IntaRNA::VrnaHandler Class Reference

#include <VrnaHandler.h>

Public Member Functions
	VrnaHandler (Z_type temperature=37.0, const std::string &vrnaParamFile=std::string(Turner04), const bool noGUclosure=false, const bool noLP=false)
virtual	~VrnaHandler ()
vrna_md_t	getModel (const int max_bp_span=-1, const int window_size=-1, const double pfScale=getPfScaleDefault()) const
Z_type	getRT () const

Static Public Member Functions
static Z_type	getRT (const Z_type temperature)
static double	getPfScaleDefault ()
static std::mutex &	getSetupMutex ()

Static Public Attributes
static constexpr const char *	Turner99 = "Turner99"
static constexpr const char *	Turner04 = "Turner04"
static constexpr const char *	Andronescu07 = "Andronescu07"

Protected Attributes
vrna_md_t	model
	VRNA parameter model.
Z_type	RT
	the RT constant used for the current setup

Detailed Description

Central hub for Vienna RNA package related stuff

Author

Martin Mann

Constructor & Destructor Documentation

VrnaHandler()

IntaRNA::VrnaHandler::VrnaHandler	(	Z_type	temperature = 37.0,
		const std::string &	vrnaParamFile = std::string(Turner04),
		const bool	noGUclosure = false,
		const bool	noLP = false
	)

Construction with global VRNA folding parameter setup Complete parameter loading before starting concurrent folding computations. The first handler also installs a mutex for logging without changing output callbacks. Retain this logging lock for all subsequent concurrent folding; logger resets remove it.

Parameters

vrnaParamFile	name of a VRNA parameter file to be used for parameter setup
temperature	Folding temperature in Celsius
noGUclosue	whether or not GU base pairs are allowed at helix ends
noLP	whether or not lonely base pairs are considered

~VrnaHandler()

virtual IntaRNA::VrnaHandler::~VrnaHandler ( )

virtual

destruction

Member Function Documentation

getModel()

vrna_md_t IntaRNA::VrnaHandler::getModel	(	const int	max_bp_span = -1,
		const int	window_size = -1,
		const double	pfScale = getPfScaleDefault()
	)		const

Generates a new VRNA parameter model according to the global and local settings

Pass the returned model explicitly to ViennaRNA APIs; do not broadcast it through global model defaults while other threads are folding.

Parameters

max_bp_span	Maximal distance between base pair partners within one RNA or -1 if no constraint needed
window_size	Size of the sliding window for locally folding within one RNA or -1 if no constraint needed @oaram pfScale can be used to scale pf_scale of VRNA partition function computation. Note: only used for values >= 1.0, all other values are ignored.

Returns

the model to be used for VRNA computations

getPfScaleDefault()

static double IntaRNA::VrnaHandler::getPfScaleDefault ( )

static

Provides the default value of the ViennaRNA package for the pf_scale factor model.sfact to be used in argument parsing etc.

Returns

the default model.sfact value from the ViennaRNA package

getRT() [1/2]

Z_type IntaRNA::VrnaHandler::getRT ( ) const

inline

Provides RT for the current setup

Returns

R*temperature

getRT() [2/2]

static Z_type IntaRNA::VrnaHandler::getRT ( const Z_type  temperature )

static

Provides RT for the given temperature

Returns

R*temperature

getSetupMutex()

static std::mutex & IntaRNA::VrnaHandler::getSetupMutex ( )

static

Provides the process-wide lock for ViennaRNA's shared initialization state. Hold this lock while creating parameters and fold compounds, adding constraints, and preparing folding. Global MFE/PF calls also require it. Prepared window computations may run concurrently with OpenMP-enabled ViennaRNA, provided energy parameters are not reloaded during folding.

Returns

the mutex shared by all IntaRNA ViennaRNA callers

Member Data Documentation

Andronescu07

constexpr const char* IntaRNA::VrnaHandler::Andronescu07 = "Andronescu07"

staticconstexpr

model

vrna_md_t IntaRNA::VrnaHandler::model

protected

VRNA parameter model.

RT

Z_type IntaRNA::VrnaHandler::RT

protected

the RT constant used for the current setup

Turner04

constexpr const char* IntaRNA::VrnaHandler::Turner04 = "Turner04"

staticconstexpr

Turner99

constexpr const char* IntaRNA::VrnaHandler::Turner99 = "Turner99"

staticconstexpr

---

The documentation for this class was generated from the following file:

• src/IntaRNA/VrnaHandler.h