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b233cf7 fd5ba83 b233cf7 fd5ba83 b233cf7 fd5ba83 b233cf7 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 | from __future__ import annotations
import logging
from typing import Any
from rdkit import Chem
from rdkit.Chem import Descriptors
from .materials import resolve_material
from .models import Ingredient, IngredientResolutionError
from .registry import AromaRegistry
logger = logging.getLogger("pino.structures")
class IngredientResolver:
"""
High-level resolver that combines a pre-computed SQLite registry with a
live fallback to RDKit / PubChem / ugropy.
Resolution order:
1. AromaRegistry lookup (fast, no network)
2. Live PubChem CAS -> SMILES + MW
3. Live ugropy Dortmund-UNIFAC fragmentation
"""
def __init__(self, registry: AromaRegistry | None = None) -> None:
self.registry = registry or AromaRegistry()
def resolve(self, identifier: str, weight_fraction: float, *, name: str | None = None) -> Ingredient:
"""Resolve a single raw formula component into a validated Ingredient."""
# Registry lookup first
record = self.registry.get(identifier)
if record is None and name:
record = self.registry.get(name)
if record:
logger.debug("Resolved %s from registry", identifier)
return self._ingredient_from_record(record, weight_fraction)
# Known standard-material fallback: trade names in materials.py provide
# a canonical SMILES, so we can build a record without a network round-trip.
for lookup in (name, identifier):
if not lookup:
continue
material = resolve_material(lookup)
if material and not material.get("accord"):
smiles = material.get("smiles")
if smiles:
logger.debug("Resolved %s from standard materials library", lookup)
record = AromaRegistry.validate_smiles(smiles)
if record is None:
raise IngredientResolutionError(
f"Standard material {lookup} has an invalid SMILES", cas=identifier
)
record["name"] = material.get("name", lookup)
record["cas"] = material.get("cas", identifier)
if material.get("vapor_pressure_pa") is not None:
record["vapor_pressure_pa"] = material["vapor_pressure_pa"]
if material.get("boiling_point_k") is not None:
record["boiling_point_k"] = material["boiling_point_k"]
if material.get("odor_threshold_ug_m3") is not None:
record["odor_threshold_ug_m3"] = material["odor_threshold_ug_m3"]
self.registry.add(record)
return self._ingredient_from_record(record, weight_fraction)
# Live fallback
logger.info("Registry miss for %s; falling back to PubChem/ugropy", identifier)
try:
live = AromaRegistry.build_record(identifier, "cas")
except Exception as exc:
raise IngredientResolutionError(
f"Unable to resolve {identifier} from registry or live sources: {exc}",
cas=identifier,
) from exc
# Add to registry so future lookups are fast
self.registry.add(live)
return self._ingredient_from_record(live, weight_fraction)
def resolve_formula(
self,
formula: list[dict[str, Any]],
*,
skip_unresolved: bool = False,
) -> tuple[list[Ingredient], list[IngredientResolutionError]]:
"""
Resolve a list of raw formula components.
Returns (ingredients, errors). If skip_unresolved is False, the first
error is raised immediately.
"""
ingredients: list[Ingredient] = []
errors: list[IngredientResolutionError] = []
for comp in formula:
if "weight_fraction" not in comp:
raise ValueError(f"Formula component missing weight_fraction: {comp}")
wf = float(comp["weight_fraction"])
ident = str(comp.get("cas", comp.get("smiles", comp.get("name", ""))))
try:
ing = self.resolve(ident, wf, name=comp.get("name"))
ingredients.append(ing)
except IngredientResolutionError as exc:
logger.warning("Out of applicability domain for %s: %s", ident, exc)
errors.append(exc)
if not skip_unresolved:
raise
return ingredients, errors
def resolve_formula_pairs(
self,
formula: list[dict[str, Any]],
*,
skip_unresolved: bool = False,
) -> tuple[list[tuple[dict[str, Any], Ingredient]], list[IngredientResolutionError]]:
"""
Resolve formula components and return (record, ingredient) pairs.
This is useful when the caller needs to keep the original record
alongside the resolved ingredient so that weight fractions stay aligned
after filtering out unresolved materials.
"""
pairs: list[tuple[dict[str, Any], Ingredient]] = []
errors: list[IngredientResolutionError] = []
for comp in formula:
if "weight_fraction" not in comp:
raise ValueError(f"Formula component missing weight_fraction: {comp}")
wf = float(comp["weight_fraction"])
ident = str(comp.get("cas", comp.get("smiles", comp.get("name", ""))))
try:
ing = self.resolve(ident, wf, name=comp.get("name"))
pairs.append((comp, ing))
except IngredientResolutionError as exc:
logger.warning("Out of applicability domain for %s: %s", ident, exc)
errors.append(exc)
if not skip_unresolved:
raise
return pairs, errors
def _ingredient_from_record(self, record: dict[str, Any], weight_fraction: float) -> Ingredient:
"""Construct an Ingredient from a registry/live record."""
smiles = record["smiles"]
mw = record.get("molecular_weight")
if mw is None:
mw = molecular_weight_from_smiles(smiles)
logp = record.get("logp")
if logp is None:
try:
mol = Chem.MolFromSmiles(smiles)
logp = float(Descriptors.MolLogP(mol)) if mol else None
except Exception:
logp = None
return Ingredient(
name=record.get("name", smiles),
cas=record.get("cas", ""),
smiles=smiles,
molecular_weight=float(mw),
vapor_pressure_pa=float(record.get("vapor_pressure_pa") or 1.0),
boiling_point_k=float(record["boiling_point_k"]) if record.get("boiling_point_k") is not None else None,
odor_threshold_ug_m3=float(record["odor_threshold_ug_m3"]) if record.get("odor_threshold_ug_m3") is not None else None,
logp=logp,
unifac_groups={str(k): int(v) for k, v in record.get("unifac_groups", {}).items()},
)
def canonicalize_smiles(smiles: str) -> str:
mol = Chem.MolFromSmiles(smiles)
if mol is None:
raise IngredientResolutionError(f"Invalid SMILES: {smiles}", smiles=smiles)
return Chem.MolToSmiles(mol, canonical=True)
def molecular_weight_from_smiles(smiles: str) -> float:
mol = Chem.MolFromSmiles(smiles)
if mol is None:
raise IngredientResolutionError(f"Invalid SMILES: {smiles}", smiles=smiles)
return Descriptors.MolWt(mol)
def ingredient_from_smiles(
name: str,
cas: str,
smiles: str,
vapor_pressure_pa: float,
boiling_point_k: float | None = None,
odor_threshold_ug_m3: float | None = None,
) -> Ingredient:
"""Build an Ingredient directly from a SMILES string (with live fragmentation)."""
resolver = IngredientResolver()
record = AromaRegistry.build_record(smiles, "smiles", vapor_pressure_pa, boiling_point_k, odor_threshold_ug_m3)
record["name"] = name
record["cas"] = cas
return resolver._ingredient_from_record(record, 0.0)
def ingredient_from_data(data: dict[str, Any]) -> Ingredient:
"""Build an Ingredient from a dict (with optional precomputed registry groups)."""
resolver = IngredientResolver()
if "cas" in data or "smiles" in data or "name" in data:
return resolver.resolve(
str(data.get("cas", data.get("smiles", data.get("name", "")))),
float(data.get("weight_fraction", 0.0)),
name=data.get("name"),
)
raise IngredientResolutionError("No identifier (cas, smiles, name) provided in data")
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