keggtools.models

KEGG pathway models to parse object relational.

Classes

Alt	Alt model.
Component	Component model.
Entry	Entry model class.
Graphics	Graphics information for rendering.
Pathway	KEGG Pathway object.
Product	Reaction Product model.
Reaction	Reaction model.
Relation	Relation model class.
Substrate	reaction Substrate model.
Subtype	Subtype model class.

Module Contents

class keggtools.models.Alt(/, **data)

Bases: pydantic_xml.BaseXmlModel

Alt model.

Parameters:

data (Any)

name: str

class keggtools.models.Component(/, **data)

Bases: pydantic_xml.BaseXmlModel

Component model.

Parameters:

data (Any)

id: str

class keggtools.models.Entry(/, **data)

Bases: pydantic_xml.BaseXmlModel

Entry model class.

Parameters:

data (Any)

components: list[Component] = []

get_gene_id()

Parse variable ‘name’ of Entry into KEGG id.

Returns:

List of KEGG identifier.

Return type:

list[str]

graphics: Graphics | None = None

has_multiple_names()

Checks if entry has multiple names that are space seperated.

Returns:

Retruns True if entry has multiple names.

Return type:

bool

id: str

link: str | None

name: str

reaction: str | None

type: keggtools._types.EntryTypeAlias

class keggtools.models.Graphics(/, **data)

Bases: pydantic_xml.BaseXmlModel

Graphics information for rendering.

Parameters:

data (Any)

bgcolor: str | None

coords: str | None

fgcolor: str | None

height: int | None

name: str | None

type: keggtools._types.GraphicTypeAlias | None

width: int | None

x: int | None

y: int | None

class keggtools.models.Pathway(/, **data)

Bases: pydantic_xml.BaseXmlModel

KEGG Pathway object.

The KEGG pathway object stores graphics information and related objects.

Parameters:

data (Any)

entries: list[Entry] = []

get_entry_by_id(entry_id)

Get pathway Entry object by id.

Parameters:

entry_id (str) – Id of Entry.

Returns:

Returns Entry instance if id is found in Pathway. Otherwise returns None.

Return type:

Optional[Entry]

get_genes()

List all genes from pathway.

Returns:

List of entry ids with type gene.

Return type:

List[str]

image: str | None

link: str | None

name: str

number: str

org: str

reactions: list[Reaction] = []

relations: list[Relation] = []

title: str | None

class keggtools.models.Product(/, **data)

Bases: pydantic_xml.BaseXmlModel

Reaction Product model.

Parameters:

data (Any)

alt: Alt | None = None

id: str

name: str

class keggtools.models.Reaction(/, **data)

Bases: pydantic_xml.BaseXmlModel

Reaction model.

Parameters:

data (Any)

id: str

name: str

products: list[Product] = []

substrates: list[Substrate] = []

type: keggtools._types.ReactionTypeAlias

class keggtools.models.Relation(/, **data)

Bases: pydantic_xml.BaseXmlModel

Relation model class.

Parameters:

data (Any)

entry1: str

entry2: str

subtypes: list[Subtype] = []

type: keggtools._types.RelationTypeAlias

class keggtools.models.Substrate(/, **data)

Bases: pydantic_xml.BaseXmlModel

reaction Substrate model.

Parameters:

data (Any)

alt: Alt | None = None

id: str

name: str

class keggtools.models.Subtype(/, **data)

Bases: pydantic_xml.BaseXmlModel

Subtype model class.

Parameters:

data (Any)

name: keggtools._types.RelationSubtypeAlias

value: str