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from typing import Sequence |
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import numpy as np |
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from mandos.model.apis.pubchem_api import PubchemApi |
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from mandos.search.pubchem import PubchemSearch |
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from mandos.model.concrete_hits import AcuteEffectHit, Ld50Hit |
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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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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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weight = -np.log10(dd.mg_per_kg) |
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source = self._format_source( |
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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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test_type=dd.test_type, |
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) |
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predicate = self._format_predicate( |
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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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test_type=dd.test_type, |
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) |
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results.append( |
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self._create_hit( |
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inchikey=inchikey, |
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c_id=str(data.cid), |
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c_origin=inchikey, |
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c_matched=data.names_and_identifiers.inchikey, |
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c_name=data.name, |
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data_source=source, |
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predicate=predicate, |
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object_id=effect_name, |
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object_name=effect_name, |
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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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weight=weight, |
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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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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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weight = -np.log10(dd.mg_per_kg) |
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results.append( |
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self._create_hit( |
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inchikey=inchikey, |
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c_id=str(data.cid), |
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c_origin=inchikey, |
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c_matched=data.names_and_identifiers.inchikey, |
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c_name=data.name, |
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data_source="ChemIDplus", |
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predicate="has LD50", |
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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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weight=weight, |
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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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) |
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) |
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return results |
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__all__ = ["AcuteEffectSearch", "Ld50Search"] |
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dmyersturnbull /
mandos
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