> ## Documentation Index > Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt > Use this file to discover all available pages before exploring further. # RNA Structural Motif Similarity > Compare RNA structural motifs (stems, hairpins, bulges) using Jaccard similarity.

**License:** ViennaRNA is licensed under Custom (ViennaRNA Package License) and may require explicit attribution when utilized. Please refer to [the license](https://github.com/ViennaRNA/ViennaRNA/blob/master/COPYING) for full terms.

This constraint is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.

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evo-design/proto-language/proto\_language/constraint/rna\_secondary\_structure/structure\_similarity\_constraint.py

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```bibtex theme={null} @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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Compare structural motifs (stems, hairpins, bulges) between proposals and. reference using Jaccard similarity. Returns 1 - similarity (so 0 is perfect match, 1 is worst). ## API Reference

ConfigRNAMotifSimilarityConfig Source

Configuration for structural motif similarity constraint. Compares extracted structural motifs (stems, hairpins, bulges, nesting depth, unpaired regions) using Jaccard similarity. Inherits from `RNAStructureConstraintBaseConfig`. Reference RNA/DNA sequence to compare against Folding temperature in Celsius

ReturnsConstraintOutput

Per-proposal score (`1 - similarity`) with metadata for reference, candidate, and shared motif sets plus the predicted structure.

## Usage ```python python icon="python" theme={null} from proto_language.core import Constraint from proto_language.constraint import rna_motif_similarity_constraint, RNAMotifSimilarityConfig constraint = Constraint( inputs=[segment], function=rna_motif_similarity_constraint, function_config=RNAMotifSimilarityConfig( # Configure parameters here ), ) scores = constraint.evaluate() ``` ## Metadata | Property | Value | | --------------- | --------------------------------- | | Key | `rna-motif-similarity` | | Function | `rna_motif_similarity_constraint` | | Category | `rna_secondary_structure` | | Mode | `discrete` | | Uses GPU | `False` | | Supported Types | `dna`, `rna` |