model.h File Reference

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 multi-branch 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 multi-branch 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 co-variance contribution assessment. More...
#define	VRNA_MODEL_DEFAULT_ALI_CV_FACT   1.
	Default model behavior for weighting the co-variance 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...
vrna_md_t *	vrna_md_copy (vrna_md_t *md_to, const vrna_md_t *md_from)
	Copy/Clone a vrna_md_t model. 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 multi-branch loops using a logarithmic model. More...
int	vrna_md_defaults_logML_get (void)
	Get default behavior recomputing free energies of multi-branch 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 multi-branch loop prediction. More...
int	vrna_md_defaults_uniq_ML_get (void)
	Get default behavior for creating additional matrix for unique multi-branch 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 co-variance scaling factor used in comparative structure prediction. More...
double	vrna_md_defaults_cv_fact_get (void)
	Get the default co-variance 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	uniq_ML
	do ML decomposition uniquely (for subopt)
int	energy_set
	0 = BP; 1=any with GC; 2=any with 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.