mandos.model.concrete_hits

Complexity

Total Complexity

2

Size/Duplication

Total Lines	245
Duplicated Lines	0 %

Importance

Changes

0

1 Method

Rating	Name	Duplication	Size	Complexity
A	GoType.of()	0	5	2

from __future__ import annotations

Missing module docstring

import abc
import enum
from dataclasses import dataclass
from typing import Optional, Union

from mandos.model import ReflectionUtils
from mandos.model.hits import AbstractHit


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class ChemblHit(AbstractHit, metaclass=abc.ABCMeta):
    """ """


@dataclass(frozen=True, order=True, repr=True)
class ProteinHit(ChemblHit, metaclass=abc.ABCMeta):
    """
    A protein target entry for a compound.
    """

    exact_target_id: str


@dataclass(frozen=True, order=True, repr=True)
class _ActivityHit(ProteinHit):
    taxon_id: int
    taxon_name: str
    src_id: str


@dataclass(frozen=True, order=True, repr=True)
class AtcHit(ChemblHit):
    """
    An ATC code found for a compound.
    """

    level: int


@dataclass(frozen=True, order=True, repr=True)
class BindingHit(_ActivityHit):
    """
    An "activity" hit for a compound.
    """

    pchembl: float
    std_type: str
    standard_relation: str


@dataclass(frozen=True, order=True, repr=True)
class FunctionalHit(_ActivityHit):
    """
    An "activity" hit of type "F" for a compound.
    """

    tissue: Optional[str]
    cell_type: Optional[str]
    subcellular_region: Optional[str]


class GoType(enum.Enum):

Missing class docstring

    component = enum.auto()
    function = enum.auto()
    process = enum.auto()

    @classmethod
    def of(cls, s: Union[str, GoType]) -> GoType:

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

Missing function or method docstring

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

        if isinstance(s, GoType):
            return s
        return GoType[s.lower()]


@dataclass(frozen=True, order=True, repr=True)
class GoHit(ChemblHit, metaclass=abc.ABCMeta):
    """
    A mechanism entry for a compound.
    """

    go_type: str
    binding: BindingHit


@dataclass(frozen=True, order=True, repr=True)
class IndicationHit(ChemblHit):
    """
    An indication with a MESH term.
    """

    max_phase: int


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

    action_type: str


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class G2pHit(AbstractHit, metaclass=abc.ABCMeta):
    """ """


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class G2pInteractionHit(G2pHit):
    """ """

    action: str
    selective: str
    primary: str
    endogenous: str
    species: str
    affinity: float
    measurement: str


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class PubchemHit(AbstractHit, metaclass=abc.ABCMeta):
    """ """


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class AcuteEffectHit(PubchemHit):
    """ """

    organism: str
    human: bool
    test_type: str
    route: str
    effect: str
    mg_per_kg: float


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class Ld50Hit(PubchemHit):
    """ """

    organism: str
    human: bool


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

Too many instance attributes (8/7)

class BioactivityHit(PubchemHit):
    """ """

    target_abbrev: Optional[str]
    activity: str
    assay_type: str
    micromolar: float
    relation: str
    species: Optional[str]
    compound_name_in_assay: str
    referrer: str


@dataclass(frozen=True, order=True, repr=True)

Missing class docstring

class ComputedPropertyHit(PubchemHit):
    pass


@dataclass(frozen=True, order=True, repr=True)

Missing class docstring

class CoOccurrenceHit(PubchemHit, metaclass=abc.ABCMeta):
    score: int
    intersect_count: int
    query_count: int
    neighbor_count: int


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class DiseaseCoOccurrenceHit(CoOccurrenceHit):
    """ """


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class GeneCoOccurrenceHit(CoOccurrenceHit):
    """ """


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class ChemicalCoOccurrenceHit(CoOccurrenceHit):
    """ """


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class CtdGeneHit(PubchemHit):
    """ """

    taxon_id: Optional[int]
    taxon_name: Optional[str]


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class DgiHit(PubchemHit):
    """ """


@dataclass(frozen=True, order=True, repr=True)

Missing class docstring

class DiseaseHit(PubchemHit):
    evidence_type: str


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class DrugbankDdiHit(PubchemHit):
    """ """

    type: str
    effect_target: Optional[str]
    change: Optional[str]
    description: str


@dataclass(frozen=True, order=True, repr=True)
class _DrugbankInteractionHit(PubchemHit):
    """ """

    gene_symbol: str
    protein_id: str
    target_type: str
    target_name: str
    general_function: str


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class DrugbankTargetHit(_DrugbankInteractionHit):
    """ """


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class DrugbankGeneralFunctionHit(_DrugbankInteractionHit):
    """ """


@dataclass(frozen=True, order=True, repr=True)

Missing class docstring

class TrialHit(PubchemHit):
    phase: float
    status: str
    interventions: str


HIT_CLASSES = ReflectionUtils.subclass_dict(AbstractHit, concrete=True)