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from dataclasses import dataclass |
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from typing import Sequence, Optional, Set |
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from mandos.model.pubchem_api import PubchemApi |
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from mandos.model.pubchem_support.pubchem_data import PubchemData |
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from mandos.model.pubchem_support.pubchem_models import Activity, AssayType, Bioactivity |
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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 BioactivityHit(PubchemHit): |
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"""""" |
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activity: str |
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confirmatory: bool |
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micromolar: float |
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relation: str |
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compound_name_in_assay: str |
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referrer: str |
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class BioactivitySearch(PubchemSearch[BioactivityHit]): |
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"""""" |
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def __init__( |
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self, |
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key: str, |
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api: PubchemApi, |
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answers: Set[Activity], |
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assay_types: Set[AssayType], |
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min_micromolar: Optional[float], |
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max_micromolar: Optional[float], |
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relations: Set[str], |
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compound_name_must_match: bool, |
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): |
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super().__init__(key, api) |
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self.answers = answers |
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self.assay_types = assay_types |
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self.min_micromolar, self.max_micromolar = min_micromolar, max_micromolar |
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self.relations = relations |
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self.compound_name_must_match = compound_name_must_match |
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@property |
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def data_source(self) -> str: |
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return "PubChem" |
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def find(self, inchikey: str) -> Sequence[BioactivityHit]: |
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data = self.api.fetch_data(inchikey) |
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results = [] |
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for dd in data.biological_test_results.bioactivity: |
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results.append(self.process(inchikey, data, dd)) |
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return results |
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def process(self, inchikey: str, data: PubchemData, dd: Bioactivity) -> BioactivityHit: |
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return BioactivityHit( |
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record_id=None, |
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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=f"bioactivity", |
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object_id=dd.gene_id, |
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object_name=dd.target_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 + " : " + dd.assay_ref, |
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activity=dd.activity.name.lower(), |
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confirmatory=dd.assay_type is AssayType.confirmatory, |
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micromolar=dd.activity_value, |
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relation=dd.activity_name, |
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compound_name_in_assay=dd.compound_name, |
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referrer=dd.assay_ref, |
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) |
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__all__ = ["BioactivityHit", "BioactivitySearch"] |
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dmyersturnbull /
mandos
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