mandos.search.chembl.mechanism_search

Complexity

Total Complexity

6

Size/Duplication

Total Lines	76
Duplicated Lines	0 %

Importance

Changes

0

5 Methods

Rating	Name	Duplication	Size	Complexity
A	MechanismSearch.should_include()	0	7	2
A	MechanismSearch.query()	0	2	1
A	MechanismSearch.to_hit()	0	19	1
A	MechanismHit.predicate()	0	3	1
A	MechanismSearch.default_traversal_strategy()	0	3	1

import logging

Missing module docstring

from dataclasses import dataclass
from typing import Sequence

from pocketutils.core.dot_dict import NestedDotDict

Unable to import 'pocketutils.core.dot_dict'

from mandos.model import ChemblCompound
from mandos.model.targets import Target
from mandos.search.chembl.protein_search import ProteinHit, ProteinSearch
from mandos.search.chembl.target_traversal_strategy import (
    TargetTraversalStrategy,
    TargetTraversalStrategies,
)

logger = logging.getLogger("mandos")


@dataclass(frozen=True, order=True, repr=True)
class MechanismHit(ProteinHit):
    """
    A mechanism entry for a compound.
    """

    action_type: str
    direct_interaction: bool
    description: str
    exact_target_id: str

    @property
    def predicate(self) -> str:
        return self.action_type.lower()


class MechanismSearch(ProteinSearch[MechanismHit]):
    """
    Search for ``mechanisms``.
    """

    @property
    def default_traversal_strategy(self) -> TargetTraversalStrategy:

Missing function or method docstring

        return TargetTraversalStrategies.strategy0(self.api)

    def query(self, parent_form: ChemblCompound) -> Sequence[NestedDotDict]:

Missing function or method docstring

        return list(self.api.mechanism.filter(parent_molecule_chembl_id=parent_form.chid))

    def should_include(

Missing function or method docstring

        self, lookup: str, compound: ChemblCompound, data: NestedDotDict, target: Target

Wrong hanging indentation before block (add 4 spaces).

The argument lookup seems to be unused.

The argument compound seems to be unused.

The argument data seems to be unused.

    ) -> bool:
        if target.type.name.lower() not in {s.lower() for s in self.config.allowed_target_types}:
            logger.warning(f"Excluding {target} with type {target.type}")

Use lazy % formatting in logging functions

            return False
        return True

    def to_hit(

Missing function or method docstring

This method could be written as a function/class method.

        self, lookup: str, compound: ChemblCompound, data: NestedDotDict, target: Target

Wrong hanging indentation before block (add 4 spaces).

    ) -> Sequence[MechanismHit]:
        # these must match the constructor of the Hit,
        # EXCEPT for object_id and object_name, which come from traversal
        x = NestedDotDict(

Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            dict(
                record_id=data["mec_id"],
                compound_id=compound.chid,
                inchikey=compound.inchikey,
                compound_name=compound.name,
                compound_lookup=lookup,
                action_type=data["action_type"],
                direct_interaction=data["direct_interaction"],
                description=data["mechanism_of_action"],
                exact_target_id=data["target_chembl_id"],
            )
        )
        return [MechanismHit(**x, object_id=target.chembl, object_name=target.name)]


__all__ = ["MechanismHit", "MechanismSearch"]