Fine-tuning of the Implemented Models

Functions and data structures to fine-tune the implemented secondary structure evaluation model. More...

Detailed Description

Functions and data structures to fine-tune the implemented secondary structure evaluation model.

Collaboration diagram for Fine-tuning of the Implemented Models:

Files
file	model.h
	The model details data structure and its corresponding modifiers.

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

---

Data Structure Documentation

struct vrna_md_s

The data structure that contains the complete model details used throughout the calculations.

For convenience reasons, we provide the type name vrna_md_t to address this data structure without the use of the struct keyword

See also

vrna_md_set_default(), set_model_details(), vrna_md_update(), vrna_md_t

SWIG Wrapper Notes:

This data structure is wrapped as an object md with multiple related functions attached as methods.

A new set of default parameters can be obtained by calling the constructure of md:

• md() – Initialize with default settings

The resulting object has a list of attached methods which directly correspond to functions that mainly operate on the corresponding C data structure:

• reset() – vrna_md_set_default()
• set_from_globals() – set_model_details()
• option_string() – vrna_md_option_string()

Note, that default parameters can be modified by directly setting any of the following global variables. Internally, getting/setting default parameters using their global variable representative translates into calls of the following functions, therefore these wrappers for these functions do not exist in the scripting language interface(s):

global variable	C getter	C setter
temperature	vrna_md_defaults_temperature_get()	vrna_md_defaults_temperature()
dangles	vrna_md_defaults_dangles_get()	vrna_md_defaults_dangles()
betaScale	vrna_md_defaults_betaScale_get()	vrna_md_defaults_betaScale()
tetra_loop	this is an alias of special_hp
special_hp	vrna_md_defaults_special_hp_get()	vrna_md_defaults_special_hp()
noLonelyPairs	this is an alias of noLP
noLP	vrna_md_defaults_noLP_get()	vrna_md_defaults_noLP()
noGU	vrna_md_defaults_noGU_get()	vrna_md_defaults_noGU()
no_closingGU	this is an alias of noGUclosure
noGUclosure	vrna_md_defaults_noGUclosure_get()	vrna_md_defaults_noGUclosure()
logML	vrna_md_defaults_logML_get()	vrna_md_defaults_logML()
circ	vrna_md_defaults_circ_get()	vrna_md_defaults_circ()
gquad	vrna_md_defaults_gquad_get()	vrna_md_defaults_gquad()
uniq_ML	vrna_md_defaults_uniq_ML_get()	vrna_md_defaults_uniq_ML()
energy_set	vrna_md_defaults_energy_set_get()	vrna_md_defaults_energy_set()
backtrack	vrna_md_defaults_backtrack_get()	vrna_md_defaults_backtrack()
backtrack_type	vrna_md_defaults_backtrack_type_get()	vrna_md_defaults_backtrack_type()
do_backtrack	this is an alias of compute_bpp
compute_bpp	vrna_md_defaults_compute_bpp_get()	vrna_md_defaults_compute_bpp()
max_bp_span	vrna_md_defaults_max_bp_span_get()	vrna_md_defaults_max_bp_span()
min_loop_size	vrna_md_defaults_min_loop_size_get()	vrna_md_defaults_min_loop_size()
window_size	vrna_md_defaults_window_size_get()	vrna_md_defaults_window_size()
oldAliEn	vrna_md_defaults_oldAliEn_get()	vrna_md_defaults_oldAliEn()
ribo	vrna_md_defaults_ribo_get()	vrna_md_defaults_ribo()
cv_fact	vrna_md_defaults_cv_fact_get()	vrna_md_defaults_cv_fact()
nc_fact	vrna_md_defaults_nc_fact_get()	vrna_md_defaults_nc_fact()
sfact	vrna_md_defaults_sfact_get()	vrna_md_defaults_sfact()

