Converting Energy Parameter Files

Detailed Documentation

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

Global 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

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)

Macros

#define VRNA_CONVERT_OUTPUT_ALL
Flag to indicate printing of a complete parameter set
#define VRNA_CONVERT_OUTPUT_BULGE
Flag to indicate printing of bulge loop contribution
#define VRNA_CONVERT_OUTPUT_DANGLE3
Flag to indicate printing of 3’ dangle contribution
#define VRNA_CONVERT_OUTPUT_DANGLE5
Flag to indicate printing of 5’ dangle conctribution
#define VRNA_CONVERT_OUTPUT_DUMP
Flag to indicate dumping the energy contributions from the library instead of an input file
#define VRNA_CONVERT_OUTPUT_HP
Flag to indicate printing of hairpin contributions
#define VRNA_CONVERT_OUTPUT_INT
Flag to indicate printing of interior loop contribution
#define VRNA_CONVERT_OUTPUT_INT_11
Flag to indicate printing of 1:1 interior loop contribution
#define VRNA_CONVERT_OUTPUT_INT_21
Flag to indicate printing of 2:1 interior loop contribution
#define VRNA_CONVERT_OUTPUT_INT_22
Flag to indicate printing of 2:2 interior loop contribution
#define VRNA_CONVERT_OUTPUT_MISC
Flag to indicate printing of misc contributions (such as terminalAU)
#define VRNA_CONVERT_OUTPUT_ML
Flag to indicate printing of multi loop contribution
#define VRNA_CONVERT_OUTPUT_MM_EXT
Flag to indicate printing of exterior loop mismatch contribution
#define VRNA_CONVERT_OUTPUT_MM_HP
Flag to indicate printing of hairpin mismatch contribution
#define VRNA_CONVERT_OUTPUT_MM_INT
Flag to indicate printing of interior loop mismatch contribution
#define VRNA_CONVERT_OUTPUT_MM_INT_1N
Flag to indicate printing of 1:n interior loop mismatch contribution
#define VRNA_CONVERT_OUTPUT_MM_INT_23
Flag to indicate printing of 2:3 interior loop mismatch contribution
#define VRNA_CONVERT_OUTPUT_MM_MULTI
Flag to indicate printing of multi loop mismatch contribution
#define VRNA_CONVERT_OUTPUT_NINIO
Flag to indicate printing of interior loop asymmetry contribution
#define VRNA_CONVERT_OUTPUT_SPECIAL_HP
Flag to indicate printing of special hairpin contributions (tri-, tetra-, hexa-loops)
#define VRNA_CONVERT_OUTPUT_STACK
Flag to indicate printing of base pair stack contributions
#define VRNA_CONVERT_OUTPUT_VANILLA

Flag to indicate printing of given parameters only

Note

This option overrides all other output options, except VRNA_CONVERT_OUTPUT_DUMP !