feat(validation): add SQLModel database models

pixi.toml

@@ -19,6 +19,7 @@ rdkit = ">=2025.9.1,<2026"
 pandas = ">=2.3.3,<3"
 numpy = ">=2.3.4,<3"
 matplotlib = ">=3.10,<4"
+sqlmodel = ">=0.0.37,<0.0.38"
 
 [pypi-dependencies]
 macro_lactone_toolkit = { path = ".", editable = true }

src/macro_lactone_toolkit/validation/models.py

@@ -0,0 +1,99 @@
+from __future__ import annotations
+
+from datetime import datetime
+from enum import Enum
+from typing import List, Optional
+
+from sqlmodel import Field, Relationship, SQLModel
+
+
+class ClassificationType(str, Enum):
+    STANDARD = "standard_macrolactone"
+    NON_STANDARD = "non_standard_macrocycle"
+    NOT_MACROLACTONE = "not_macrolactone"
+
+
+class ProcessingStatus(str, Enum):
+    PENDING = "pending"
+    SUCCESS = "success"
+    FAILED = "failed"
+    SKIPPED = "skipped"
+
+
+class ParentMolecule(SQLModel, table=True):
+    """Original molecule information."""
+
+    __tablename__ = "parent_molecules"
+
+    id: Optional[int] = Field(default=None, primary_key=True)
+    source_id: str = Field(index=True)
+    molecule_name: Optional[str] = None
+    smiles: str = Field(index=True)
+    classification: ClassificationType = Field(index=True)
+    ring_size: Optional[int] = Field(default=None, index=True)
+    primary_reason_code: Optional[str] = None
+    primary_reason_message: Optional[str] = None
+    processing_status: ProcessingStatus = Field(default=ProcessingStatus.PENDING)
+    error_message: Optional[str] = None
+    num_sidechains: Optional[int] = None
+    cleavage_positions: Optional[str] = None
+    numbered_image_path: Optional[str] = None
+    created_at: datetime = Field(default_factory=datetime.utcnow)
+    processed_at: Optional[datetime] = None
+
+    fragments: List["SideChainFragment"] = Relationship(back_populates="parent")
+    numbering: Optional["RingNumbering"] = Relationship(back_populates="parent")
+
+
+class RingNumbering(SQLModel, table=True):
+    """Ring numbering details."""
+
+    __tablename__ = "ring_numberings"
+
+    id: Optional[int] = Field(default=None, primary_key=True)
+    parent_id: int = Field(foreign_key="parent_molecules.id", unique=True)
+    ring_size: int
+    carbonyl_carbon_idx: int
+    ester_oxygen_idx: int
+    position_to_atom: str
+    atom_to_position: str
+
+    parent: Optional[ParentMolecule] = Relationship(back_populates="numbering")
+
+
+class SideChainFragment(SQLModel, table=True):
+    """Side chain fragments from cleavage."""
+
+    __tablename__ = "side_chain_fragments"
+
+    id: Optional[int] = Field(default=None, primary_key=True)
+    parent_id: int = Field(foreign_key="parent_molecules.id", index=True)
+    fragment_id: str = Field(index=True)
+    cleavage_position: int = Field(index=True)
+    attachment_atom_idx: int
+    attachment_atom_symbol: str
+    fragment_smiles_labeled: str
+    fragment_smiles_plain: str
+    dummy_isotope: int
+    atom_count: int
+    heavy_atom_count: int
+    molecular_weight: float
+    original_bond_type: str
+    image_path: Optional[str] = None
+
+    parent: Optional[ParentMolecule] = Relationship(back_populates="fragments")
+
+
+class ValidationResult(SQLModel, table=True):
+    """Manual validation records."""
+
+    __tablename__ = "validation_results"
+
+    id: Optional[int] = Field(default=None, primary_key=True)
+    parent_id: int = Field(foreign_key="parent_molecules.id")
+    numbering_correct: Optional[bool] = None
+    cleavage_correct: Optional[bool] = None
+    classification_correct: Optional[bool] = None
+    notes: Optional[str] = None
+    validated_by: Optional[str] = None
+    validated_at: Optional[datetime] = None