Data Fields
double	temperature
	The temperature used to scale the thermodynamic parameters.
double	betaScale
	A scaling factor for the thermodynamic temperature of the Boltzmann factors.
int	pf_smooth
	A flat specifying whether energies in Boltzmann factors need to be smoothed.
int	dangles
	Specifies the dangle model used in any energy evaluation (0,1,2 or 3) More...
int	special_hp
	Include special hairpin contributions for tri, tetra and hexaloops.
int	noLP
	Only consider canonical structures, i.e. no 'lonely' base pairs.
int	noGU
	Do not allow GU pairs.
int	noGUclosure
	Do not allow loops to be closed by GU pair.
int	logML
	Use logarithmic scaling for multiloops.
int	circ
	Assume RNA to be circular instead of linear.
int	gquad
	Include G-quadruplexes in structure prediction.
int	uniq_ML
	Flag to ensure unique multi-branch loop decomposition during folding.
int	energy_set
	Specifies the energy set that defines set of compatible base pairs.
int	backtrack
	Specifies whether or not secondary structures should be backtraced.
char	backtrack_type
	Specifies in which matrix to backtrack.
int	compute_bpp
	Specifies whether or not backward recursions for base pair probability (bpp) computation will be performed.
char	nonstandards [64]
	contains allowed non standard bases
int	max_bp_span
	maximum allowed base pair span
int	min_loop_size
	Minimum size of hairpin loops. More...
int	window_size
	Size of the sliding window for locally optimal structure prediction.
int	oldAliEn
	Use old alifold energy model.
int	ribo
	Use ribosum scoring table in alifold energy model.
double	cv_fact
	Co-variance scaling factor for consensus structure prediction.
double	nc_fact
	Scaling factor to weight co-variance contributions of non-canonical pairs.
double	sfact
	Scaling factor for partition function scaling.
int	rtype [8]
	Reverse base pair type array.
short	alias [MAXALPHA+1]
	alias of an integer nucleotide representation
int	pair [MAXALPHA+1][MAXALPHA+1]
	Integer representation of a base pair.

Field Documentation

int vrna_md_s::dangles

Specifies the dangle model used in any energy evaluation (0,1,2 or 3)

If set to 0 no stabilizing energies are assigned to bases adjacent to helices in free ends and multiloops (so called dangling ends). Normally (dangles = 1) dangling end energies are assigned only to unpaired bases and a base cannot participate simultaneously in two dangling ends. In the partition function algorithm vrna_pf() these checks are neglected. To provide comparability between free energy minimization and partition function algorithms, the default setting is 2. This treatment of dangling ends gives more favorable energies to helices directly adjacent to one another, which can be beneficial since such helices often do engage in stabilizing interactions through co-axial stacking.
If set to 3 co-axial stacking is explicitly included for adjacent helices in multiloops. The option affects only mfe folding and energy evaluation (vrna_mfe() and vrna_eval_structure()), as well as suboptimal folding (vrna_subopt()) via re-evaluation of energies. Co-axial stacking with one intervening mismatch is not considered so far.

Note

Some function do not implement all dangle model but only a subset of (0,1,2,3). In particular, partition function algorithms can only handle 0 and 2. Read the documentation of the particular recurrences or energy evaluation function for information about the provided dangle model.

int vrna_md_s::min_loop_size

Minimum size of hairpin loops.

Note

The default value for this field is TURN, however, it may be 0 in cofolding context.

Macro Definition Documentation

#define VRNA_MODEL_DEFAULT_TEMPERATURE   37.0

#include <ViennaRNA/model.h>

Default temperature for structure prediction and free energy evaluation in °C

See also

vrna_md_t.temperature, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_PF_SCALE   -1

#include <ViennaRNA/model.h>

Default scaling factor for partition function computations.

See also

vrna_exp_param_t.pf_scale, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_BETA_SCALE   1.

#include <ViennaRNA/model.h>

Default scaling factor for absolute thermodynamic temperature in Boltzmann factors.

