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from dataclasses import dataclass |
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from typing import Sequence, Optional |
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from mandos.model.pubchem_api import PubchemApi |
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from mandos.search.pubchem import PubchemHit, PubchemSearch |
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@dataclass(frozen=True, order=True, repr=True) |
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class AcuteEffectHit(PubchemHit): |
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"""""" |
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organism: str |
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human: bool |
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test_type: str |
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route: str |
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effect: str |
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mg_per_kg: float |
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@dataclass(frozen=True, order=True, repr=True) |
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class Ld50Hit(PubchemHit): |
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"""""" |
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organism: str |
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human: bool |
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class AcuteEffectSearch(PubchemSearch[AcuteEffectHit]): |
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"""""" |
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def __init__(self, key: str, api: PubchemApi, top_level: bool): |
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super().__init__(key, api) |
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self.top_level = top_level |
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@property |
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def data_source(self) -> str: |
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return "ChemIDplus" |
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def find(self, inchikey: str) -> Sequence[AcuteEffectHit]: |
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data = self.api.fetch_data(inchikey) |
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results = [] |
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for dd in data.toxicity.acute_effects: |
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for effect in dd.effects: |
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effect_name = effect.category.lower() if self.top_level else effect.lower() |
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results.append( |
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AcuteEffectHit( |
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record_id=str(dd.gid), |
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origin_inchikey=inchikey, |
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matched_inchikey=data.names_and_identifiers.inchikey, |
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compound_id=str(data.cid), |
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compound_name=data.name, |
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predicate="causes acute effect", |
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object_id=effect_name, |
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object_name=effect_name, |
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search_key=self.key, |
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search_class=self.search_class, |
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data_source=self.data_source, |
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effect=effect.lower(), |
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organism=dd.organism, |
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human=dd.organism.is_human, |
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route=dd.route, |
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mg_per_kg=dd.mg_per_kg, |
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test_type=dd.test_type, |
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) |
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) |
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return results |
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class Ld50Search(PubchemSearch[Ld50Hit]): |
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@property |
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def data_source(self) -> str: |
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return "ChemIDplus" |
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def find(self, inchikey: str) -> Sequence[Ld50Hit]: |
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data = self.api.fetch_data(inchikey) |
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results = [] |
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for dd in data.toxicity.acute_effects: |
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if dd.test_type != "LD50": |
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continue |
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results.append( |
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Ld50Hit( |
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record_id=str(dd.gid), |
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origin_inchikey=inchikey, |
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matched_inchikey=data.names_and_identifiers.inchikey, |
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compound_id=str(data.cid), |
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compound_name=data.name, |
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predicate="has LD50 for " + dd.organism, |
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object_id=str(dd.mg_per_kg), |
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object_name=str(dd.mg_per_kg), |
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search_key=self.key, |
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search_class=self.search_class, |
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data_source=self.data_source, |
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organism=dd.organism, |
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human=dd.organism.is_human, |
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) |
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) |
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return results |
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__all__ = ["AcuteEffectHit", "AcuteEffectSearch", "Ld50Hit", "Ld50Search"] |
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dmyersturnbull /
mandos
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