Fold Report

Fold Report: Fields

Name	Data Type
Sample	str
Branches	dict[str, str]
Reference	str
Region	str
Profile	str
Only generate the fold command and input files; do not run folding	bool
Model RNA structures using RNAstructure (Fold/ShapeKnots) or ViennaRNA (RNAfold/RNAsubopt); auto selects RNAstructure for DMS and ViennaRNA for other probes	str
Use this method to incorporate reactivities into folding energies. auto selects Cordero for DMS and Eddy for other probes; Eddy requires –fold-backend=ViennaRNA; Cordero requires –fold-backend=RNAstructure	str
Slope (kcal/mol) for SHAPE reactivities using Deigan method; used only with –fold-energy-method=Deigan	float
Intercept (kcal/mol) for SHAPE reactivities using Deigan method; used only with –fold-energy-method=Deigan	float
Normalize and winsorize reactivities to this quantile for folding	float
Allow isolated (non-stacked) base pairs when folding	bool
Predict structures at this temperature (Celsius)	float
Limit base pair distances to this number of bases (0 for no limit)	int
Predict only the minimum free energy (MFE) structure	bool
Output at most this many structures (overriden by –fold-mfe)	int
Stop outputting structures when the % difference in energy exceeds this value (overriden by –fold-mfe)	float
Maximum absolute energy difference (kcal/mol) from the MFE for suboptimal structures output by RNAsubopt (overriden by –fold-mfe)	float
Predict pseudoknotted structures (requires –fold-backend=RNAstructure; uses ShapeKnots when set, Fold otherwise)	bool
Checksum of the ViennaRNA command file (SHA-512)	str
Checksum of the constraints file (SHA-512)	str
Checksum of the Eddy paired-prior file (SHA-512)	str
Checksum of the Eddy unpaired-prior file (SHA-512)	str
Time began	str
Time ended	str
Time taken (minutes)	float
Version of SEISMIC-RNA	str

Fold Report: Example

{
    "Sample": "sample1",
    "Branches": {
        "align": "",
        "idmut": "",
        "filter": "",
        "fold": ""
    },
    "Reference": "myref",
    "Region": "full",
    "Profile": "full__average",
    "Only generate the fold command and input files; do not run folding": false,
    "Model RNA structures using RNAstructure (Fold/ShapeKnots) or ViennaRNA (RNAfold/RNAsubopt); auto selects RNAstructure for DMS and ViennaRNA for other probes": "RNAstructure",
    "Use this method to incorporate reactivities into folding energies. auto selects Cordero for DMS and Eddy for other probes; Eddy requires --fold-backend=ViennaRNA; Cordero requires --fold-backend=RNAstructure": "Cordero",
    "Slope (kcal/mol) for SHAPE reactivities using Deigan method; used only with --fold-energy-method=Deigan": 1.8,
    "Intercept (kcal/mol) for SHAPE reactivities using Deigan method; used only with --fold-energy-method=Deigan": -0.6,
    "Normalize and winsorize reactivities to this quantile for folding": 0.95,
    "Allow isolated (non-stacked) base pairs when folding": false,
    "Predict structures at this temperature (Celsius)": 37.0,
    "Limit base pair distances to this number of bases (0 for no limit)": 0,
    "Predict only the minimum free energy (MFE) structure": false,
    "Output at most this many structures (overriden by --fold-mfe)": 20,
    "Stop outputting structures when the % difference in energy exceeds this value (overriden by --fold-mfe)": 20.0,
    "Maximum absolute energy difference (kcal/mol) from the MFE for suboptimal structures output by RNAsubopt (overriden by --fold-mfe)": 1.0,
    "Predict pseudoknotted structures (requires --fold-backend=RNAstructure; uses ShapeKnots when set, Fold otherwise)": false,
    "Checksum of the ViennaRNA command file (SHA-512)": "",
    "Checksum of the constraints file (SHA-512)": "",
    "Checksum of the Eddy paired-prior file (SHA-512)": "",
    "Checksum of the Eddy unpaired-prior file (SHA-512)": "",
    "Time began": "2026-05-31 at 12:59:24",
    "Time ended": "2026-05-31 at 12:59:24",
    "Time taken (minutes)": 0.01,
    "Version of SEISMIC-RNA": "0.25.3"
}