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from typing import Sequence |
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from mandos.model.apis.pubchem_api import PubchemApi |
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from mandos.model.apis.pubchem_support.pubchem_data import PubchemData |
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from mandos.model.apis.pubchem_support.pubchem_models import Bioactivity |
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from mandos.search.pubchem import PubchemSearch |
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from mandos.model.concrete_hits import BioactivityHit |
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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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compound_name_must_match: bool, |
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): |
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super().__init__(key, api) |
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self.compound_name_must_match = compound_name_must_match |
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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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if not self.compound_name_must_match or dd.compound_name.lower() == data.name.lower(): |
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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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target_name, target_abbrev, species = dd.target_name_abbrev_species |
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action = dd.activity.name.lower() |
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source = self._format_source( |
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assay_type=dd.assay_type, |
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species=species, |
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) |
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predicate = self._format_predicate( |
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action=action, |
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assay_type=dd.assay_type, |
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species=species, |
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) |
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return 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=dd.gene_id, |
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object_name=target_name, |
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target_abbrev=target_abbrev, |
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activity=action, |
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assay_type=dd.assay_type, |
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micromolar=dd.activity_value, |
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relation=dd.activity_name, |
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species=species, |
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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__ = ["BioactivitySearch"] |
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dmyersturnbull /
mandos
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