2.1.2

.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
.TH RNAPARCONV "1" "July 2013" "RNAparconv 2.1.2" "User Commands"
.SH NAME
RNAparconv \- manual page for RNAparconv 2.1.2
.SH SYNOPSIS
.B RNAparconv
[\fIoptions\fR] [\fI<input file>\fR] [\fI<output file>\fR]
.SH DESCRIPTION
RNAparconv 2.1.2
.PP
Convert energy parameter files from ViennaRNA 1.8.4 to 2.0 format
.PP
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.
.TP
\fB\-h\fR, \fB\-\-help\fR
Print help and exit
.TP
\fB\-\-full\-help\fR
Print help, including hidden options, and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
Print version and exit
.TP
\fB\-o\fR, \fB\-\-output\fR=\fIfilename\fR
Specify an output file name. If argument is missing
the converted energy parameters are printed to
\&'stdout'.
.TP
\fB\-i\fR, \fB\-\-input\fR=\fIfilename\fR
Specify an input file name. If argument is missing
the energy parameter input can be supplied via
\&'stdin'.
.TP
\fB\-\-vanilla\fR
Print just as much as needed to represent the given
energy parameters data set.
This option overrides all other output settings!
.IP
(default=off)
.TP
\fB\-\-dump\fR
Just dump Vienna 1.8.4 energy parameters in format
used since 2.0.
This option skips any energy parameter input!
.IP
(default=off)
.TP
\fB\-\-silent\fR
Print just energy parameters and appropriate comment
lines but suppress all other output
.IP
(default=off)
.TP
\fB\-\-without\-HairpinE\fR
Do not print converted hairpin energies and
enthalpies
.IP
(default=off)
.TP
\fB\-\-without\-StackE\fR
Do not print converted stacking energies and
enthalpies
.IP
(default=off)
.TP
\fB\-\-without\-IntE\fR
Do not print converted interior loop energies,
enthalpies and asymetry factors
.IP
(default=off)
.TP
\fB\-\-without\-BulgeE\fR
Do not print converted bulge loop energies and
enthalpies
.IP
(default=off)
.TP
\fB\-\-without\-MultiE\fR
Do not print converted multi loop energies and
enthalpies
.IP
(default=off)
.TP
\fB\-\-without\-MismatchE\fR
Do not print converted exterior loop mismatch
energies and enthalpies
.IP
(default=off)
.TP
\fB\-\-without\-MismatchH\fR
Do not print converted hairpin mismatch energies and
enthalpies
.IP
(default=off)
.TP
\fB\-\-without\-MismatchI\fR
Do not print converted interior loop mismatch
energies and enthalpies
.IP
(default=off)
.TP
\fB\-\-without\-MismatchM\fR
Do not print converted multi loop mismatch energies
and enthalpies
.IP
(default=off)
.TP
\fB\-\-without\-Dangle5\fR
Do not print converted 5' dangle energies and
enthalpies
.IP
(default=off)
.TP
\fB\-\-without\-Dangle3\fR
Do not print converted 3' dangle energies and
enthalpies
.IP
(default=off)
.TP
\fB\-\-without\-Misc\fR
Do not print converted Misc energies and enthalpies
(TerminalAU, DuplexInit, lxc)
.IP
(default=off)
.SH AUTHOR

Ronny Lorenz
.SH REFERENCES
.I 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


.I 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
.SH "REPORTING BUGS"
If in doubt our program is right, nature is at fault.
.br
Comments should be sent to rna@tbi.univie.ac.at.