See also

vrna_exp_param_t.alpha, vrna_md_t.betaScale, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_DANGLES   2

#include <ViennaRNA/model.h>

Default dangling end model.

See also

vrna_md_t.dangles, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_SPECIAL_HP   1

#include <ViennaRNA/model.h>

Default model behavior for lookup of special tri-, tetra-, and hexa-loops.

See also

vrna_md_t.special_hp, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_NO_LP   0

#include <ViennaRNA/model.h>

Default model behavior for so-called 'lonely pairs'.

See also

vrna_md_t.noLP, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_NO_GU   0

#include <ViennaRNA/model.h>

Default model behavior for G-U base pairs.

See also

vrna_md_t.noGU, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE   0

#include <ViennaRNA/model.h>

Default model behavior for G-U base pairs closing a loop.

See also

vrna_md_t.noGUclosure, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_CIRC   0

#include <ViennaRNA/model.h>

Default model behavior to treat a molecule as a circular RNA (DNA)

See also

vrna_md_t.circ, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_GQUAD   0

#include <ViennaRNA/model.h>

Default model behavior regarding the treatment of G-Quadruplexes.

See also

vrna_md_t.gquad, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_UNIQ_ML   0

#include <ViennaRNA/model.h>

Default behavior of the model regarding unique multi-branch loop decomposition.

See also

vrna_md_t.uniq_ML, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_ENERGY_SET   0

#include <ViennaRNA/model.h>

Default model behavior on which energy set to use.

See also

vrna_md_t.energy_set, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_BACKTRACK   1

#include <ViennaRNA/model.h>

Default model behavior with regards to backtracking of structures.

See also

vrna_md_t.backtrack, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE   'F'

#include <ViennaRNA/model.h>

Default model behavior on what type of backtracking to perform.

See also

vrna_md_t.backtrack_type, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_COMPUTE_BPP   1

#include <ViennaRNA/model.h>

Default model behavior with regards to computing base pair probabilities.

See also

vrna_md_t.compute_bpp, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_MAX_BP_SPAN   -1

#include <ViennaRNA/model.h>

Default model behavior for the allowed maximum base pair span.

See also

vrna_md_t.max_bp_span, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_WINDOW_SIZE   -1

#include <ViennaRNA/model.h>

Default model behavior for the sliding window approach.

See also

vrna_md_t.window_size, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_LOG_ML   0

#include <ViennaRNA/model.h>

Default model behavior on how to evaluate the energy contribution of multi-branch loops.

See also

vrna_md_t.logML, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_ALI_OLD_EN   0

#include <ViennaRNA/model.h>

Default model behavior for consensus structure energy evaluation.

See also

vrna_md_t.oldAliEn, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_ALI_RIBO   0

#include <ViennaRNA/model.h>

Default model behavior for consensus structure co-variance contribution assessment.

See also

vrna_md_t.ribo, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_ALI_CV_FACT   1.

#include <ViennaRNA/model.h>

Default model behavior for weighting the co-variance score in consensus structure prediction.

See also

vrna_md_t.cv_fact, vrna_md_defaults_reset(), vrna_md_set_default()

#define VRNA_MODEL_DEFAULT_ALI_NC_FACT   1.

#include <ViennaRNA/model.h>

Default model behavior for weighting the nucleotide conservation? in consensus structure prediction.

See also

vrna_md_t.nc_fact, vrna_md_defaults_reset(), vrna_md_set_default()

Function Documentation

void vrna_md_set_default

(

vrna_md_t *

md

)

#include <ViennaRNA/model.h>

Apply default model details to a provided vrna_md_t data structure.

Use this function to initialize a vrna_md_t data structure with its default values

Parameters

md	A pointer to the data structure that is about to be initialized

void vrna_md_update

(

vrna_md_t *

md

)

#include <ViennaRNA/model.h>

Update the model details data structure.

