Converting Energy Parameter Files
Energy Parameter Sets and Boltzmann Factors » Reading/Writing Energy Parameter Sets from/to File

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

Collaboration diagram for Converting Energy Parameter Files:

## Files

file | convert_epars.h
| Functions and definitions for energy parameter file format conversion.

## 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)

## 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

## Macro Definition Documentation

#define VRNA_CONVERT_OUTPUT_ALL 1U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of a complete parameter set

#define VRNA_CONVERT_OUTPUT_HP 2U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of hairpin contributions

#define VRNA_CONVERT_OUTPUT_STACK 4U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of base pair stack contributions

#define VRNA_CONVERT_OUTPUT_MM_HP 8U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of hairpin mismatch contribution

#define VRNA_CONVERT_OUTPUT_MM_INT 16U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of interior loop mismatch contribution

#define VRNA_CONVERT_OUTPUT_MM_INT_1N 32U

`#include <ViennaRNA/convert_epars.h>`

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

#define VRNA_CONVERT_OUTPUT_MM_INT_23 64U

`#include <ViennaRNA/convert_epars.h>`

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

#define VRNA_CONVERT_OUTPUT_MM_MULTI 128U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of multi loop mismatch contribution

#define VRNA_CONVERT_OUTPUT_MM_EXT 256U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of exterior loop mismatch contribution

#define VRNA_CONVERT_OUTPUT_DANGLE5 512U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of 5' dangle conctribution

#define VRNA_CONVERT_OUTPUT_DANGLE3 1024U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of 3' dangle contribution

#define VRNA_CONVERT_OUTPUT_INT_11 2048U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of 1:1 interior loop contribution

#define VRNA_CONVERT_OUTPUT_INT_21 4096U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of 2:1 interior loop contribution

#define VRNA_CONVERT_OUTPUT_INT_22 8192U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of 2:2 interior loop contribution

#define VRNA_CONVERT_OUTPUT_BULGE 16384U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of bulge loop contribution

#define VRNA_CONVERT_OUTPUT_INT 32768U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of interior loop contribution

#define VRNA_CONVERT_OUTPUT_ML 65536U

`#include <ViennaRNA/convert_epars.h>`

Flag to indicate printing of multi loop contribution

#define VRNA_CONVERT_OUTPUT_MISC 131072U

`#include <ViennaRNA/convert_epars.h>`

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

#define VRNA_CONVERT_OUTPUT_SPECIAL_HP 262144U

`#include <ViennaRNA/convert_epars.h>`

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

#define VRNA_CONVERT_OUTPUT_VANILLA 524288U

`#include <ViennaRNA/convert_epars.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/convert_epars.h>`

Flag to indicate printing of interior loop asymmetry contribution

#define VRNA_CONVERT_OUTPUT_DUMP 2097152U

`#include <ViennaRNA/convert_epars.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/convert_epars.h>`

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)