Read and Write energy parameter sets from and to files or strings. More...

Detailed Description

Read and Write energy parameter sets from and to files or strings.

Collaboration diagram for Reading/Writing Energy Parameter Sets from/to File:

Modules
	Converting Energy Parameter Files
	Convert energy parameter files into the latest format.

Macros
#define	VRNA_PARAMETER_FORMAT_DEFAULT 0
	Default Energy Parameter File format. More...

Functions
int	vrna_params_load (const char fname[], unsigned int options)
	Load energy parameters from a file. More...

int	vrna_params_save (const char fname[], unsigned int options)
	Save energy parameters to a file. More...

int	vrna_params_load_from_string (const char string, const char name, unsigned int options)
	Load energy paramters from string. More...

int	vrna_params_load_defaults (void)
	Load default RNA energy parameter set. More...

int	vrna_params_load_RNA_Turner2004 (void)
	Load Turner 2004 RNA energy parameter set. More...

int	vrna_params_load_RNA_Turner1999 (void)
	Load Turner 1999 RNA energy parameter set. More...

int	vrna_params_load_RNA_Andronescu2007 (void)
	Load Andronsecu 2007 RNA energy parameter set. More...

int	vrna_params_load_RNA_Langdon2018 (void)
	Load Langdon 2018 RNA energy parameter set. More...

int	vrna_params_load_RNA_misc_special_hairpins (void)
	Load Misc Special Hairpin RNA energy parameter set. More...

int	vrna_params_load_DNA_Mathews2004 (void)
	Load Mathews 2004 DNA energy parameter set. More...

int	vrna_params_load_DNA_Mathews1999 (void)
	Load Mathews 1999 DNA energy parameter set. More...

const char *	last_parameter_file (void)
	Get the file name of the parameter file that was most recently loaded. More...

void	read_parameter_file (const char fname[])
	Read energy parameters from a file. More...

void	write_parameter_file (const char fname[])
	Write energy parameters to a file. More...

Macro Definition Documentation

#define VRNA_PARAMETER_FORMAT_DEFAULT 0

#include <ViennaRNA/params/io.h>

Default Energy Parameter File format.

See also: vrna_params_load(), vrna_params_load_from_string(), vrna_params_save()

Function Documentation

int vrna_params_load	(	const char	fname[],
		unsigned int	options
	)

#include <ViennaRNA/params/io.h>

Load energy parameters from a file.

See also: vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_defaults(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

Parameters

fname	The path to the file containing the energy parameters
options	File format bit-mask (usually VRNA_PARAMETER_FORMAT_DEFAULT)

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as overloaded function params_load(fname="", options=VRNA_PARAMETER_FORMAT_DEFAULT). Here, the empty filename string indicates to load default RNA parameters, i.e. this is equivalent to calling vrna_params_load_defaults().

int vrna_params_save	(	const char	fname[],
		unsigned int	options
	)

#include <ViennaRNA/params/io.h>

Save energy parameters to a file.

See also: vrna_params_load()

Parameters

fname	A filename (path) for the file where the current energy parameters will be written to
options	File format bit-mask (usually VRNA_PARAMETER_FORMAT_DEFAULT)

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as overloaded function params_save(fname, options=VRNA_PARAMETER_FORMAT_DEFAULT).

int vrna_params_load_from_string	(	const char *	string,
		const char *	name,
		unsigned int	options
	)

#include <ViennaRNA/params/io.h>

Load energy paramters from string.

The string must follow the default energy parameter file convention! The optional name argument allows one to specify a name for the parameter set which is stored internally.

See also: vrna_params_load(), vrna_params_save(), vrna_params_load_defaults(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

Parameters

string	A 0-terminated string containing energy parameters
name	A name for the parameter set in `string` (Maybe `NULL`)
options	File format bit-mask (usually VRNA_PARAMETER_FORMAT_DEFAULT)

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as overloaded function params_load_from_string(string, name="", options=VRNA_PARAMETER_FORMAT_DEFAULT).

int vrna_params_load_defaults ( void )

#include <ViennaRNA/params/io.h>

Load default RNA energy parameter set.

This is a convenience function to load the Turner 2004 RNA free energy parameters. It's the same as calling vrna_params_load_RNA_Turner2004()

See also: vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as overloaded function params_load().

int vrna_params_load_RNA_Turner2004 ( void )

#include <ViennaRNA/params/io.h>

Load Turner 2004 RNA energy parameter set.

See also: vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_defaults(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as function params_load_RNA_Turner2004().

int vrna_params_load_RNA_Turner1999 ( void )

#include <ViennaRNA/params/io.h>

Load Turner 1999 RNA energy parameter set.

See also: vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_defaults(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as function params_load_RNA_Turner1999().

int vrna_params_load_RNA_Andronescu2007 ( void )

#include <ViennaRNA/params/io.h>

Load Andronsecu 2007 RNA energy parameter set.

See also: vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_defaults(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as function params_load_RNA_Andronescu2007().

int vrna_params_load_RNA_Langdon2018 ( void )

#include <ViennaRNA/params/io.h>

Load Langdon 2018 RNA energy parameter set.

See also: vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_defaults(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as function params_load_RNA_Langdon2018().

int vrna_params_load_RNA_misc_special_hairpins ( void )

#include <ViennaRNA/params/io.h>

Load Misc Special Hairpin RNA energy parameter set.

See also: vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_defaults(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_DNA_Mathews1999()

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as function params_load_RNA_misc_special_hairpins().

int vrna_params_load_DNA_Mathews2004 ( void )

#include <ViennaRNA/params/io.h>

Load Mathews 2004 DNA energy parameter set.

See also: vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_defaults(), vrna_params_load_DNA_Mathews1999()

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as function params_load_DNA_Mathews2004().

int vrna_params_load_DNA_Mathews1999 ( void )

#include <ViennaRNA/params/io.h>

Load Mathews 1999 DNA energy parameter set.

See also: vrna_params_load(), vrna_params_load_from_string(), vrna_params_save(), vrna_params_load_RNA_Turner2004(), vrna_params_load_RNA_Turner1999(), vrna_params_load_RNA_Andronescu2007(), vrna_params_load_RNA_Langdon2018(), vrna_params_load_RNA_misc_special_hairpins(), vrna_params_load_DNA_Mathews2004(), vrna_params_load_defaults()

Returns: Non-zero on success, 0 on failure

SWIG Wrapper Notes:: This function is available as function params_load_DNA_Mathews1999().

const char* last_parameter_file ( void )

#include <ViennaRNA/params/io.h>

Get the file name of the parameter file that was most recently loaded.

Returns: The file name of the last parameter file, or NULL if parameters are still at defaults

void read_parameter_file ( const char fname[] )

#include <ViennaRNA/params/io.h>

Read energy parameters from a file.

Deprecated:: Use vrna_params_load() instead!

Parameters

fname The path to the file containing the energy parameters

void write_parameter_file ( const char fname[] )

#include <ViennaRNA/params/io.h>

Write energy parameters to a file.

Deprecated:: Use vrna_params_save() instead!

Parameters

fname A filename (path) for the file where the current energy parameters will be written to

Detailed Description

Modules

Macros

Functions

Macro Definition Documentation

Function Documentation