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RNAstructure Command Line Help

EDcalculator is used to calculate the Ensemble Defect (ED) of a structure or structures in a CT file or Dot-Bracket file. This is the average number of nucleotides (as estimated by a partition function calculation) that will not be paired as expected in the structure, for the specific sequence and structure in the input ct or dot-bracket file.

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

The program outputs both the total ED and the normalized ED (NED; i.e. the total divided by the number of nucleotides in the sequence). The program can also calculate the ED for a local region of the structure. The region is specified using --start and --end (inclusive), and the normalized ED is the ED divided by the fragment length. The default behavior is to use the full length of the sequence.

USAGE: EDcalculator <structure file> [options]

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

Required parameters:

<structure file> The name of a CT file or Dot-Bracket file containing the input structure. The ED is calculated for this sequence to fold to the structure encoded in the input file.

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.
-s -S --start Specify a start nucleotide for a local calculation. The default is to start at the first nucleotide (nucleotide 1).
-e -E --end Specify an end nucleotide for a local calculation. The default is to end at the last nucleotide of the sequence.

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.


  1. Reuter, J.S. and Mathews, D.H.
    "RNAstructure: software for RNA secondary structure prediction and analysis."
    BMC Bioinformatics, 11:129. (2010).
  2. Bellaousov, S., Kayedkhordeh, M., Peterson, R. J. and Mathews, D. H.
    "Accelerated RNA Secondary Structure Design Using Pre-Selected Sequences for Helices and Loops."
    RNA. 24: 1555-1567. (2018).
  3. Zadeh, J.N., Wolfe, B.R., and Pierce, N.A.
    "Nucleic acid sequence design via efficient ensemble defect optimization."
    J. Comput. Chem., 32: 439-452. (2011).