RNAlib-2.5.1
model.h
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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
22typedef 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
166#define MAXALPHA 20
167#endif
168
169#endif
170
180struct vrna_md_s {
181 double temperature;
182 double betaScale;
209 int noLP;
210 int noGU;
212 int logML;
213 int circ;
214 int gquad;
220 char nonstandards[64];
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 float pair_dist[7][7];
237};
238
239
248void
250
251
264void
266
267
278vrna_md_t *
280 const vrna_md_t *md_from);
281
282
288char *
290
291
292void
293vrna_md_set_nonstandards(vrna_md_t *md,
294 const char *ns_bases);
295
296
314void
316
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323void
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332double
334
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343void
345
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353double
355
356
357void
358vrna_md_defaults_pf_smooth(int s);
359
360
361int
362vrna_md_defaults_pf_smooth_get(void);
363
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370void
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746#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
747
748#define model_detailsT vrna_md_t /* restore compatibility of struct rename */
749
750/* BEGIN deprecated global variables: */
751
761extern double temperature;
762
774extern double pf_scale;
775
797extern int dangles;
798
804extern int tetra_loop;
805
813extern int noLonelyPairs;
814
818extern int noGU;
819
823extern int no_closingGU;
824
828extern int circ;
829
833extern int gquad;
834
838extern int uniq_ML;
839
847extern int energy_set;
848
855extern int do_backtrack;
856
864extern char backtrack_type;
865
873extern char *nonstandards;
874
880extern int max_bp_span;
881
885extern int oldAliEn;
886
890extern int ribo;
891
892extern double cv_fact;
893
894extern double nc_fact;
895
897extern int logML;
898
899/* END deprecated global variables: */
900
914void
916
917
918char *
919option_string(void);
920
921
922#endif
927#endif
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
double betaScale
A scaling factor for the thermodynamic temperature of the Boltzmann factors.
Definition: model.h:182
int backtrack
Specifies whether or not secondary structures should be backtraced.
Definition: model.h:217
int ribo
Use ribosum scoring table in alifold energy model.
Definition: model.h:229
char nonstandards[64]
contains allowed non standard bases
Definition: model.h:220
int energy_set
Specifies the energy set that defines set of compatible base pairs.
Definition: model.h:216
double temperature
The temperature used to scale the thermodynamic parameters.
Definition: model.h:181
double cv_fact
Co-variance scaling factor for consensus structure prediction.
Definition: model.h:230
int max_bp_span
maximum allowed base pair span
Definition: model.h:221
short alias[MAXALPHA+1]
alias of an integer nucleotide representation
Definition: model.h:234
int noLP
Only consider canonical structures, i.e. no 'lonely' base pairs.
Definition: model.h:209
int noGUclosure
Do not allow loops to be closed by GU pair.
Definition: model.h:211
int circ
Assume RNA to be circular instead of linear.
Definition: model.h:213
float pair_dist[7][7]
Base pair dissimilarity, a.k.a. distance matrix.
Definition: model.h:236
int pf_smooth
A flat specifying whether energies in Boltzmann factors need to be smoothed.
Definition: model.h:183
int min_loop_size
Minimum size of hairpin loops.
Definition: model.h:223
int compute_bpp
Specifies whether or not backward recursions for base pair probability (bpp) computation will be perf...
Definition: model.h:219
int pair[MAXALPHA+1][MAXALPHA+1]
Integer representation of a base pair.
Definition: model.h:235
int oldAliEn
Use old alifold energy model.
Definition: model.h:228
double sfact
Scaling factor for partition function scaling.
Definition: model.h:232
char backtrack_type
Specifies in which matrix to backtrack.
Definition: model.h:218
double nc_fact
Scaling factor to weight co-variance contributions of non-canonical pairs.
Definition: model.h:231
int window_size
Size of the sliding window for locally optimal structure prediction.
Definition: model.h:227
int rtype[8]
Reverse base pair type array.
Definition: model.h:233
int noGU
Do not allow GU pairs.
Definition: model.h:210
int dangles
Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
Definition: model.h:184
int special_hp
Include special hairpin contributions for tri, tetra and hexaloops.
Definition: model.h:208
int uniq_ML
Flag to ensure unique multi-branch loop decomposition during folding.
Definition: model.h:215
int logML
Use logarithmic scaling for multiloops.
Definition: model.h:212
int gquad
Include G-quadruplexes in structure prediction.
Definition: model.h:214
int vrna_md_defaults_energy_set_get(void)
Get default energy set.
#define MAXALPHA
Maximal length of alphabet.
Definition: model.h:166
int ribo
use ribosum matrices
void vrna_md_defaults_gquad(int flag)
Set default behavior for treatment of G-Quadruplexes.
int noLonelyPairs
Global switch to avoid/allow helices of length 1.
char vrna_md_defaults_backtrack_type_get(void)
Get default backtrack type, i.e. which DP matrix is used.
int vrna_md_defaults_ribo_get(void)
Get default behavior for whether to use Ribosum Scoring in comparative structure prediction.
int max_bp_span
Maximum allowed base pair span.
int vrna_md_defaults_special_hp_get(void)
Get default behavior for lookup of tabulated free energies for special hairpin loops,...
