Protein Max Identity

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Tools Used Tools Used Source Source

evo-design/proto-language/proto_language/constraint/protein_quality/protein_max_identity_constraint.py

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Constraint contributors

Require top-hit MMseqs2 identity to remain below a maximum threshold.

API Reference

ConfigProteinMaxIdentityConfig Source

Configuration for maximum identity to a protein reference set.

string

required

Path to MMseqs2 target database (FASTA file or MMseqs2 createdb output).

number

default:"90.0"

Maximum allowed percent identity (0-100, inclusive) to the top reference hit.

boolean

default:"True"

If True, proposals with no MMseqs2 hit pass as novel sequences.

string

Optional FASTA file for recovering the top hit sequence by target ID.

Mmseqs2SearchProteinsConfig

Advanced MMseqs2 protein search configuration.

ReturnsConstraintOutput

One output per proposal. A score of 0.0 passes and 1.0 fails. Metadata contains top-hit identity, target ID, target sequence when available, and selected ORF details for DNA.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import protein_max_identity_constraint, ProteinMaxIdentityConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	`protein-max-identity`
Function	`protein_max_identity_constraint`
Category	`protein_quality`
Mode	`discrete`
Uses GPU	`False`
Supported Types	`dna`, `protein`

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Protein Max Identity

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