1 #ifndef __VIENNA_RNA_PACKAGE_MODEL_H__
2 #define __VIENNA_RNA_PACKAGE_MODEL_H__
5 #define DEPRECATED(func) func __attribute__ ((deprecated))
7 #define DEPRECATED(func) func
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.
261 void vrna_md_set_nonstandards(
model_detailsT *md,
const char *ns);
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
double cv_fact
Covariance scaling factor for consensus structure prediction.
Definition: model.h:239
int oldAliEn
use old alifold energies (with gaps)