RNAlib-2.5.1
Reading/Writing Energy Parameter Sets from/to File

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

◆ VRNA_PARAMETER_FORMAT_DEFAULT

#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

◆ vrna_params_load()

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
fnameThe path to the file containing the energy parameters
optionsFile 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().

◆ vrna_params_save()

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
fnameA filename (path) for the file where the current energy parameters will be written to
optionsFile 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).

◆ vrna_params_load_from_string()

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
stringA 0-terminated string containing energy parameters
nameA name for the parameter set in string (Maybe NULL)
optionsFile 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).

◆ vrna_params_load_defaults()

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().

◆ vrna_params_load_RNA_Turner2004()

int vrna_params_load_RNA_Turner2004 ( void  )

◆ vrna_params_load_RNA_Turner1999()

int vrna_params_load_RNA_Turner1999 ( void  )

◆ vrna_params_load_RNA_Andronescu2007()

int vrna_params_load_RNA_Andronescu2007 ( void  )

◆ vrna_params_load_RNA_Langdon2018()

int vrna_params_load_RNA_Langdon2018 ( void  )

◆ vrna_params_load_RNA_misc_special_hairpins()

int vrna_params_load_RNA_misc_special_hairpins ( void  )

◆ vrna_params_load_DNA_Mathews2004()

int vrna_params_load_DNA_Mathews2004 ( void  )

◆ vrna_params_load_DNA_Mathews1999()

int vrna_params_load_DNA_Mathews1999 ( void  )

◆ last_parameter_file()

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

◆ read_parameter_file()

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
fnameThe path to the file containing the energy parameters

◆ write_parameter_file()

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