1 #ifndef VIENNA_RNA_PACKAGE_MODEL_H
2 #define VIENNA_RNA_PACKAGE_MODEL_H
4 #ifdef DEPRECATION_WARNINGS
6 # define DEPRECATED(func) func __attribute__ ((deprecated))
8 # define DEPRECATED(func) func
11 # define DEPRECATED(func) func
16 #define VRNA_BACKWARD_COMPAT
39 #define VRNA_MODEL_DEFAULT_TEMPERATURE 37.0
45 #define VRNA_MODEL_DEFAULT_PF_SCALE -1
51 #define VRNA_MODEL_DEFAULT_BETA_SCALE 1.
56 #define VRNA_MODEL_DEFAULT_DANGLES 2
62 #define VRNA_MODEL_DEFAULT_SPECIAL_HP 1
68 #define VRNA_MODEL_DEFAULT_NO_LP 0
74 #define VRNA_MODEL_DEFAULT_NO_GU 0
80 #define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE 0
86 #define VRNA_MODEL_DEFAULT_CIRC 0
92 #define VRNA_MODEL_DEFAULT_GQUAD 0
94 #define VRNA_MODEL_DEFAULT_CANONICAL_BP 0
100 #define VRNA_MODEL_DEFAULT_UNIQ_ML 0
106 #define VRNA_MODEL_DEFAULT_ENERGY_SET 0
112 #define VRNA_MODEL_DEFAULT_BACKTRACK 1
118 #define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE 'F'
124 #define VRNA_MODEL_DEFAULT_COMPUTE_BPP 1
130 #define VRNA_MODEL_DEFAULT_MAX_BP_SPAN -1
136 #define VRNA_MODEL_DEFAULT_WINDOW_SIZE -1
142 #define VRNA_MODEL_DEFAULT_LOG_ML 0
148 #define VRNA_MODEL_DEFAULT_ALI_OLD_EN 0
154 #define VRNA_MODEL_DEFAULT_ALI_RIBO 0
160 #define VRNA_MODEL_DEFAULT_ALI_CV_FACT 1.
165 #define VRNA_MODEL_DEFAULT_ALI_NC_FACT 1.
168 #ifdef VRNA_BACKWARD_COMPAT
281 vrna_md_set_nonstandards(
vrna_md_t *md,
const char *ns);
677 #ifdef VRNA_BACKWARD_COMPAT
679 #define model_detailsT vrna_md_t
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...
int backtrack
Specifies whether or not secondary structures should be backtraced.
Definition: model.h:224
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.
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_max_bp_span_get(void)
Get default maximal base pair span.
char nonstandards[33]
contains allowed non standard bases
Definition: model.h:227
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 ...
short alias[MAXALPHA+1]
alias of an integer nucleotide representation
Definition: model.h:241
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 special_hp
Include special hairpin contributions for tri, tetra and hexaloops.
Definition: model.h:214
int compute_bpp
Specifies whether or not backward recursions for base pair probability (bpp) computation will be perf...
Definition: model.h:226
void vrna_md_defaults_circ(int flag)
Set default behavior whether input sequences are circularized.
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.
double temperature
Rescale energy parameters to a temperature in degC.
char * nonstandards
contains allowed non standard base pairs
int ribo
use ribosum matrices
int do_backtrack
do backtracking, i.e. compute secondary structures or base pair probabilities
int noLP
Only consider canonical structures, i.e. no 'lonely' base pairs.
Definition: model.h:215
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 uniq_ML
Flag to ensure unique multibranch loop decomposition during folding.
Definition: model.h:222
int vrna_md_defaults_oldAliEn_get(void)
Get default behavior for whether to use old energy model for comparative structure prediction...
int noGU
Do not allow GU pairs.
Definition: model.h:216
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 cv_fact
Covariance scaling factor for consensus structure prediction.
Definition: model.h:237
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 oldAliEn
Use old alifold energy model.
Definition: model.h:235
int window_size
Size of the sliding window for locally optimal structure predition.
Definition: model.h:234
int vrna_md_defaults_ribo_get(void)
Get default behavior for whether to use Ribosum Scoring in comparative structure prediction.
int logML
Use logarithmic scaling for multi loops.
Definition: model.h:218
void vrna_md_defaults_uniq_ML(int flag)
Set default behavior for creating additional matrix for unique multibranch loop prediction.
int max_bp_span
maximum allowed base pair span
Definition: model.h:228
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 rtype[8]
Reverse base pair type array.
Definition: model.h:240
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.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:187
void vrna_md_defaults_energy_set(int e)
Set default energy set.
double sfact
Scaling factor for partition function scaling.
Definition: model.h:239
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.
void vrna_md_defaults_logML(int flag)
Set default behavior recomputing free energies of multibranch loops using a logarithmic model...
int gquad
Include G-quadruplexes in structure prediction.
Definition: model.h:220
void vrna_md_defaults_noLP(int flag)
Set default behavior for prediction of canonical secondary structures.
#define MAXALPHA
Maximal length of alphabet.
Definition: model.h:174
void vrna_md_defaults_window_size(int size)
Set default window size for sliding window structure prediction approaches.
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)
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.
char backtrack_type
Specifies in which matrix to backtrack.
Definition: model.h:225
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 ribo
Use ribosum scoring table in alifold energy model.
Definition: model.h:236
int vrna_md_defaults_compute_bpp_get(void)
Get the default behavior for whether to compute base pair probabilities after partition function comp...
int pair[MAXALPHA+1][MAXALPHA+1]
Integer representation of a base pair.
Definition: model.h:242
double vrna_md_defaults_cv_fact_get(void)
Get the default covariance scaling factor used in comparative structure prediction.
double temperature
The temperature used to scale the thermodynamic parameters.
Definition: model.h:188
int dangles
Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
Definition: model.h:190
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 circ
Assume RNA to be circular instead of linear.
Definition: model.h:219
int vrna_md_defaults_gquad_get(void)
Get default behavior for treatment of G-Quadruplexes.
int canonicalBPonly
remove non-canonical bp's from constraint structures
Definition: model.h:221
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)
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 vrna_md_defaults_logML_get(void)
Get default behavior recomputing free energies of multibranch loops using a logarithmic model...
int noGUclosure
Do not allow loops to be closed by GU pair.
Definition: model.h:217
int circ
backward compatibility variable.. this does not effect anything
int energy_set
Specifies the energy set that defines set of compatible base pairs.
Definition: model.h:223
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
int min_loop_size
Minimum size of hairpin loops.
Definition: model.h:230
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.
double betaScale
A scaling factor for the thermodynamic temperature of the Boltzmann factors.
Definition: model.h:189