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_oldAliEn_get(void)
Get default behavior for whether to use old energy model for comparative structure prediction.
int gquad
Allow G-quadruplex formation.
char * nonstandards
contains allowed non standard base pairs
void vrna_md_defaults_noLP(int flag)
Set default behavior for prediction of canonical secondary structures.
void vrna_md_update(vrna_md_t *md)
Update the model details data structure.
void vrna_md_defaults_logML(int flag)
Set default behavior recomputing free energies of multi-branch loops using a logarithmic model.
void vrna_md_defaults_sfact(double factor)
Set the default scaling factor used to avoid under-/overflows in partition function computation.
void vrna_md_defaults_oldAliEn(int flag)
Set default behavior for whether to use old energy model for comparative structure prediction.
void vrna_md_defaults_max_bp_span(int span)
Set default maximal base pair span.
void vrna_md_defaults_circ(int flag)
Set default behavior whether input sequences are circularized.
int tetra_loop
Include special stabilizing energies for some tri-, tetra- and hexa-loops;.
int vrna_md_defaults_noGUclosure_get(void)
Get default behavior for G-U pairs as closing pair for loops.
void vrna_md_defaults_uniq_ML(int flag)
Set default behavior for creating additional matrix for unique multi-branch loop prediction.
int vrna_md_defaults_min_loop_size_get(void)
Get default minimal loop size.
int vrna_md_defaults_noGU_get(void)
Get default behavior for treatment of G-U wobble pairs.
int vrna_md_defaults_window_size_get(void)
Get default window size for sliding window structure prediction approaches.
int vrna_md_defaults_dangles_get(void)
Get default dangle model for structure prediction.
void vrna_md_defaults_backtrack_type(char t)
Set default backtrack type, i.e. which DP matrix is used.
int uniq_ML
do ML decomposition uniquely (for subopt)
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.
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
double vrna_md_defaults_nc_fact_get(void)
void vrna_md_defaults_window_size(int size)
Set default window size for sliding window structure prediction approaches.
int logML
if nonzero use logarithmic ML energy in energy_of_struct
char backtrack_type
A backtrack array marker for inverse_fold()
void vrna_md_set_default(vrna_md_t *md)
Apply default model details to a provided vrna_md_t data structure.
void vrna_md_defaults_energy_set(int e)
Set default energy set.
int vrna_md_defaults_backtrack_get(void)
Get default behavior for whether to backtrack secondary structures.
int vrna_md_defaults_noLP_get(void)
Get default behavior for prediction of canonical secondary structures.
void vrna_md_defaults_ribo(int flag)
Set default behavior for whether to use Ribosum Scoring in comparative structure prediction.
int vrna_md_defaults_logML_get(void)
Get default behavior recomputing free energies of multi-branch loops using a logarithmic model.
double vrna_md_defaults_temperature_get(void)
Get default temperature for energy evaluation of loops.
void vrna_md_defaults_backtrack(int flag)
Set default behavior for whether to backtrack secondary structures.
void vrna_md_defaults_noGU(int flag)
Set default behavior for treatment of G-U wobble pairs.
int vrna_md_defaults_compute_bpp_get(void)
Get the default behavior for whether to compute base pair probabilities after partition function comp...
int vrna_md_defaults_max_bp_span_get(void)
Get default maximal base pair span.
vrna_md_t * vrna_md_copy(vrna_md_t *md_to, const vrna_md_t *md_from)
Copy/Clone a vrna_md_t model.
int no_closingGU
GU allowed only inside stacks if set to 1.
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_uniq_ML_get(void)
Get default behavior for creating additional matrix for unique multi-branch loop prediction.
double temperature
Rescale energy parameters to a temperature in degC.
void set_model_details(vrna_md_t *md)
Set default model details.
double vrna_md_defaults_betaScale_get(void)
Get default scaling factor of thermodynamic temperature in Boltzmann factors.
int noGU
Global switch to forbid/allow GU base pairs at all.
void vrna_md_defaults_min_loop_size(int size)
Set default minimal loop size.
void vrna_md_defaults_nc_fact(double factor)
int oldAliEn
use old alifold energies (with gaps)
void vrna_md_defaults_dangles(int d)
Set default dangle model for structure prediction.
void vrna_md_defaults_cv_fact(double factor)
Set the default co-variance scaling factor used in comparative structure prediction.
int vrna_md_defaults_circ_get(void)
Get default behavior whether input sequences are circularized.
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
int do_backtrack
do backtracking, i.e. compute secondary structures or base pair probabilities
void vrna_md_defaults_noGUclosure(int flag)
Set default behavior for G-U pairs as closing pair for loops.
double vrna_md_defaults_cv_fact_get(void)
Get the default co-variance scaling factor used in comparative structure prediction.
int vrna_md_defaults_gquad_get(void)
Get default behavior for treatment of G-Quadruplexes.
void vrna_md_defaults_betaScale(double b)
Set default scaling factor of thermodynamic temperature in Boltzmann factors.
void vrna_md_defaults_compute_bpp(int flag)
Set the default behavior for whether to compute base pair probabilities after partition function comp...
int circ
backward compatibility variable.. this does not effect anything
void vrna_md_defaults_temperature(double T)
Set default temperature for energy evaluation of loops.
int energy_set
0 = BP; 1=any with GC; 2=any with AU-parameter
void vrna_md_defaults_special_hp(int flag)
Set default behavior for lookup of tabulated free energies for special hairpin loops,...
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:180