Overall Protein Quality

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

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Constraint contributors

Evaluate overall protein quality using multiple configurable sub-constraints. This constraint function provides a comprehensive assessment of protein quality by evaluating multiple aspects including sequence length, structural complexity, repetitiveness, amino acid diversity, and balanced amino acid representation. For DNA sequences, it first predicts protein-coding regions using Prodigal, then evaluates all predicted proteins. For protein sequences, it evaluates them directly. The function aggregates scores from enabled sub-constraints by averaging them and clipping to [0.0, 1.0]. Use the native Constraint(threshold=...) parameter for pass/fail filtering.

API Reference

ConfigOverallProteinQualityConfig Source

Configuration for the overall protein quality constraint.This configuration class orchestrates multiple protein quality sub-constraints that can be enabled or disabled individually. It provides a flexible framework for comprehensive protein quality assessment by combining various metrics including sequence length, structural complexity, repetitiveness, amino acid diversity, and balanced amino acid representation.The configuration uses a nested structure where all sub-constraint parameters are exposed through a single protein_quality_config attribute of type ProteinQualitySubConfig. This design allows for easy serialization in UI/API schemas while maintaining clear organization of constraint-specific parameters.At least one sub-constraint must be enabled for the configuration to be valid. This is enforced through a model validator that runs after initialization.

The nested protein_quality_config provides access to:

Length constraint: Validates protein length against min/max range or target value
Complexity constraint: Detects low-complexity regions using segmasker
Repetitiveness constraint: Identifies repeated k-mer patterns
Diversity constraint: Ensures adequate amino acid type diversity
Balanced amino acids constraint: Checks for underrepresented amino acid types

Each sub-constraint can be independently enabled/disabled and configured with specific parameters. See ProteinQualitySubConfig documentation for complete parameter details.For more details, see:

ProteinQualitySubConfig: Detailed documentation of all sub-constraint parameters and configuration options
overall_protein_quality_constraint: The constraint function that uses this configuration
SequenceLengthConfig: Configuration for length constraint
ProteinComplexityConfig: Configuration for complexity constraint
ProteinRepetitivenessConfig: Configuration for repetitiveness constraint
ProteinDiversityConfig: Configuration for diversity constraint
BalancedAaConfig: Configuration for balanced amino acids constraint

ProteinQualitySubConfig

required

Nested configuration for protein quality checks

ReturnsConstraintOutput

One result per sequence. Scores range from 0.0 (best) to 1.0 (worst) and represent the average of all enabled sub-constraint scores, clipped to [0.0, 1.0]. For DNA sequences, the score reflects the average quality across all predicted proteins. metadata carries:For DNA sequences:

prodigal_proteins: List of dicts of predicted proteins from Prodigal, each with protein ID, sequence, length, etc. (or None if no ORFs were predicted)
prodigal_protein_count: Integer count of predicted ORFs
predicted_protein_count: Integer count of proteins (same as prodigal_protein_count)
avg_constraint_score: Float average quality score across all predicted proteins
protein_quality_details: List of dictionaries, one per predicted protein, each containing:
- protein_id: String identifier from Prodigal
- length: Integer protein length in amino acids
- avg_constraint_score: Float average across enabled constraints
- quality_scores: Dictionary mapping constraint names to scores
- metadata: Dictionary of additional constraint-specific metadata

For protein sequences:

protein_quality_scores: Dictionary mapping constraint names (e.g., “length”, “complexity”, “repetitiveness”, “diversity”, “balanced_aas”) to their individual scores
avg_constraint_score: Float average across all enabled constraints

Usage

Using all available constraints with custom thresholds:

python

>>> quality_config = ProteinQualitySubConfig(
...     enable_length=True,
...     length_target_length=300,
...     enable_complexity=True,
...     complexity_max_low_complexity=0.25,
...     enable_repetitiveness=True,
...     repetitiveness_max_repetitiveness=0.08,
...     repetitiveness_min_repeat_length=3,
...     enable_diversity=True,
...     diversity_min_diversity=0.75,
...     enable_balanced_aas=True,
...     balanced_min_aa_frequency=0.03,
...     balanced_max_underrepresented_count=2,
... )
>>> overall_cfg = OverallProteinQualityConfig(protein_quality_config=quality_config)
>>> protein_seq = Sequence("MKYIVAVAG...", "protein")
>>> results = overall_protein_quality_constraint([(protein_seq,)], overall_cfg)

Metadata

Property	Value
Key	`overall-protein-quality`
Function	`overall_protein_quality_constraint`
Category	`protein_quality`
Mode	`discrete`
Uses GPU	`False`
Supported Types	`dna`, `protein`

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Overall Protein Quality

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