"""Digital Evolution Engine (`dee`) — PLM-guided directed evolution toolkit.

Pipeline (Phase 1 -> Phase 4):
  1. Parse + validate + translate input DNA (dee.core.sequence)
  2. Zero-shot single-site scoring with ESM-2 (dee.models.scorer)
  3. Combinatorial multi-mutant search under an epistatic threshold (dee.optimizer.search)
  4. Reverse-translate, codon-optimize, and clean restriction sites (dee.core.codon)
"""

from dee.core.sequence import (
    SequenceRecord,
    looks_like_protein,
    parse_input,
    parse_protein,
    translate_dna,
    validate_dna,
)

__version__ = "0.1.0"

__all__ = [
    "SequenceRecord",
    "looks_like_protein",
    "parse_input",
    "parse_protein",
    "translate_dna",
    "validate_dna",
    "__version__",
]