This function should be called after changing the vrna_md_t.energy_set attribute since it re-initializes base pairing related arrays within the vrna_md_t data structure. In particular, vrna_md_t.pair, vrna_md_t.alias, and vrna_md_t.rtype are set to the values that correspond to the specified vrna_md_t.energy_set option

See also

vrna_md_t, vrna_md_t.energy_set, vrna_md_t.pair, vrna_md_t.rtype, vrna_md_t.alias, vrna_md_set_default()

vrna_md_t* vrna_md_copy	(	vrna_md_t *	md_to,
		const vrna_md_t *	md_from
	)

#include <ViennaRNA/model.h>

Copy/Clone a vrna_md_t model.

Use this function to clone a given model either inplace (target container md_to given) or create a copy by cloning the source model and returning it (md_to == NULL).

Parameters

md_to	The model to be overwritten (if non-NULL and md_to != md_from)
md_from	The model to copy (if non-NULL)

Returns

A pointer to the copy model (or NULL if md_from == NULL)

char* vrna_md_option_string

(

vrna_md_t *

md

)

#include <ViennaRNA/model.h>

Get a corresponding commandline parameter string of the options in a vrna_md_t.

Note

This function is not threadsafe!

void vrna_md_defaults_reset

(

vrna_md_t *

md_p

)

#include <ViennaRNA/model.h>

Reset the global default model details to a specific set of parameters, or their initial values.

This function resets the global default model details to their initial values, i.e. as specified by the ViennaRNA Package release, upon passing NULL as argument. Alternatively it resets them according to a set of provided parameters.

Note

The global default parameters affect all function calls of RNAlib where model details are not explicitly provided. Hence, any change of them is not considered threadsafe

Warning

This function first resets the global default settings to factory defaults, and only then applies user provided settings (if any). User settings that do not meet specifications are skipped.

See also

vrna_md_set_default(), vrna_md_t

Parameters

md_p	A set of model details to use as global default (if NULL is passed, factory defaults are restored)

void vrna_md_defaults_temperature

(

double

T

)

#include <ViennaRNA/model.h>

Set default temperature for energy evaluation of loops.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_TEMPERATURE

Parameters

T	Temperature in centigrade

double vrna_md_defaults_temperature_get

(

void

)

#include <ViennaRNA/model.h>

Get default temperature for energy evaluation of loops.

See also

vrna_md_defaults_temperature(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_TEMPERATURE

Returns

The global default settings for temperature in centigrade

void vrna_md_defaults_betaScale

(

double

b

)

#include <ViennaRNA/model.h>

Set default scaling factor of thermodynamic temperature in Boltzmann factors.

Bolzmann factors are then computed as .

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_BETA_SCALE

Parameters

b	The scaling factor, default is 1.0

double vrna_md_defaults_betaScale_get

(

void

)

#include <ViennaRNA/model.h>

Get default scaling factor of thermodynamic temperature in Boltzmann factors.

See also

vrna_md_defaults_betaScale(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_BETA_SCALE

Returns

The global default thermodynamic temperature scaling factor

void vrna_md_defaults_dangles

(

int

d

)

#include <ViennaRNA/model.h>

Set default dangle model for structure prediction.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_DANGLES

Parameters

d	The dangle model

int vrna_md_defaults_dangles_get

(

void

)

#include <ViennaRNA/model.h>

Get default dangle model for structure prediction.

See also

vrna_md_defaults_dangles(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_DANGLES

Returns

The global default settings for the dangle model

void vrna_md_defaults_special_hp

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_SPECIAL_HP

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_special_hp_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops.

See also

vrna_md_defaults_special_hp(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_SPECIAL_HP

Returns

The global default settings for the treatment of special hairpin loops

void vrna_md_defaults_noLP

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior for prediction of canonical secondary structures.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_NO_LP

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_noLP_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior for prediction of canonical secondary structures.

