NAME

ct-energy — evaluate the energy of a .ct file

SYNOPSIS

ct-energy [OPTION]... [FILE]...

DESCRIPTION

ct-energy evaluates the energy of each structure in each FILE, such as those produced by mfold or by hybrid-min or hybrid-ss-min. In its default mode it prints the energy of each structure followed by a carriage return (but see the --verbose option below).

When no FILE is specified, or if FILE is -, ct-energy reads standard input.

OPTIONS

-n, --NA=RNA2|RNA3|RNA|DNA
set nucleic acid type to RNA or DNA. Default is RNA.
-t, --temperature=REAL
set temperature to REAL °C. Default is 37.
-N, --sodium=REAL
set Sodium ion concentration to REAL molar. Default is 1.
-M, --magnesium=REAL
set Magnesium ion concentration to REAL molar. Default is 0.
-p, --polymer
use salt corrections for polymers instead of oligomers (the default).
-s, --suffix=STRING
use energy rules with the suffix STRING. Overrides --temperature, --sodium, --magnesium and --polymer.
-v, --verbose
output detailed information about each loop in the structure. Specify twice for even more verbosity.
-L, --logarithmic
make the penalty for multibranch loops logarithmic rather than linear.

OBSCURE OPTIONS

--nodangle
remove single-base stacking from consideration.
--simple
make the penalty for multibranch loops constant rather than affine.
--Vienna
consider single-base stacking in "Vienna mode", in which a single-stranded base that may stack on an adjacent basepair must always do so. By default, two states are considered for each such base: dangling and not dangling.
--coaxial
consider coaxial stacking.

ENVIRONMENT

UNAFOLDDAT
an alternate location from which to read the energy rules. The default energy rules can be overridden with files in the current directory or in the directory pointed to by UNAFOLDDAT. ct-energy looks for each file first in the current directory, then in the directory specified by UNAFOLDDAT and last in /usr/local/share/unafold (or wherever the energy rules were installed).

REFERENCES

Markham, N. R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. In Keith, J. M., editor, Bioinformatics, Volume II. Structure, Functions and Applications, number 453 in Methods in Molecular Biology, chapter 1, pages 3-31. Humana Press, Totowa, NJ. ISBN 978-1-60327-428-9.

Other references which may be useful may be found at http://www.unafold.org/Dinamelt/dinamelt-references.php

SEE ALSO

hybrid-min(1), hybrid-ss-min(1)

AUTHORS

Nick Markham <markham@alum.rpi.edu> and Michael Zuker <zukerm@alum.mit.edu>

COPYRIGHT

Copyright (c) 2006-2021, Rensselaer Polytechnic Institute.

AVAILABILITY

UNAFold is available from http://www.unafold.org/Dinamelt/software/obtaining-unafold.php. Commercial use requires a license; see https://ipo.rpi.edu/invention/unafold-version-40.