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EDcalculator

EDcalculator is used to calculate the Ensemble Defect (ED) of a structure or structures in a CT file or Dot-Bracket file. This is a measure of how much a single structure deviates from the basepair probabilities calculated for the ensemble of possible structures with the same sequence.

EDcalculator-smp is a parallel processing version for use on multi-core computers.

The program outputs both the total ED and the"normalized" ED (i.e. the total divided by the number of nucleotides in the sequence).

USAGE: EDcalculator <structure file> [options]

OR: EDcalculator-smp <structure file> <energy file> [options]

Required parameters:

<structure file> The name of a CT file or Dot-Bracket file containing the input structure.

Options that do not require added values:

-d, -D, --DNA Specify that the sequence is DNA, and DNA parameters are to be used.
Default is to use RNA parameters.
-h, -H, --help Display the usage details message.
-r, --raw Output just the *Normalized* ensemble defect as a pure number (with no
    additional description).
-v -V --version Display version and copyright information for this interface.

Options that require added values:

-a, -A, --alphabet Specify the name of a folding alphabet and associated nearest neighbor parameters. The alphabet is the prefix for the thermodynamic parameter files, e.g. "rna" for RNA parameters or "dna" for DNA parameters or a custom extended/modified alphabet. The thermodynamic parameters need to reside in the at the location indicated by environment variable DATAPATH.
The default is "rna" (i.e. use RNA parameters). This option overrides the --DNA flag.
-c -C --constraint Specify a folding constraints file to be applied.
-f --file Output the results to the specified file instead of to the screen (stdout).
-n --number Specify the index of a particular structure for which to calculate the defect. The default is -1, which means to calculate the defect for all structures in the input file.

Notes for smp:

The -smp, by default, will use all available compute cores for processing. The number of cores used can be controlled by setting the OMP_NUM_THREADS environment variable.

Visit The Mathews Lab RNAstructure Page for updates and latest information.