Minimum Free Energy

License: ViennaRNA is licensed under Custom (ViennaRNA Package License) and may require explicit attribution when utilized. Please refer to the license for full terms.

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evo-design/proto-language

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@articlelorenz2011viennarna

@article{lorenz2011viennarna,
  title={ViennaRNA Package 2.0},
  author={Lorenz, Ronny and Bernhart, Stephan H and H{\"o}ner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F and Hofacker, Ivo L},
  journal={Algorithms for Molecular Biology},
  volume={6},
  number={1},
  pages={26},
  year={2011},
  publisher={BioMed Central},
  doi={10.1186/1748-7188-6-26}
}

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Constraint contributors

Score sequences by ViennaRNA minimum free energy.

API Reference

ConfigMFEConfig Source

Configuration for the minimum-free-energy (MFE) constraint.

enum

default:"min"

‘min’ rewards more-negative MFE (more stable); ‘max’ rewards less structure.Options: min, max

number

default:"-30.0"

MFE (kcal/mol) mapped to energy 0.5; length-dependent, tune per sequence length.

number

default:"10.0"

Positive float32-safe width of the sigmoid transform in kcal/mol; larger is gentler.

number

default:"37.0"

ViennaRNA folding temperature in Celsius.

ReturnsConstraintOutput

One result per sequence. score is in [0.0, 1.0] (lower is better in the requested direction); metadata carries the raw mfe (kcal/mol) and the ViennaRNA dot-bracket structure.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import mfe_constraint, MFEConfig

constraint = Constraint(
    inputs=[segment],
    function=mfe_constraint,
    function_config=MFEConfig(
        # Configure parameters here
    ),
)

scores = constraint.evaluate()

Metadata

Property	Value
Key	`mfe`
Function	`mfe_constraint`
Category	`rna_secondary_structure`
Mode	`discrete`
Uses GPU	`False`
Supported Types	`dna`, `rna`

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