model.h File Reference
Manipulation of the Prediction Models

The model details data structure and its corresponding modifiers. More...

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## Data Structures

struct | vrna_md_s
| The data structure that contains the complete model details used throughout the calculations. More...

## Macros

#define | VRNA_MODEL_DEFAULT_TEMPERATURE 37.0
| Default temperature for structure prediction and free energy evaluation in °C More...
#define | VRNA_MODEL_DEFAULT_PF_SCALE -1
| Default scaling factor for partition function computations. More...
#define | VRNA_MODEL_DEFAULT_BETA_SCALE 1.
| Default scaling factor for absolute thermodynamic temperature in Boltzmann factors. More...
#define | VRNA_MODEL_DEFAULT_DANGLES 2
| Default dangling end model. More...
#define | VRNA_MODEL_DEFAULT_SPECIAL_HP 1
| Default model behavior for lookup of special tri-, tetra-, and hexa-loops. More...
#define | VRNA_MODEL_DEFAULT_NO_LP 0
| Default model behavior for so-called 'lonely pairs'. More...
#define | VRNA_MODEL_DEFAULT_NO_GU 0
| Default model behavior for G-U base pairs. More...
#define | VRNA_MODEL_DEFAULT_NO_GU_CLOSURE 0
| Default model behavior for G-U base pairs closing a loop. More...
#define | VRNA_MODEL_DEFAULT_CIRC 0
| Default model behavior to treat a molecule as a circular RNA (DNA) More...
#define | VRNA_MODEL_DEFAULT_GQUAD 0
| Default model behavior regarding the treatment of G-Quadruplexes. More...
#define | VRNA_MODEL_DEFAULT_UNIQ_ML 0
| Default behavior of the model regarding unique multibranch loop decomposition. More...
#define | VRNA_MODEL_DEFAULT_ENERGY_SET 0
| Default model behavior on which energy set to use. More...
#define | VRNA_MODEL_DEFAULT_BACKTRACK 1
| Default model behavior with regards to backtracking of structures. More...
#define | VRNA_MODEL_DEFAULT_BACKTRACK_TYPE 'F'
| Default model behavior on what type of backtracking to perform. More...
#define | VRNA_MODEL_DEFAULT_COMPUTE_BPP 1
| Default model behavior with regards to computing base pair probabilities. More...
#define | VRNA_MODEL_DEFAULT_MAX_BP_SPAN -1
| Default model behavior for the allowed maximum base pair span. More...
#define | VRNA_MODEL_DEFAULT_WINDOW_SIZE -1
| Default model behavior for the sliding window approach. More...
#define | VRNA_MODEL_DEFAULT_LOG_ML 0
| Default model behavior on how to evaluate the energy contribution of multibranch loops. More...
#define | VRNA_MODEL_DEFAULT_ALI_OLD_EN 0
| Default model behavior for consensus structure energy evaluation. More...
#define | VRNA_MODEL_DEFAULT_ALI_RIBO 0
| Default model behavior for consensus structure covariance contribution assessment. More...
#define | VRNA_MODEL_DEFAULT_ALI_CV_FACT 1.
| Default model behavior for weighting the covariance score in consensus structure prediction. More...
#define | VRNA_MODEL_DEFAULT_ALI_NC_FACT 1.
| Default model behavior for weighting the nucleotide conservation? in consensus structure prediction. More...
#define | MAXALPHA 20
| Maximal length of alphabet.

## Typedefs

typedef struct vrna_md_s | vrna_md_t
| Typename for the model details data structure vrna_md_s.

