Converting Energy Parameter Files

Convert energy parameter files into the latest format. More...

Detailed Description

Convert energy parameter files into the latest format.

To preserve some backward compatibility the RNAlib also provides functions to convert energy parameter files from the format used in version 1.4-1.8 into the new format used since version 2.0

Collaboration diagram for Converting Energy Parameter Files:

Files
file	1.8.4_epars.h
	Free energy parameters for parameter file conversion.
file	1.8.4_intloops.h
	Free energy parameters for interior loop contributions needed by the parameter file conversion functions.

Macros
#define	VRNA_CONVERT_OUTPUT_ALL   1U
#define	VRNA_CONVERT_OUTPUT_HP   2U
#define	VRNA_CONVERT_OUTPUT_STACK   4U
#define	VRNA_CONVERT_OUTPUT_MM_HP   8U
#define	VRNA_CONVERT_OUTPUT_MM_INT   16U
#define	VRNA_CONVERT_OUTPUT_MM_INT_1N   32U
#define	VRNA_CONVERT_OUTPUT_MM_INT_23   64U
#define	VRNA_CONVERT_OUTPUT_MM_MULTI   128U
#define	VRNA_CONVERT_OUTPUT_MM_EXT   256U
#define	VRNA_CONVERT_OUTPUT_DANGLE5   512U
#define	VRNA_CONVERT_OUTPUT_DANGLE3   1024U
#define	VRNA_CONVERT_OUTPUT_INT_11   2048U
#define	VRNA_CONVERT_OUTPUT_INT_21   4096U
#define	VRNA_CONVERT_OUTPUT_INT_22   8192U
#define	VRNA_CONVERT_OUTPUT_BULGE   16384U
#define	VRNA_CONVERT_OUTPUT_INT   32768U
#define	VRNA_CONVERT_OUTPUT_ML   65536U
#define	VRNA_CONVERT_OUTPUT_MISC   131072U
#define	VRNA_CONVERT_OUTPUT_SPECIAL_HP   262144U
#define	VRNA_CONVERT_OUTPUT_VANILLA   524288U
#define	VRNA_CONVERT_OUTPUT_NINIO   1048576U
#define	VRNA_CONVERT_OUTPUT_DUMP   2097152U

Functions
void	convert_parameter_file (const char *iname, const char *oname, unsigned int options)

Macro Definition Documentation

#define VRNA_CONVERT_OUTPUT_ALL   1U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of a complete parameter set

#define VRNA_CONVERT_OUTPUT_HP   2U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of hairpin contributions

#define VRNA_CONVERT_OUTPUT_STACK   4U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of base pair stack contributions

#define VRNA_CONVERT_OUTPUT_MM_HP   8U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of hairpin mismatch contribution

#define VRNA_CONVERT_OUTPUT_MM_INT   16U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of interior loop mismatch contribution

#define VRNA_CONVERT_OUTPUT_MM_INT_1N   32U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of 1:n interior loop mismatch contribution

#define VRNA_CONVERT_OUTPUT_MM_INT_23   64U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of 2:3 interior loop mismatch contribution

#define VRNA_CONVERT_OUTPUT_MM_MULTI   128U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of multi loop mismatch contribution

#define VRNA_CONVERT_OUTPUT_MM_EXT   256U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of exterior loop mismatch contribution

#define VRNA_CONVERT_OUTPUT_DANGLE5   512U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of 5' dangle conctribution

#define VRNA_CONVERT_OUTPUT_DANGLE3   1024U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of 3' dangle contribution

#define VRNA_CONVERT_OUTPUT_INT_11   2048U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of 1:1 interior loop contribution

#define VRNA_CONVERT_OUTPUT_INT_21   4096U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of 2:1 interior loop contribution

#define VRNA_CONVERT_OUTPUT_INT_22   8192U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of 2:2 interior loop contribution

#define VRNA_CONVERT_OUTPUT_BULGE   16384U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of bulge loop contribution

#define VRNA_CONVERT_OUTPUT_INT   32768U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of interior loop contribution

#define VRNA_CONVERT_OUTPUT_ML   65536U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of multi loop contribution

#define VRNA_CONVERT_OUTPUT_MISC   131072U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of misc contributions (such as terminalAU)

#define VRNA_CONVERT_OUTPUT_SPECIAL_HP   262144U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of special hairpin contributions (tri-, tetra-, hexa-loops)

#define VRNA_CONVERT_OUTPUT_VANILLA   524288U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of given parameters only

Note

This option overrides all other output options, except VRNA_CONVERT_OUTPUT_DUMP !

#define VRNA_CONVERT_OUTPUT_NINIO   1048576U

#include <ViennaRNA/params/convert.h>

Flag to indicate printing of interior loop asymmetry contribution

#define VRNA_CONVERT_OUTPUT_DUMP   2097152U

#include <ViennaRNA/params/convert.h>

Flag to indicate dumping the energy contributions from the library instead of an input file

Function Documentation

void convert_parameter_file	(	const char *	iname,
		const char *	oname,
		unsigned int	options
	)

#include <ViennaRNA/params/convert.h>

Convert/dump a Vienna 1.8.4 formatted energy parameter file

The options argument allows one to control the different output modes.
Currently available options are:
VRNA_CONVERT_OUTPUT_ALL, VRNA_CONVERT_OUTPUT_HP, VRNA_CONVERT_OUTPUT_STACK
VRNA_CONVERT_OUTPUT_MM_HP, VRNA_CONVERT_OUTPUT_MM_INT, VRNA_CONVERT_OUTPUT_MM_INT_1N
VRNA_CONVERT_OUTPUT_MM_INT_23, VRNA_CONVERT_OUTPUT_MM_MULTI, VRNA_CONVERT_OUTPUT_MM_EXT
VRNA_CONVERT_OUTPUT_DANGLE5, VRNA_CONVERT_OUTPUT_DANGLE3, VRNA_CONVERT_OUTPUT_INT_11
VRNA_CONVERT_OUTPUT_INT_21, VRNA_CONVERT_OUTPUT_INT_22, VRNA_CONVERT_OUTPUT_BULGE
VRNA_CONVERT_OUTPUT_INT, VRNA_CONVERT_OUTPUT_ML, VRNA_CONVERT_OUTPUT_MISC
VRNA_CONVERT_OUTPUT_SPECIAL_HP, VRNA_CONVERT_OUTPUT_VANILLA, VRNA_CONVERT_OUTPUT_NINIO
VRNA_CONVERT_OUTPUT_DUMP

The defined options are fine for bitwise compare- and assignment-operations, e. g.: pass a collection of options as a single value like this:

convert_parameter_file(ifile, ofile, option_1 | option_2 | option_n) 

Parameters

iname	The input file name (If NULL input is read from stdin)
oname	The output file name (If NULL output is written to stdout)
options	The options (as described above)