for consensus structure prediction.
Definition: model.h:230
noGU
int noGU
Global switch to forbid/allow GU base pairs at all.
ribo
int ribo
use ribosum matrices
vrna_md_defaults_circ_get
int vrna_md_defaults_circ_get(void)
Get default behavior whether input sequences are circularized.