## Functions

void | vrna_md_set_default (vrna_md_t *md)
| Apply default model details to a provided vrna_md_t data structure. More...
void | vrna_md_update (vrna_md_t *md)
| Update the model details data structure. More...
char * | vrna_md_option_string (vrna_md_t *md)
| Get a corresponding commandline parameter string of the options in a vrna_md_t. More...
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. More...
void | vrna_md_defaults_temperature (double T)
| Set default temperature for energy evaluation of loops. More...
double | vrna_md_defaults_temperature_get (void)
| Get default temperature for energy evaluation of loops. More...
void | vrna_md_defaults_betaScale (double b)
| Set default scaling factor of thermodynamic temperature in Boltzmann factors. More...
double | vrna_md_defaults_betaScale_get (void)
| Get default scaling factor of thermodynamic temperature in Boltzmann factors. More...
void | vrna_md_defaults_dangles (int d)
| Set default dangle model for structure prediction. More...
int | vrna_md_defaults_dangles_get (void)
| Get default dangle model for structure prediction. More...
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. More...
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. More...
void | vrna_md_defaults_noLP (int flag)
| Set default behavior for prediction of canonical secondary structures. More...
int | vrna_md_defaults_noLP_get (void)
| Get default behavior for prediction of canonical secondary structures. More...
void | vrna_md_defaults_noGU (int flag)
| Set default behavior for treatment of G-U wobble pairs. More...
int | vrna_md_defaults_noGU_get (void)
| Get default behavior for treatment of G-U wobble pairs. More...
void | vrna_md_defaults_noGUclosure (int flag)
| Set default behavior for G-U pairs as closing pair for loops. More...
int | vrna_md_defaults_noGUclosure_get (void)
| Get default behavior for G-U pairs as closing pair for loops. More...
void | vrna_md_defaults_logML (int flag)
| Set default behavior recomputing free energies of multibranch loops using a logarithmic model. More...
int | vrna_md_defaults_logML_get (void)
| Get default behavior recomputing free energies of multibranch loops using a logarithmic model. More...
void | vrna_md_defaults_circ (int flag)
| Set default behavior whether input sequences are circularized. More...
int | vrna_md_defaults_circ_get (void)
| Get default behavior whether input sequences are circularized. More...
void | vrna_md_defaults_gquad (int flag)
| Set default behavior for treatment of G-Quadruplexes. More...
int | vrna_md_defaults_gquad_get (void)
| Get default behavior for treatment of G-Quadruplexes. More...
void | vrna_md_defaults_uniq_ML (int flag)
| Set default behavior for creating additional matrix for unique multibranch loop prediction. More...
int | vrna_md_defaults_uniq_ML_get (void)
| Get default behavior for creating additional matrix for unique multibranch loop prediction. More...
void | vrna_md_defaults_energy_set (int e)
| Set default energy set. More...
int | vrna_md_defaults_energy_set_get (void)
| Get default energy set. More...
void | vrna_md_defaults_backtrack (int flag)
| Set default behavior for whether to backtrack secondary structures. More...
int | vrna_md_defaults_backtrack_get (void)
| Get default behavior for whether to backtrack secondary structures. More...
void | vrna_md_defaults_backtrack_type (char t)
| Set default backtrack type, i.e. which DP matrix is used. More...
char | vrna_md_defaults_backtrack_type_get (void)
| Get default backtrack type, i.e. which DP matrix is used. More...
void | vrna_md_defaults_compute_bpp (int flag)
| Set the default behavior for whether to compute base pair probabilities after partition function computation. More...
int | vrna_md_defaults_compute_bpp_get (void)
| Get the default behavior for whether to compute base pair probabilities after partition function computation. More...
void | vrna_md_defaults_max_bp_span (int span)
| Set default maximal base pair span. More...
int | vrna_md_defaults_max_bp_span_get (void)
| Get default maximal base pair span. More...
void | vrna_md_defaults_min_loop_size (int size)
| Set default minimal loop size. More...
int | vrna_md_defaults_min_loop_size_get (void)
| Get default minimal loop size. More...
void | vrna_md_defaults_window_size (int size)
| Set default window size for sliding window structure prediction approaches. More...
int | vrna_md_defaults_window_size_get (void)
| Get default window size for sliding window structure prediction approaches. More...
void | vrna_md_defaults_oldAliEn (int flag)
| Set default behavior for whether to use old energy model for comparative structure prediction. More...
int | vrna_md_defaults_oldAliEn_get (void)
| Get default behavior for whether to use old energy model for comparative structure prediction. More...
void | vrna_md_defaults_ribo (int flag)
| Set default behavior for whether to use Ribosum Scoring in comparative structure prediction. More...
int | vrna_md_defaults_ribo_get (void)
| Get default behavior for whether to use Ribosum Scoring in comparative structure prediction. More...
void | vrna_md_defaults_cv_fact (double factor)
| Set the default covariance scaling factor used in comparative structure prediction. More...
double | vrna_md_defaults_cv_fact_get (void)
| Get the default covariance scaling factor used in comparative structure prediction. More...
void | vrna_md_defaults_nc_fact (double factor)
double | vrna_md_defaults_nc_fact_get (void)
void | vrna_md_defaults_sfact (double factor)
| Set the default scaling factor used to avoid under-/overflows in partition function computation. More...
double | vrna_md_defaults_sfact_get (void)
| Get the default scaling factor used to avoid under-/overflows in partition function computation. More...
void | set_model_details (vrna_md_t *md)
| Set default model details. More...

## Variables

double | temperature
| Rescale energy parameters to a temperature in degC. More...
double | pf_scale
| A scaling factor used by pf_fold() to avoid overflows. More...
int | dangles
| Switch the energy model for dangling end contributions (0, 1, 2, 3) More...
int | tetra_loop
| Include special stabilizing energies for some tri-, tetra- and hexa-loops;. More...
int | noLonelyPairs
| Global switch to avoid/allow helices of length 1. More...
int | noGU
| Global switch to forbid/allow GU base pairs at all.
int | no_closingGU
| GU allowed only inside stacks if set to 1.
int | circ
| backward compatibility variable.. this does not effect anything
int | gquad
| Allow G-quadruplex formation.
int | canonicalBPonly
int | uniq_ML
| do ML decomposition uniquely (for subopt)
int | energy_set
| 0 = BP; 1=any mit GC; 2=any mit AU-parameter More...
int | do_backtrack
| do backtracking, i.e. compute secondary structures or base pair probabilities More...
char | backtrack_type
| A backtrack array marker for inverse_fold() More...
char * | nonstandards
| contains allowed non standard base pairs More...
int | max_bp_span
| Maximum allowed base pair span. More...
int | oldAliEn
| use old alifold energies (with gaps)
int | ribo
| use ribosum matrices
int | logML
| if nonzero use logarithmic ML energy in energy_of_struct

## Detailed Description

The model details data structure and its corresponding modifiers.