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import abc |
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import logging |
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from dataclasses import dataclass |
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from typing import Sequence, TypeVar, Mapping, Any |
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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_targets import TargetFactory |
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from mandos.model.chembl_support.chembl_target_graphs import ( |
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ChemblTargetGraph, |
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ChemblTargetGraphFactory, |
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) |
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from mandos.model.chembl_support.chembl_utils import ChemblUtils |
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from mandos.model.taxonomy import Taxonomy |
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from mandos.search.chembl import ChemblHit, ChemblSearch |
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from mandos.search.chembl.target_traversal import TargetTraversalStrategies, TargetTraversalStrategy |
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logger = logging.getLogger("mandos") |
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@dataclass(frozen=True, order=True, repr=True) |
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class ProteinHit(ChemblHit, metaclass=abc.ABCMeta): |
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""" |
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A protein target entry for a compound. |
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""" |
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H = TypeVar("H", bound=ProteinHit, covariant=True) |
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class ProteinSearch(ChemblSearch[H], metaclass=abc.ABCMeta): |
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""" |
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Abstract search. |
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""" |
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def __init__(self, chembl_api: ChemblApi, taxa: Sequence[Taxonomy], traversal_strategy: str): |
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super().__init__(chembl_api) |
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self.taxa = taxa |
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self._traversal_strategy = TargetTraversalStrategies.by_name(traversal_strategy, self.api) |
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def get_params(self) -> Mapping[str, Any]: |
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# TODO not robust |
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return { |
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key: value |
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for key, value in vars(self).items() |
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if not key.startswith("_") and key != "path" |
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} |
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def get_params_str(self) -> str: |
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return ", ".join([k + "=" + str(v) for k, v in self.get_params()]) |
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def is_in_taxa(self, species: str) -> bool: |
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""" |
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Returns true if the ChEMBL species is contained in any of our taxonomies. |
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""" |
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return any((taxon.contains(species) for taxon in self.taxa)) |
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def __repr__(self) -> str: |
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return self.__class__.__name__ + "(" + self.get_params_str() + ")" |
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def __str__(self) -> str: |
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return self.__class__.__name__ + "(" + self.get_params_str() + ")" |
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def find_all(self, compounds: Sequence[str]) -> Sequence[H]: |
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logger.info( |
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f"Using traversal strategy {self.traversal_strategy.__class__.__name__} for {self.search_name}" |
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) |
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return super().find_all(compounds) |
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def query(self, parent_form: ChemblCompound) -> Sequence[NestedDotDict]: |
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raise NotImplementedError() |
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@property |
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def traversal_strategy(self) -> TargetTraversalStrategy: |
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return self._traversal_strategy |
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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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""" |
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Filter based on the returned (activity/mechanism) data. |
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IGNORE filters about the target itself, including whether it's a valid target. |
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Return True in these cases (better yet, don't check). |
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Args: |
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lookup: |
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compound: |
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data: |
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target: |
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Returns: |
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""" |
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raise NotImplementedError() |
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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[H]: |
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""" |
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Gets the desired data as a NestedDotDict from the data from a single element |
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returned by ``api_endpoint.filter``. |
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This MUST MATCH the constructor, EXCEPT for object_id and object_name, |
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which come from traversal and should be added by ``ProteinSearch.to_hit`` (parameter ``best_target``). |
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Turns the final data into ``H``. |
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Note that this has a default behavior but could be overridden to split into multiple hits |
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and/or to add additional attributes that might come from ``best_target``. |
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Args: |
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lookup: |
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compound: |
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data: |
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best_target: |
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Returns: |
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A sequence of hits. |
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""" |
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h = self.get_h() |
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return [h(**data, object_id=best_target.chembl, object_name=best_target.name)] |
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View Code Duplication |
def find(self, lookup: str) -> Sequence[H]: |
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""" |
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Args: |
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lookup: |
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Returns:e |
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""" |
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form = ChemblUtils(self.api).get_compound(lookup) |
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results = self.query(form) |
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hits = [] |
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for result in results: |
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result = NestedDotDict(result) |
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hits.extend(self.process(lookup, form, result)) |
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return hits |
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def process(self, lookup: str, compound: ChemblCompound, data: NestedDotDict) -> Sequence[H]: |
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""" |
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Args: |
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lookup: |
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compound: |
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data: |
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Returns: |
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""" |
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if data.get("target_chembl_id") is None: |
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logger.debug(f"target_chembl_id missing from mechanism '{data}' for compound {lookup}") |
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return [] |
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chembl_id = data["target_chembl_id"] |
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factory = TargetFactory(self.api) |
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target_obj = factory.find(chembl_id) |
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graph_factory = ChemblTargetGraphFactory.create(self.api, factory) |
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graph = graph_factory.at_target(target_obj) |
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if not self.should_include(lookup, compound, data, graph): |
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return [] |
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# traverse() will return the source target if it's a non-traversable type (like DNA) |
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# and the subclass decided whether to filter those |
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# so don't worry about that here |
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ancestors = self.traversal_strategy(graph) |
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lst = [] |
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for ancestor in ancestors: |
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lst.extend(self.to_hit(lookup, compound, data, ancestor)) |
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return lst |
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__all__ = ["ProteinHit", "ProteinSearch"] |
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dmyersturnbull /
mandos
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