See also

vrna_md_defaults_noLP(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_NO_LP

Returns

The global default settings for predicting canonical secondary structures

void vrna_md_defaults_noGU

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior for treatment of G-U wobble pairs.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_NO_GU

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_noGU_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior for treatment of G-U wobble pairs.

See also

vrna_md_defaults_noGU(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_NO_GU

Returns

The global default settings for treatment of G-U wobble pairs

void vrna_md_defaults_noGUclosure

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior for G-U pairs as closing pair for loops.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_NO_GU_CLOSURE

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_noGUclosure_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior for G-U pairs as closing pair for loops.

See also

vrna_md_defaults_noGUclosure(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_NO_GU_CLOSURE

Returns

The global default settings for treatment of G-U pairs closing a loop

void vrna_md_defaults_logML

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior recomputing free energies of multi-branch loops using a logarithmic model.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_LOG_ML

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_logML_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior recomputing free energies of multi-branch loops using a logarithmic model.

See also

vrna_md_defaults_logML(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_LOG_ML

Returns

The global default settings for logarithmic model in multi-branch loop free energy evaluation

void vrna_md_defaults_circ

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior whether input sequences are circularized.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_CIRC

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_circ_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior whether input sequences are circularized.

See also

vrna_md_defaults_circ(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_CIRC

Returns

The global default settings for treating input sequences as circular

void vrna_md_defaults_gquad

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior for treatment of G-Quadruplexes.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_GQUAD

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_gquad_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior for treatment of G-Quadruplexes.

See also

vrna_md_defaults_gquad(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_GQUAD

Returns

The global default settings for treatment of G-Quadruplexes

void vrna_md_defaults_uniq_ML

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior for creating additional matrix for unique multi-branch loop prediction.

Note

Activating this option usually results in higher memory consumption!

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_UNIQ_ML

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_uniq_ML_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior for creating additional matrix for unique multi-branch loop prediction.

See also

vrna_md_defaults_uniq_ML(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_UNIQ_ML

Returns

The global default settings for creating additional matrices for unique multi-branch loop prediction

void vrna_md_defaults_energy_set

(

int

e

)

#include <ViennaRNA/model.h>

Set default energy set.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_ENERGY_SET

Parameters

e	Energy set (0, 1, 2, 3)

int vrna_md_defaults_energy_set_get

(

void

)

#include <ViennaRNA/model.h>

Get default energy set.

See also

vrna_md_defaults_energy_set(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_ENERGY_SET

Returns

The global default settings for the energy set

void vrna_md_defaults_backtrack

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior for whether to backtrack secondary structures.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_BACKTRACK

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_backtrack_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior for whether to backtrack secondary structures.

See also

vrna_md_defaults_backtrack(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_BACKTRACK

Returns

The global default settings for backtracking structures

void vrna_md_defaults_backtrack_type

(

char

t

)

#include <ViennaRNA/model.h>

Set default backtrack type, i.e. which DP matrix is used.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_BACKTRACK_TYPE

Parameters

t	The type ('F', 'C', or 'M')

char vrna_md_defaults_backtrack_type_get

(

void

)

#include <ViennaRNA/model.h>

Get default backtrack type, i.e. which DP matrix is used.

See also

vrna_md_defaults_backtrack_type(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_BACKTRACK_TYPE

Returns

The global default settings that specify which DP matrix is used for backtracking

void vrna_md_defaults_compute_bpp

(

int

flag

)

#include <ViennaRNA/model.h>

Set the default behavior for whether to compute base pair probabilities after partition function computation.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_COMPUTE_BPP

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_compute_bpp_get

(

void

)

#include <ViennaRNA/model.h>

Get the default behavior for whether to compute base pair probabilities after partition function computation.

See also

vrna_md_defaults_compute_bpp(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_COMPUTE_BPP

Returns

The global default settings that specify whether base pair probabilities are computed together with partition function

void vrna_md_defaults_max_bp_span

(

int

span

)

#include <ViennaRNA/model.h>

Set default maximal base pair span.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_MAX_BP_SPAN

Parameters

span	Maximal base pair span

int vrna_md_defaults_max_bp_span_get

(

void

)

#include <ViennaRNA/model.h>

Get default maximal base pair span.

