Gyration Radius

Filter structures by radius of gyration (compactness)

License: Structure Metrics is open source and free for academic and commercial use under an Apache-2.0 license. 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.

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proto-bio/proto-language/proto_language/constraint/protein_structure/gyration_radius_constraint.py

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@misc{structuremetrics2024,
  title={Structure quality metrics for protein structure prediction filtering},
  author={Internal},
  year={2024},
  note={Internal proto-tools tool using biotite for SSE annotation}
}

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Filter structures by radius of gyration.

API Reference

ConfigGyrationRadiusConfig Source

Configuration for gyration radius constraint.

max_gyration_radius · number · default: "45.0"

Maximum acceptable radius of gyration in Ångströms (lower values are more compact).

ReturnsConstraintOutput

Per-proposal score in [0.0, 1.0] with gyration_radius and longest_alpha_helix metadata. Sequences without a structure receive MAX_ENERGY and no metadata.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import gyration_radius_constraint, GyrationRadiusConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	gyration-radius
Function	gyration_radius_constraint
Category	protein_structure
Mode	discrete
Uses GPU	False
Supported Types	protein, dna