Gyration Radius

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evo-design/proto-language/proto_language/constraint/protein_structure/gyration_radius_constraint.py

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@article{kunzmann2023biotite,
  title={Biotite: new tools for a versatile {Python} bioinformatics library},
  author={Kunzmann, Patrick and M{\"u}ller, Tom David and Greil, Maximilian and Krumbach, Jan Hendrik and Anter, Jacob Marcel and Bauer, Daniel and Islam, Faisal and Hamacher, Kay},
  journal={BMC Bioinformatics},
  volume={24},
  number={1},
  pages={236},
  year={2023},
  publisher={BioMed Central},
  doi={10.1186/s12859-023-05345-6}
}

@article{labesse1997psea,
  title={{P-SEA}: a new efficient assignment of secondary structure from {C}$\alpha$ trace of proteins},
  author={Labesse, Gilles and Colloc'h, Nathalie and Pothier, Joel and Mornon, Jean-Paul},
  journal={Bioinformatics},
  volume={13},
  number={3},
  pages={291--295},
  year={1997},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/13.3.291}
}

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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`

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Usage

Metadata