RNAlib-2.2.0RC0
model.h
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1 #ifndef __VIENNA_RNA_PACKAGE_MODEL_H__
2 #define __VIENNA_RNA_PACKAGE_MODEL_H__
3 
4 #ifdef __GNUC__
5 #define DEPRECATED(func) func __attribute__ ((deprecated))
6 #else
7 #define DEPRECATED(func) func
8 #endif
9 
10 #ifndef MAXALPHA
11 
14 #define MAXALPHA 20
15 #endif
16 
17 #define VRNA_MODEL_DEFAULT_TEMPERATURE 37.0
18 #define VRNA_MODEL_DEFAULT_PF_SCALE -1
19 #define VRNA_MODEL_DEFAULT_BETA_SCALE 1.
20 #define VRNA_MODEL_DEFAULT_DANGLES 2
21 #define VRNA_MODEL_DEFAULT_SPECIAL_HP 1
22 #define VRNA_MODEL_DEFAULT_NO_LP 0
23 #define VRNA_MODEL_DEFAULT_NO_GU 0
24 #define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE 0
25 #define VRNA_MODEL_DEFAULT_CIRC 0
26 #define VRNA_MODEL_DEFAULT_GQUAD 0
27 #define VRNA_MODEL_DEFAULT_CANONICAL_BP 0
28 #define VRNA_MODEL_DEFAULT_UNIQ_ML 0
29 #define VRNA_MODEL_DEFAULT_ENERGY_SET 0
30 #define VRNA_MODEL_DEFAULT_BACKTRACK 1
31 #define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE 'F'
32 #define VRNA_MODEL_DEFAULT_COMPUTE_BPP 1
33 #define VRNA_MODEL_DEFAULT_MAX_BP_SPAN -1
34 #define VRNA_MODEL_DEFAULT_LOG_ML 0
35 #define VRNA_MODEL_DEFAULT_ALI_OLD_EN 0
36 #define VRNA_MODEL_DEFAULT_ALI_RIBO 0
37 #define VRNA_MODEL_DEFAULT_ALI_CV_FACT 1.
38 #define VRNA_MODEL_DEFAULT_ALI_NC_FACT 1.
39 
40 
49 /* BEGIN deprecated global variables: */
50 
57 extern double temperature;
58 
70 extern double pf_scale;
71 
93 extern int dangles;
94 
100 extern int tetra_loop;
101 
109 extern int noLonelyPairs;
110 
114 extern int noGU;
115 
119 extern int no_closingGU;
120 
124 extern int circ;
125 
129 extern int gquad;
130 
134 extern int canonicalBPonly;
135 
139 extern int uniq_ML;
140 
148 extern int energy_set;
149 
156 extern int do_backtrack;
157 
165 extern char backtrack_type;
166 
174 extern char *nonstandards;
175 
181 extern int max_bp_span;
182 
186 extern int oldAliEn;
187 
191 extern int ribo;
192 
193 extern double cv_fact;
194 
195 extern double nc_fact;
196 
198 extern int logML;
199 
200 /* END deprecated global variables: */
201 
206 typedef struct{
207  double temperature;
208  double betaScale;
209  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[33];
237  int oldAliEn;
238  int ribo;
239  double cv_fact;
240  double nc_fact;
241  double sfact;
242  int rtype[8];
243  short alias[MAXALPHA+1];
244  int pair[MAXALPHA+1][MAXALPHA+1];
246 
247 
259 
260 
261 void vrna_md_set_nonstandards(model_detailsT *md, const char *ns);
262 
263 
264 void vrna_md_set_dangles(model_detailsT *md, int d);
265 
266 
267 int vrna_md_get_dangles(model_detailsT *md);
268 
269 
270 void vrna_md_set_temperature(model_detailsT *md, double T);
271 
272 
273 double vrna_md_get_temperature(model_detailsT *md);
274 
275 
276 void vrna_md_set_special_hp(model_detailsT *md, int shp);
277 
278 
279 int vrna_md_get_special_hp(model_detailsT *md);
280 
281 
282 void vrna_md_set_gquad(model_detailsT *md, int g);
283 
284 
285 int vrna_md_get_gquad(model_detailsT *md);
286 
287 
288 void vrna_md_set_nolp(model_detailsT *md, int nolp);
289 
290 
291 int vrna_md_get_nolp(model_detailsT *md);
292 
293 
294 void vrna_md_set_betascale(model_detailsT *md, double b);
295 
296 
297 double vrna_md_get_betascale(model_detailsT *md);
298 
303 
315 
316 #endif
int do_backtrack
do backtracking, i.e. compute secondary structures or base pair probabilities
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
int logML
if nonzero use logarithmic ML energy in energy_of_struct
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
int ribo
use ribosum matrices
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_update(model_detailsT *md)
Update the model details.
int min_loop_size
Minimum size of hairpin loops.
Definition: model.h:231
double betaScale
A scaling factor for the thermodynamic temperature of the Boltzmann factors.
Definition: model.h:208
int uniq_ML
do ML decomposition uniquely (for subopt)
int ribo
Use ribosum scoring table in alifold energy model.
Definition: model.h:238
int special_hp
Include special hairpin contributions for tri, tetra and hexaloops.
Definition: model.h:215
int uniq_ML
Flag to ensure unique multibranch loop decomposition during folding.
Definition: model.h:223
double temperature
The temperature used to scale the thermodynamic parameters.
Definition: model.h:207
char backtrack_type
Specifies in which matrix to backtrack.
Definition: model.h:226
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
int max_bp_span
maximum allowed base pair span
Definition: model.h:229
int oldAliEn
Use old alifold energy model.
Definition: model.h:237
int energy_set
0 = BP; 1=any mit GC; 2=any mit AU-parameter
int backtrack
Specifies whether or not secondary structures should be backtraced.
Definition: model.h:225
void set_model_details(model_detailsT *md)
Set default model details.
int noGU
Do not allow GU pairs.
Definition: model.h:217
void vrna_md_set_default(model_detailsT *md)
Set default model details.
int canonicalBPonly
remove non-canonical bp's from constraint structures
Definition: model.h:222
int noGUclosure
Do not allow loops to be closed by GU pair.
Definition: model.h:218
char backtrack_type
A backtrack array marker for inverse_fold()
int max_bp_span
Maximum allowed base pair span.
#define MAXALPHA
Maximal length of alphabet.
Definition: model.h:14
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
char * nonstandards
contains allowed non standard base pairs
int gquad
Include G-quadruplexes in structure prediction.
Definition: model.h:221
int dangles
Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
Definition: model.h:209
int tetra_loop
Include special stabilizing energies for some tri-, tetra- and hexa-loops;.
double sfact
Scaling factor for partition function scaling.
Definition: model.h:241
int noLonelyPairs
Global switch to avoid/allow helices of length 1.
int no_closingGU
GU allowed only inside stacks if set to 1.
int circ
backward compatibility variable.. this does not effect anything
int logML
Use logarithmic scaling for multi loops.
Definition: model.h:219
int gquad
Allow G-quadruplex formation.
int noGU
Global switch to forbid/allow GU base pairs at all.
int noLP
Only consider canonical structures, i.e. no 'lonely' base pairs.
Definition: model.h:216
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:206
double temperature
Rescale energy parameters to a temperature in degC.
int energy_set
Specifies the energy set that defines set of compatible base pairs.
Definition: model.h:224
int circ
Assume RNA to be circular instead of linear.
Definition: model.h:220
int canonicalBPonly
double cv_fact
Covariance scaling factor for consensus structure prediction.
Definition: model.h:239
int oldAliEn
use old alifold energies (with gaps)