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from typing import Sequence, Set |
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3
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from pocketutils.core.dot_dict import NestedDotDict |
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4
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5
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from mandos.model.apis.chembl_support import ChemblCompound |
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from mandos.model.apis.chembl_support.chembl_target_graphs import ChemblTargetGraph |
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from mandos.search.chembl._activity_search import _ActivitySearch |
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from mandos.model.concrete_hits import BindingHit |
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10
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class BindingSearch(_ActivitySearch[BindingHit]): |
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""" |
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Search for ``activity`` of type "B". |
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""" |
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@classmethod |
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def allowed_assay_types(cls) -> Set[str]: |
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return {"B"} |
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def to_hit( |
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self, |
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lookup: str, |
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compound: ChemblCompound, |
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data: NestedDotDict, |
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best_target: ChemblTargetGraph, |
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) -> Sequence[BindingHit]: |
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# these must match the constructor of the Hit, |
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# EXCEPT for object_id and object_name, which come from traversal |
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from_super = self._extract(lookup, compound, data) |
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rel = from_super.req_as("standard_relation", str) |
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pchembl = from_super.req_as("pchembl_value", float) |
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truth = self._truth(pchembl, rel) |
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source = self._format_source( |
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src_id=from_super.req_as("src_id", str), |
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taxon_id=from_super.get("taxon_id"), |
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taxon_name=from_super.get("taxon_name"), |
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) |
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predicate = self._format_predicate( |
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src_id=from_super.req_as("src_id", str), |
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taxon_id=from_super.get("taxon_id"), |
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taxon_name=from_super.get("taxon_name"), |
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truth=truth, |
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rel=rel, |
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) |
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hit = self._create_hit( |
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c_origin=lookup, |
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c_matched=compound.inchikey, |
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c_id=compound.chid, |
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c_name=compound.name, |
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data_source=source, |
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predicate=predicate, |
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object_id=best_target.chembl, |
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object_name=best_target.name, |
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record_id=from_super.req_as("activity_id", str), |
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exact_target_id=from_super.req_as("target_chembl_id", str), |
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taxon_id=from_super.get("taxon_id"), |
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taxon_name=from_super.get("taxon_name"), |
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src_id=from_super.req_as("src_id", str), |
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pchembl=pchembl, |
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std_type=from_super.req_as("standard_type", str), |
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standard_relation=rel, |
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) |
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return [hit] |
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def _truth(self, pchembl: float, rel: str) -> str: |
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if ( |
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self.binds_cutoff is not None |
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and pchembl >= self.binds_cutoff |
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and rel in {"=", "~", "<", "<="} |
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): |
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return "yes" |
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elif ( |
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self.does_not_bind_cutoff is not None |
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and pchembl <= self.does_not_bind_cutoff |
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and rel in {"=", "~", ">", ">="} |
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): |
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return "no" |
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return rel |
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80
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81
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__all__ = ["BindingSearch"] |
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dmyersturnbull /
mandos
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