| ## RNAstructure Command Line Help EDcalculator | ### Contents ### Index
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. ### References: Reuter, J.S. and Mathews, D.H. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC Bioinformatics, 11:129. (2010). 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). 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).