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from __future__ import annotations |
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import abc |
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import enum |
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import logging |
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from dataclasses import dataclass |
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from typing import Sequence, Union |
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from pocketutils.core.dot_dict import NestedDotDict |
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from mandos import logger |
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from mandos.model.chembl_api import ChemblApi |
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from mandos.search.chembl import ChemblHit, ChemblSearch |
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from mandos.search.chembl.binding_search import BindingSearch, BindingHit |
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class GoType(enum.Enum): |
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component = enum.auto() |
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function = enum.auto() |
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process = enum.auto() |
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@classmethod |
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def of(cls, s: Union[str, GoType]) -> GoType: |
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if isinstance(s, GoType): |
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return s |
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return GoType[s.lower()] |
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@dataclass(frozen=True, order=True, repr=True) |
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class GoHit(ChemblHit, metaclass=abc.ABCMeta): |
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""" |
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A mechanism entry for a compound. |
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""" |
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go_type: str |
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binding: BindingHit |
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class GoSearch(ChemblSearch[GoHit]): |
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""" |
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Search for GO terms. |
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""" |
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def __init__(self, key: str, api: ChemblApi, go_type: GoType, binding_search: BindingSearch): |
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super().__init__(key, api) |
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self.go_type = go_type |
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self.binding_search = binding_search |
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@property |
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def data_source(self) -> str: |
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return "ChEMBL :: GO terms" |
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53
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def find(self, compound: str) -> Sequence[GoHit]: |
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matches = self.binding_search.find(compound) |
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terms = [] |
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for match in matches: |
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target = self.api.target.get(match.object_id) |
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terms.extend(self._process(compound, match, target)) |
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return terms |
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61
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def _process(self, lookup: str, match: BindingHit, target: NestedDotDict) -> Sequence[GoHit]: |
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terms = set() |
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if target.get("target_components") is not None: |
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for comp in target["target_components"]: |
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if comp.get("target_component_xrefs") is not None: |
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for xref in comp["target_component_xrefs"]: |
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if xref["xref_src_db"] == f"Go{self.go_type.name.capitalize()}": |
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terms.add((xref["xref_id"], xref["xref_name"])) |
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hits = [] |
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for xref_id, xref_name in terms: |
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hits.append( |
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GoHit( |
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None, |
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origin_inchikey=lookup, |
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matched_inchikey=match.matched_inchikey, |
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compound_id=match.compound_id, |
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compound_name=match.compound_name, |
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predicate=f"is associated with {self.go_type.name} term", |
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object_id=xref_id, |
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object_name=xref_name, |
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search_key=self.key, |
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search_class=self.search_class, |
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data_source=self.data_source, |
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go_type=self.go_type.name, |
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binding=match, |
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) |
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) |
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return hits |
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90
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91
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__all__ = ["GoHit", "GoSearch", "GoType"] |
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dmyersturnbull /
mandos
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