Converting Energy Parameter Files — ViennaRNA Package

# Converting Energy Parameter Files

Converting 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

  Defines

  VRNA_CONVERT_OUTPUT_ALL

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of a complete parameter set

  VRNA_CONVERT_OUTPUT_HP

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of hairpin contributions

  VRNA_CONVERT_OUTPUT_STACK

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of base pair stack contributions

  VRNA_CONVERT_OUTPUT_MM_HP

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of hairpin mismatch contribution

  VRNA_CONVERT_OUTPUT_MM_INT

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of internal loop mismatch contribution

  VRNA_CONVERT_OUTPUT_MM_INT_1N

        #include <ViennaRNA/params/convert.h>

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

  VRNA_CONVERT_OUTPUT_MM_INT_23

        #include <ViennaRNA/params/convert.h>

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

  VRNA_CONVERT_OUTPUT_MM_MULTI

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of multi loop mismatch contribution

  VRNA_CONVERT_OUTPUT_MM_EXT

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of exterior loop mismatch contribution

  VRNA_CONVERT_OUTPUT_DANGLE5

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of 5’ dangle conctribution

  VRNA_CONVERT_OUTPUT_DANGLE3

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of 3’ dangle contribution

  VRNA_CONVERT_OUTPUT_INT_11

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of 1:1 internal loop contribution

  VRNA_CONVERT_OUTPUT_INT_21

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of 2:1 internal loop contribution

  VRNA_CONVERT_OUTPUT_INT_22

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of 2:2 internal loop contribution

  VRNA_CONVERT_OUTPUT_BULGE

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of bulge loop contribution

  VRNA_CONVERT_OUTPUT_INT

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of internal loop contribution

  VRNA_CONVERT_OUTPUT_ML

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of multi loop contribution

  VRNA_CONVERT_OUTPUT_MISC

        #include <ViennaRNA/params/convert.h>

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

  VRNA_CONVERT_OUTPUT_SPECIAL_HP

        #include <ViennaRNA/params/convert.h>

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

  VRNA_CONVERT_OUTPUT_VANILLA

        #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 !

  VRNA_CONVERT_OUTPUT_NINIO

        #include <ViennaRNA/params/convert.h>

    Flag to indicate printing of internal loop asymmetry contribution

  VRNA_CONVERT_OUTPUT_DUMP

        #include <ViennaRNA/params/convert.h>

    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)

        #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)