NAME

       RNAparconv - manual page for RNAparconv 2.6.4

SYNOPSIS

       RNAparconv [options] [<input file>] [<output file>]

DESCRIPTION

       RNAparconv 2.6.4

       Convert energy parameter files from ViennaRNA 1.8.4 to 2.0 format

       Converts  energy  parameter  files  from "old" ViennaRNAPackage 1.8.4 format to the new format used since
       ViennaRNAPackage 2.0.  The Program reads a valid energy parameter file or valid  energy  parameters  from
       stdin  and  prints the converted energy parameters to stdout or a specified output file. Per default, the
       converted output file contains the whole set of energy parameters used throughout ViennaRNAPackage 1.8.4.
       The user can specify sets of energy parameters that should not be included in the output.

       -h, --help
              Print help and exit

       --full-help
              Print help, including hidden options, and exit

       -V, --version
              Print version and exit

   I/O Options:
              Command line options for input and output (pre-)processing

       -i, --input=filename
              Specify an input file name. If argument is missing the energy parameter input can be supplied  via
              'stdin'.

       -o, --output=filename
              Specify an output file name. If argument is missing the converted energy parameters are printed to
              'stdout'.

       --vanilla
              Print  just  as  much  as  needed  to represent the given energy parameters data set.  This option
              overrides all other output settings!

              (default=off)

       --dump Just dump Vienna 1.8.4 energy parameters in format used since 2.0.  This option skips  any  energy
              parameter input!

              (default=off)

       --silent
              Print just energy parameters and appropriate comment lines but suppress all other output

              (default=off)

       --without-HairpinE
              Do not print converted hairpin energies and enthalpies

              (default=off)

       --without-StackE
              Do not print converted stacking energies and enthalpies

              (default=off)

       --without-IntE
              Do not print converted interior loop energies, enthalpies and asymetry factors

              (default=off)

       --without-BulgeE
              Do not print converted bulge loop energies and enthalpies

              (default=off)

       --without-MultiE
              Do not print converted multi loop energies and enthalpies

              (default=off)

       --without-MismatchE
              Do not print converted exterior loop mismatch energies and enthalpies

              (default=off)

       --without-MismatchH
              Do not print converted hairpin mismatch energies and enthalpies

              (default=off)

       --without-MismatchI
              Do not print converted interior loop mismatch energies and enthalpies

              (default=off)

       --without-MismatchM
              Do not print converted multi loop mismatch energies and enthalpies

              (default=off)

       --without-Dangle5
              Do not print converted 5' dangle energies and enthalpies

              (default=off)

       --without-Dangle3
              Do not print converted 3' dangle energies and enthalpies

              (default=off)

       --without-Misc
              Do not print converted Misc energies and enthalpies (TerminalAU, DuplexInit, lxc)

              (default=off)

REFERENCES

       If you use this program in your work you might want to cite:

       R.  Lorenz,  S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker
       (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26

       I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994), "Fast Folding  and
       Comparison of RNA Secondary Structures", Monatshefte f. Chemie: 125, pp 167-188

       R.  Lorenz,  I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and soft constraints", Algorithms
       for Molecular Biology 11:1 pp 1-13

       The energy parameters are taken from:

       D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder,  J.  Susan,  M.  Zuker,  D.H.  Turner
       (2004),  "Incorporating  chemical  modification  constraints  into  a  dynamic  programming algorithm for
       prediction of RNA secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292

       D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter database for predicting  stability
       of nucleic acid secondary structure", Nucleic Acids Research: 38, pp 280-282

AUTHOR

       Ronny Lorenz

REPORTING BUGS

       If in doubt our program is right, nature is at fault.  Comments should be sent to rna@tbi.univie.ac.at.

RNAparconv 2.6.4                                  January 2025                                     RNAPARCONV(1)