See also

vrna_md_defaults_max_bp_span(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_MAX_BP_SPAN

Returns

The global default settings for maximum base pair span

void vrna_md_defaults_min_loop_size

(

int

size

)

#include <ViennaRNA/model.h>

Set default minimal loop size.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, TURN

Parameters

size	Minimal size, i.e. number of unpaired nucleotides for a hairpin loop

int vrna_md_defaults_min_loop_size_get

(

void

)

#include <ViennaRNA/model.h>

Get default minimal loop size.

See also

vrna_md_defaults_min_loop_size(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, TURN

Returns

The global default settings for minimal size of hairpin loops

void vrna_md_defaults_window_size

(

int

size

)

#include <ViennaRNA/model.h>

Set default window size for sliding window structure prediction approaches.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_WINDOW_SIZE

Parameters

size	The size of the sliding window

int vrna_md_defaults_window_size_get

(

void

)

#include <ViennaRNA/model.h>

Get default window size for sliding window structure prediction approaches.

See also

vrna_md_defaults_window_size(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_WINDOW_SIZE

Returns

The global default settings for the size of the sliding window

void vrna_md_defaults_oldAliEn

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior for whether to use old energy model for comparative structure prediction.

Note

This option is outdated. Activating the old energy model usually results in worse consensus structure predictions.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_ALI_OLD_EN

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_oldAliEn_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior for whether to use old energy model for comparative structure prediction.

See also

vrna_md_defaults_oldAliEn(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_ALI_OLD_EN

Returns

The global default settings for using old energy model for comparative structure prediction

void vrna_md_defaults_ribo

(

int

flag

)

#include <ViennaRNA/model.h>

Set default behavior for whether to use Ribosum Scoring in comparative structure prediction.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_ALI_RIBO

Parameters

flag	On/Off switch (0 = OFF, else = ON)

int vrna_md_defaults_ribo_get

(

void

)

#include <ViennaRNA/model.h>

Get default behavior for whether to use Ribosum Scoring in comparative structure prediction.

See also

vrna_md_defaults_ribo(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_ALI_RIBO

Returns

The global default settings for using Ribosum scoring in comparative structure prediction

void vrna_md_defaults_cv_fact

(

double

factor

)

#include <ViennaRNA/model.h>

Set the default co-variance scaling factor used in comparative structure prediction.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_ALI_CV_FACT

Parameters

factor

The co-variance factor

double vrna_md_defaults_cv_fact_get

(

void

)

#include <ViennaRNA/model.h>

Get the default co-variance scaling factor used in comparative structure prediction.

See also

vrna_md_defaults_cv_fact(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_ALI_CV_FACT

Returns

The global default settings for the co-variance factor

void vrna_md_defaults_nc_fact

(

double

factor

)

#include <ViennaRNA/model.h>

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_ALI_NC_FACT

Parameters

factor

double vrna_md_defaults_nc_fact_get

(

void

)

#include <ViennaRNA/model.h>

See also

vrna_md_defaults_nc_fact(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t, VRNA_MODEL_DEFAULT_ALI_NC_FACT

Returns

void vrna_md_defaults_sfact

(

double

factor

)

#include <ViennaRNA/model.h>

Set the default scaling factor used to avoid under-/overflows in partition function computation.

See also

vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t

Parameters

factor

The scaling factor (default: 1.07)

double vrna_md_defaults_sfact_get

(

void

)

#include <ViennaRNA/model.h>

Get the default scaling factor used to avoid under-/overflows in partition function computation.

See also

vrna_md_defaults_sfact(), vrna_md_defaults_reset(), vrna_md_set_default(), vrna_md_t

Returns

The global default settings of the scaling factor

void set_model_details

(

vrna_md_t *

md

)

#include <ViennaRNA/model.h>

Set default model details.

