keggtools.models

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#
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#
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#
Contents