H/convert_epars.h File Reference

Functions and definitions for energy parameter file format conversion. More...

Go to the source code of this file.

Defines
#define	VRNA_CONVERT_OUTPUT_ALL   1U
	Flag to indicate printing of a complete parameter set.
#define	VRNA_CONVERT_OUTPUT_HP   2U
	Flag to indicate printing of hairpin contributions.
#define	VRNA_CONVERT_OUTPUT_STACK   4U
	Flag to indicate printing of base pair stack contributions.
#define	VRNA_CONVERT_OUTPUT_MM_HP   8U
	Flag to indicate printing of hairpin mismatch contribution.
#define	VRNA_CONVERT_OUTPUT_MM_INT   16U
	Flag to indicate printing of interior loop mismatch contribution.
#define	VRNA_CONVERT_OUTPUT_MM_INT_1N   32U
	Flag to indicate printing of 1:n interior loop mismatch contribution.
#define	VRNA_CONVERT_OUTPUT_MM_INT_23   64U
	Flag to indicate printing of 2:3 interior loop mismatch contribution.
#define	VRNA_CONVERT_OUTPUT_MM_MULTI   128U
	Flag to indicate printing of multi loop mismatch contribution.
#define	VRNA_CONVERT_OUTPUT_MM_EXT   256U
	Flag to indicate printing of exterior loop mismatch contribution.
#define	VRNA_CONVERT_OUTPUT_DANGLE5   512U
	Flag to indicate printing of 5' dangle conctribution.
#define	VRNA_CONVERT_OUTPUT_DANGLE3   1024U
	Flag to indicate printing of 3' dangle contribution.
#define	VRNA_CONVERT_OUTPUT_INT_11   2048U
	Flag to indicate printing of 1:1 interior loop contribution.
#define	VRNA_CONVERT_OUTPUT_INT_21   4096U
	Flag to indicate printing of 2:1 interior loop contribution.
#define	VRNA_CONVERT_OUTPUT_INT_22   8192U
	Flag to indicate printing of 2:2 interior loop contribution.
#define	VRNA_CONVERT_OUTPUT_BULGE   16384U
	Flag to indicate printing of bulge loop contribution.
#define	VRNA_CONVERT_OUTPUT_INT   32768U
	Flag to indicate printing of interior loop contribution.
#define	VRNA_CONVERT_OUTPUT_ML   65536U
	Flag to indicate printing of multi loop contribution.
#define	VRNA_CONVERT_OUTPUT_MISC   131072U
	Flag to indicate printing of misc contributions (such as terminalAU).
#define	VRNA_CONVERT_OUTPUT_SPECIAL_HP   262144U
	Flag to indicate printing of special hairpin contributions (tri-, tetra-, hexa-loops).
#define	VRNA_CONVERT_OUTPUT_VANILLA   524288U
	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
	Flag to indicate printing of interior loop asymmetry contribution.
#define	VRNA_CONVERT_OUTPUT_DUMP   2097152U
	Flag to indicate dumping the energy contributions from the library instead of an input file.
Functions
void	convert_parameter_file (const char *iname, const char *oname, unsigned int options)
	Convert/dump a Vienna 1.8.4 formatted energy parameter file.

---

Detailed Description

Functions and definitions for energy parameter file format conversion.

---

Function Documentation

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

Convert/dump a Vienna 1.8.4 formatted energy parameter file.

The options argument allows 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)