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RNAPARCONV(1)			  User Commands 		   RNAPARCONV(1)

NAME
     RNAparconv - manual page for RNAparconv 2.7.2

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

DESCRIPTION
     RNAparconv 2.7.2

     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 de-
     fault, the converted output file contains the whole set of  energy  parame-
     ters  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

     --detailed-help
	    Print help, including all details and hidden options, and exit

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

     -V, --version
	    Print version and exit

     -v, --verbose
	    Be verbose.  (default=off)

	    Lower the log level setting such that even INFO messages are  passed
	    through.

   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 para-
	    meter 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 parame-
	    ters 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 sup-
	    press 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 internal loop energies, enthalpies and asyme-
	    try 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  en-
	    thalpies

	    (default=off)

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

	    (default=off)

     --without-MismatchI
	    Do	not  print  converted  internal  loop  mismatch energies and en-
	    thalpies

	    (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, Du-
	    plexInit, lxc)

	    (default=off)

     --log-level=level
	    Set log level threshold.  (default=`2')

	    By default, any log messages are filtered such  that  only	warnings
	    (level  2)	or errors (level 3) are printed. This setting allows for
	    specifying the log level threshold, where higher  values  result  in
	    fewer  information.  Log-level 5 turns off all messages, even errors
	    and other critical information.

     --log-file[=filename]
	    Print log messages to a  file  instead  of	stderr.   (default=`RNA-
	    parconv.log')

     --log-time
	    Include time stamp in log messages.

	    (default=off)

     --log-call
	    Include file and line of log calling function.

	    (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. Su-
     san, M. Zuker, D.H. Turner  (2004),  "Incorporating  chemical  modification
     constraints into a dynamic programming algorithm for prediction of RNA sec-
     ondary 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", Nu-
     cleic 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 2.7.2		  December 2025 		   RNAPARCONV(1)

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