dmyersturnbull /
mandos
| @@ 32-71 (lines=40) @@ | ||
| 29 | return "activity" |
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| 30 | ||
| 31 | ||
| 32 | class BindingSearch(_ActivitySearch[BindingHit]): |
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| 33 | """ |
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| 34 | Search for ``activity`` of type "B". |
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| 35 | """ |
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| 36 | ||
| 37 | @classmethod |
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| 38 | def allowed_assay_types(cls) -> Set[str]: |
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| 39 | return {"B"} |
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| 40 | ||
| 41 | def to_hit( |
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| 42 | self, |
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| 43 | lookup: str, |
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| 44 | compound: ChemblCompound, |
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| 45 | data: NestedDotDict, |
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| 46 | best_target: ChemblTargetGraph, |
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| 47 | ) -> Sequence[BindingHit]: |
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| 48 | # these must match the constructor of the Hit, |
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| 49 | # EXCEPT for object_id and object_name, which come from traversal |
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| 50 | from_super = self._extract(lookup, compound, data) |
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| 51 | hit = BindingHit( |
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| 52 | record_id=from_super.req_as("activity_id", str), |
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| 53 | origin_inchikey=lookup, |
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| 54 | matched_inchikey=compound.inchikey, |
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| 55 | compound_id=compound.chid, |
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| 56 | compound_name=compound.name, |
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| 57 | predicate="binds", |
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| 58 | object_id=best_target.chembl, |
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| 59 | object_name=best_target.name, |
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| 60 | search_key=self.key, |
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| 61 | search_class=self.search_class, |
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| 62 | data_source=self.data_source, |
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| 63 | exact_target_id=from_super.req_as("target_chembl_id", str), |
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| 64 | taxon_id=from_super.get("taxon_id"), |
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| 65 | taxon_name=from_super.get("taxon_name"), |
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| 66 | src_id=from_super.req_as("src_id", str), |
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| 67 | pchembl=from_super.req_as("pchembl_value", float), |
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| 68 | std_type=from_super.req_as("standard_type", str), |
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| 69 | standard_relation=from_super.req_as("standard_relation", str), |
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| 70 | ) |
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| 71 | return [hit] |
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| 72 | ||
| 73 | ||
| 74 | __all__ = ["BindingHit", "BindingSearch"] |
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| @@ 27-66 (lines=40) @@ | ||
| 24 | subcellular_region: Optional[str] |
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| 25 | ||
| 26 | ||
| 27 | class FunctionalSearch(_ActivitySearch[FunctionalHit]): |
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| 28 | """ |
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| 29 | Search for ``activity`` of type "F". |
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| 30 | """ |
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| 31 | ||
| 32 | @classmethod |
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| 33 | def allowed_assay_types(cls) -> Set[str]: |
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| 34 | return {"F"} |
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| 35 | ||
| 36 | def to_hit( |
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| 37 | self, |
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| 38 | lookup: str, |
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| 39 | compound: ChemblCompound, |
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| 40 | data: NestedDotDict, |
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| 41 | best_target: ChemblTargetGraph, |
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| 42 | ) -> Sequence[FunctionalHit]: |
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| 43 | # these must match the constructor of the Hit, |
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| 44 | # EXCEPT for object_id and object_name, which come from traversal |
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| 45 | from_super = self._extract(lookup, compound, data) |
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| 46 | hit = FunctionalHit( |
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| 47 | record_id=from_super.req_as("activity_id", str), |
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| 48 | origin_inchikey=lookup, |
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| 49 | matched_inchikey=compound.inchikey, |
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| 50 | compound_id=compound.chid, |
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| 51 | compound_name=compound.name, |
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| 52 | predicate="functional activity", |
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| 53 | object_id=best_target.chembl, |
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| 54 | object_name=best_target.name, |
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| 55 | search_key=self.key, |
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| 56 | search_class=self.search_class, |
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| 57 | data_source=self.data_source, |
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| 58 | exact_target_id=from_super.req_as("target_chembl_id", str), |
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| 59 | taxon_id=from_super.get("taxon_id"), |
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| 60 | taxon_name=from_super.get("taxon_name"), |
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| 61 | src_id=from_super.req_as("src_id", str), |
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| 62 | tissue=from_super.get_as("tissue", str), |
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| 63 | cell_type=from_super.get_as("cell_type", str), |
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| 64 | subcellular_region=from_super.get("subcellular_region", str), |
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| 65 | ) |
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| 66 | return [hit] |
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| 67 | ||
| 68 | ||
| 69 | __all__ = ["FunctionalHit", "FunctionalSearch", "AssayType"] |
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