ct-energy

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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=RNA|DNA
sets nucleic acid type to RNA or DNA. Default is RNA.
-t, --temperature=temp
sets temperature to temp. Default is 37.
-N, --sodium=value
sets Sodium ion concentration to value molar. Default is 1.
-M, --magnesium=value
sets Magnesium ion concentration to value 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
causes ct-energy to output detailed information about each loop in the structure. Specify twice for even more verbosity.
-L, --logarithmic
make penalty for multibranch loops logarithmic rather than linear.
-V, --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.

Obscure Options

--nodangle
removes single-base stacking from consideration.
--simple
makes the penalty for multibranch loops constant rather than affine.

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).

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