WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / man / RNAparconv.1

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+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.