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import logging |
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from dataclasses import dataclass |
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from typing import Sequence, Set, Optional |
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from pocketutils.core.dot_dict import NestedDotDict |
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from mandos.model.chembl_api import ChemblApi |
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from mandos.model.chembl_support import ChemblCompound |
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from mandos.model.chembl_support.chembl_target_graphs import ChemblTargetGraph |
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from mandos.model.taxonomy import Taxonomy |
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from mandos.search.chembl._protein_search import ProteinHit, ProteinSearch |
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from mandos.search.chembl.target_traversal import TargetTraversalStrategy, TargetTraversalStrategies |
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logger = logging.getLogger("mandos") |
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@dataclass(frozen=True, order=True, repr=True) |
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class MechanismHit(ProteinHit): |
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""" |
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A mechanism entry for a compound. |
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""" |
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action_type: str |
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direct_interaction: bool |
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description: str |
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exact_target_id: str |
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@property |
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def predicate(self) -> str: |
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return self.action_type.lower() |
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class MechanismSearch(ProteinSearch[MechanismHit]): |
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""" |
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Search for ``mechanisms``. |
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""" |
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def __init__( |
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self, |
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chembl_api: ChemblApi, |
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tax: Taxonomy, |
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traversal_strategy: str, |
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allowed_target_types: Set[str], |
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min_confidence_score: Optional[int], |
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): |
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super().__init__(chembl_api, tax, traversal_strategy) |
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self.allowed_target_types = allowed_target_types |
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self.min_confidence_score = min_confidence_score |
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def query(self, parent_form: ChemblCompound) -> Sequence[NestedDotDict]: |
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return list(self.api.mechanism.filter(parent_molecule_chembl_id=parent_form.chid)) |
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def should_include( |
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self, lookup: str, compound: ChemblCompound, data: NestedDotDict, target: ChemblTargetGraph |
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) -> bool: |
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if target.type.name.lower() not in {s.lower() for s in self.allowed_target_types}: |
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logger.warning(f"Excluding {target} with type {target.type}") |
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return False |
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return True |
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def to_hit( |
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self, lookup: str, compound: ChemblCompound, data: NestedDotDict, target: ChemblTargetGraph |
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) -> Sequence[MechanismHit]: |
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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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x = NestedDotDict( |
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dict( |
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record_id=data["mec_id"], |
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compound_id=compound.chid, |
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inchikey=compound.inchikey, |
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compound_name=compound.name, |
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compound_lookup=lookup, |
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action_type=data["action_type"], |
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direct_interaction=data["direct_interaction"], |
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description=data["mechanism_of_action"], |
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exact_target_id=data["target_chembl_id"], |
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) |
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) |
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return [MechanismHit(**x, object_id=target.chembl, object_name=target.name)] |
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__all__ = ["MechanismHit", "MechanismSearch"] |
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dmyersturnbull /
mandos
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