EnsembleEnergy calculates the energy of a structure ensemble from either a partition function save file or a sequence file. This ensemble energy is -RT ln(Q), where Q is the partition function. It prints results on standard output, so no output file is generated.
USAGE: EnsembleEnergy <input file> [options]
The name of a file containing input data. This input data can be in one of two formats:
- Partition function save file (holds base pairing probability data for all pairs and can be generated using the partition interface).
Sequence file (holds raw sequence: .seq or .fasta).
Note that lowercase nucleotides are forced single-stranded in structure prediction.
Note that in order to use a squence file, the "sequence" flag must be specified (see "--sequence" below).
|-d, -D, --DNA
This flag only matters if the input file is a squence file and has been identified as such (see "--sequence" below).
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.
|-s, -S, --silent
Suppress all progress messages except the final ensemble energy result.
Note that this does NOT suppress errors, so errors will be shown even if this option is specified.
||Identify the input file format as a sequence file.
Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction and analysis."
BMC Bioinformatics, 11:129. (2010).