RNA Feature Vector Similarity

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

Tools Used Tools Used Source Source Cite Cite

Go to Tool Page

evo-design/proto-language/proto_language/constraint/rna_secondary_structure/structure_similarity_constraint.py

View source

@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}
}

Copy citation

Constraint contributors

Construct 10-dim feature vectors and compare using cosine similarity. Returns (1 - similarity) / 2, scaling cosine similarity from [-1, 1] to [0, 1].

API Reference

ConfigRNAFeatureSimilarityConfig Source

Configuration for feature vector similarity constraint.Compares 10-dimensional structural feature vectors using cosine similarity. Features include: length, number of pairs, pairing ratio, stem statistics (avg, max, count), loop statistics, MFE, MFE per nucleotide, and hairpin count.Inherits from RNAStructureConstraintBaseConfig.

string

required

Reference RNA/DNA sequence to compare against

number

default:"37.0"

Folding temperature in Celsius

ReturnsConstraintOutput

Per-proposal score ((1 - cosine) / 2) with metadata for the reference/candidate feature vectors, predicted structure, and candidate MFE.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import rna_feature_similarity_constraint, RNAFeatureSimilarityConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	`rna-feature-similarity`
Function	`rna_feature_similarity_constraint`
Category	`rna_secondary_structure`
Mode	`discrete`
Uses GPU	`False`
Supported Types	`dna`, `rna`

Language

Language Concepts

Language Guides

Constraints

Generators

Optimizers

RNA Feature Vector Similarity

API Reference

Usage

Metadata

​API Reference

​Usage

​Metadata

API Reference

Usage

Metadata