Use this function if you wish to initialize a vrna_md_t data structure with its default values, i.e. the global model settings as provided by the deprecated global variables.

Deprecated:

This function will vanish as soon as backward compatibility of RNAlib is dropped (expected in version 3). Use vrna_md_set_default() instead!

Parameters

md	A pointer to the data structure that is about to be initialized

Variable Documentation

double temperature

#include <ViennaRNA/model.h>

Rescale energy parameters to a temperature in degC.

Default is 37C. You have to call the update_..._params() functions after changing this parameter.

Deprecated:

Use vrna_md_defaults_temperature(), and vrna_md_defaults_temperature_get() to change, and read the global default temperature settings

See also

vrna_md_defaults_temperature(), vrna_md_defaults_temperature_get(), vrna_md_defaults_reset()

double pf_scale

#include <ViennaRNA/model.h>

A scaling factor used by pf_fold() to avoid overflows.

Should be set to approximately , where is an estimate for the ensemble free energy, for example the minimum free energy. You must call update_pf_params() after changing this parameter.
If pf_scale is -1 (the default) , an estimate will be provided automatically when computing partition functions, e.g. pf_fold() The automatic estimate is usually insufficient for sequences more than a few hundred bases long.

int dangles

#include <ViennaRNA/model.h>

Switch the energy model for dangling end contributions (0, 1, 2, 3)

If set to 0 no stabilizing energies are assigned to bases adjacent to helices in free ends and multiloops (so called dangling ends). Normally (dangles = 1) dangling end energies are assigned only to unpaired bases and a base cannot participate simultaneously in two dangling ends. In the partition function algorithm pf_fold() these checks are neglected. If dangles is set to 2, all folding routines will follow this convention. This treatment of dangling ends gives more favorable energies to helices directly adjacent to one another, which can be beneficial since such helices often do engage in stabilizing interactions through co-axial stacking.
If dangles = 3 co-axial stacking is explicitly included for adjacent helices in multiloops. The option affects only mfe folding and energy evaluation (fold() and energy_of_structure()), as well as suboptimal folding (subopt()) via re-evaluation of energies. Co-axial stacking with one intervening mismatch is not considered so far.

Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2

int tetra_loop

#include <ViennaRNA/model.h>

Include special stabilizing energies for some tri-, tetra- and hexa-loops;.

default is 1.

int noLonelyPairs

#include <ViennaRNA/model.h>

Global switch to avoid/allow helices of length 1.

Disallow all pairs which can only occur as lonely pairs (i.e. as helix of length 1). This avoids lonely base pairs in the predicted structures in most cases.

int energy_set

#include <ViennaRNA/model.h>

0 = BP; 1=any with GC; 2=any with AU-parameter

If set to 1 or 2: fold sequences from an artificial alphabet ABCD..., where A pairs B, C pairs D, etc. using either GC (1) or AU parameters (2); default is 0, you probably don't want to change it.

int do_backtrack

#include <ViennaRNA/model.h>

do backtracking, i.e. compute secondary structures or base pair probabilities

If 0, do not calculate pair probabilities in pf_fold(); this is about twice as fast. Default is 1.

char backtrack_type

#include <ViennaRNA/model.h>

A backtrack array marker for inverse_fold()

If set to 'C': force (1,N) to be paired, 'M' fold as if the sequence were inside a multiloop. Otherwise ('F') the usual mfe structure is computed.

char* nonstandards

#include <ViennaRNA/model.h>

contains allowed non standard base pairs

Lists additional base pairs that will be allowed to form in addition to GC, CG, AU, UA, GU and UG. Nonstandard base pairs are given a stacking energy of 0.

int max_bp_span

#include <ViennaRNA/model.h>

Maximum allowed base pair span.

A value of -1 indicates no restriction for distant base pairs.