RNAPARCONV(1)

Okay bestie, let's talk about RNAparconv, a User Commands tool that's literally about to become your new favorite 🦋✨

💖 NAME 💖

RNAparconv - manual page for RNAparconv 2.7.0 🌸

🧚 SYNOPSIS 🧚

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

🌈 DESCRIPTION 🌈

Okay so, this is RNAparconv 2.7.0 💅

It converts energy parameter files from the "old" ViennaRNAPackage 1.8.4 format into the new format we've been using since ViennaRNAPackage 2.0. 😭 It reads a valid energy parameter file, or valid energy parameters from stdin, and spits out the converted stuff to stdout or to whatever output file you name. By default, the converted output has the whole set of energy parameters that ViennaRNAPackage 1.8.4 used. Bestie, you get to pick which sets you don't want in the output, so it's giving customization 🎀

• -h, --help — Prints help and exits 🫶
• --detailed-help — Prints help with all the details and hidden options, then exits 🔥
• --full-help — Prints help including hidden options, then exits 💜
• -V, --version — Prints the version and exits 🍓
• -v, --verbose — Gets chatty. (default=off) 🗣️ This lowers the log level so even INFO messages get through.

🎀 I/O Options 🎀

Command line options for input and output (pre-)processing. These are the ones you'll be obsessed with 🫠

• -i, --input=filename — Tells it which input file to read. If you leave out the argument, the energy parameter input can come from stdin instead 🌸
• -o, --output=filename — Tells it where to save the output. If you leave out the argument, the converted energy parameters get printed to stdout 🦋
• --vanilla — Prints just enough to represent the energy parameter data set you gave it. This option overrides all other output settings, so it's the main character of the output flags 👑 (default=off)
• --dump — Dumps the Vienna 1.8.4 energy parameters in the format used since 2.0. (default=off)

This one skips any energy parameter input entirely! Don't be surprised if it ignores your input file 💀

• --silent — Prints only the energy parameters and the appropriate comment lines, and suppresses everything else. Very quiet girl energy 🤫 (default=off)
• --without-HairpinE — Doesn't print the converted hairpin energies and enthalpies. (default=off)
• --without-StackE — Doesn't print the converted stacking energies and enthalpies. (default=off)
• --without-IntE — Doesn't print the converted internal loop energies, enthalpies, and asymmetry factors. (default=off)
• --without-BulgeE — Doesn't print the converted bulge loop energies and enthalpies. (default=off)
• --without-MultiE — Doesn't print the converted multi loop energies and enthalpies. (default=off)
• --without-MismatchE — Doesn't print the converted exterior loop mismatch energies and enthalpies. (default=off)
• --without-MismatchH — Doesn't print the converted hairpin mismatch energies and enthalpies. (default=off)
• --without-MismatchI — Doesn't print the converted internal loop mismatch energies and enthalpies. (default=off)
• --without-MismatchM — Doesn't print the converted multi loop mismatch energies and enthalpies. (default=off)
• --without-Dangle5 — Doesn't print the converted 5' dangle energies and enthalpies. (default=off)
• --without-Dangle3 — Doesn't print the converted 3' dangle energies and enthalpies. (default=off)
• --without-Misc — Doesn't print the converted Misc energies and enthalpies (TerminalAU, DuplexInit, lxc). (default=off)
• --log-level=level — Sets the log level threshold. (default=(default=`2')) Okay so, by default, only warnings (level 2) or errors (level 3) get printed. Higher values mean fewer messages. Log level 5 turns off all messages, even errors and other critical info 🙈
• --log-file[=filename] — Sends log messages to a file instead of stderr. (default=(default=`RNAparconv.log'))
• --log-time — Adds a time stamp to log messages. (default=off) ⏰
• --log-call — Adds the file and line of the log-calling function to log messages. (default=off) 🔍

📚 REFERENCES 📚

If you use this program in your work, you might want to cite these iconic papers 🫶

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 you're ever unsure, our program is right and nature is at fault 💅 Send your comments to rna@tbi.univie.ac.at 🫶

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Bestie, that's the whole tea ☕🌸 RNAparconv 2.7.0, February 2026, RNAPARCONV(1), go convert those parameters and slay forever 💖✨