Reaction

This class represents metabolic reactions extracted from Rhea database.

Rhea is an expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models (https://www.rhea-db.org/). Rhea data are available under the Creative Commons License (CC BY 4.0), https://creativecommons.org/licenses/by/4.0/.

:property rhea_id: rhea accession number :type rhea_id: CharField :property master_id: master id of the reaction :type master_id: CharField :property direction: direction of the reaction :type direction: CharField (UN = undirected, LR = left-right, RL = right-left, BI = bidirectionnal) :property biocyc_ids: reaction identifier in the biocyc database :type biocyc_ids: CharField :property kegg_id: reaction identifier in the kegg databse :type kegg_id: CharField :property substrates: substrates of the reaction :type substrates: List of Compound :property products: products of the reaction :type products: List of Compound :property enzymes: enzymes of the reaction :type enzymes: List of Enzyme

Attributes

created_at: TypedDateTimeUTCdata: dictid: TypedCharFieldlast_modified_at: TypedDateTimeUTC

Functions

__init__

Initialize self. See help(type(self)) for accurate signature.

append_biocyc_id

Appends a biocyc id to the reaction

id : Any

The id

clone

coerce

_coerce : bool - True

delete_instance

recursive : bool - False

delete_nullable : bool - False

dependencies

search_nullable : bool - True

exclude_null_children : bool - False

get_id

get_name

Get the name. Alias of :meth:get_title

Return type : str

get_title

has_enzymes

is_alias

is_charge_balanced

is_dirty

is_mass_balanced

is_saved

Returns True if the model is saved in db, False otherwise

Return type : bool

refresh

Return type : ModelType

save

Sets the data set force_insert to True to force creation of the object set skip_hook to True to skip the before insert or update hook

Return type : Self

set_direction

Set the direction of the reaction

direction : Any

The direction

set_kegg_id

Set the KEGG id the reaction

kegg_id : Any

The kegg id

set_master_id

Set the master id the reaction

master_id : Any

The master id

set_name

Set the name.

name : str

set_rhea_id

Set the RHEA id the reaction

kegg_id : Any

to_dto

Return type : BaseModelDTO

unwrap

add_index @classmethod

fields : Any

after_all_tables_init @classmethod

Method call after all the table are inited

Useful when use DeferredForeignKey to create the foreign key manually latter

after_table_creation @classmethod

Method call after the table is created

Usefull to create the full text indexes

alias @classmethod

alias : Any

bind @classmethod

database : Any

bind_refs : bool - True

bind_backrefs : bool - True

_exclude : Any

bind_ctx @classmethod

database : Any

bind_refs : bool - True

bind_backrefs : bool - True

bulk_create @classmethod

model_list : Any

batch_size : Any

bulk_update @classmethod

model_list : Any

fields : Any

batch_size : Any

classname @classmethod

Returns the name of the class

slugify : bool - False

True to slugify the class name if True

snakefy : bool - False

True to snakefy the class name if True

replace_uppercase : bool - False

Replace upper cases by "-" if True

Return type : str

column_exists @classmethod

Returns True if the column exists in the table

column_name : str

The column name

Return type : bool

create @classmethod

query : Any

create_all @classmethod

Automically and safely save a list of models in the database. If an error occurs during the operation, the whole transactions is rolled back (if use_transaction=True).

model_list : list

List of models

batch_size : int - 10000

Size of each batch for bulk creation

use_transaction : bool - True

If True, wraps all batches in a single transaction. If False, each batch creates its own transaction (for MariaDB timeout issues)

Return type : list

create_foreign_key_if_not_exist @classmethod

Create a foreign key for a Foreign key field only if the foreign key does not exists

field : Any

[description]

create_full_text_index @classmethod

Method to create a full text index

columns : list

[description]

index_name : str

create_table @classmethod

Creates reaction table and related tables.

Extra parameters are passed to :meth:peewee.Model.create_table

delete @classmethod

delete_by_id @classmethod

pk : Any

drop_table @classmethod

Drops reaction table and related tables.

Extra parameters are passed to :meth:peewee.Model.drop_table

execute_sql @classmethod

Execute a raw SQL query. Can use the [TABLE_NAME] to replace by the table name

query : str

The query to execute

filter @classmethod

dq_nodes : Any

filters : Any

foreign_key_exists @classmethod

column_name : str

Return type : bool

full_classname @classmethod

Returns the full name of the class

slugify : bool - False

Slugify the returned class name if True

snakefy : bool - False

Snakefy the returned class name if True

Return type : str

get @classmethod

query : Any

filters : Any

get_by_id @classmethod

id : str

Return type : Optional

get_by_id_and_check @classmethod

Get by ID and throw 404 error if object not found

id : str

The ID of the model

Return type : ModelType

get_by_ids @classmethod

ids : list

Return type : list

get_db @classmethod

Return type : DatabaseProxy

get_db_manager @classmethod

Returns the (current) DbManager of this model

Return type : AbstractDbManager

get_metadata @classmethod

Return type : ModelMetadata

get_or_create @classmethod

get_or_none @classmethod

arg : Any

get_table_name @classmethod

Returns the table name of this class

Return type : str | None

index @classmethod

fields : Any

index_exists @classmethod

Returns True if the index exists in the table

index_name : str

The index name

Return type : bool

inheritors @classmethod

Get all the classes that inherit this class

insert @classmethod

_Model__data : Any

insert : Any

insert_all @classmethod

Insert multiple items with detailed logging

data : list

List of dictionaries to insert

batch_size : int - 10000

Number of items per batch

use_transaction : bool - True

If True, wraps all batches in a single transaction. If False, each batch uses its own transaction (for MariaDB timeout issues)

insert_from @classmethod

query : Any

fields : Any

insert_many @classmethod

rows : Any

fields : Any

is_mysql_engine @classmethod

is_table @classmethod

Returns True if the class has a table name defined

Return type : bool

noop @classmethod

raw @classmethod

sql : Any

params : Any

replace @classmethod

_Model__data : Any

insert : Any

replace_many @classmethod

rows : Any

fields : Any

save_all @classmethod

search @classmethod

Performs full-text search on the field. Must be overrided by child class to work

phrase : str

The phrase to search

modifier : str

Return type : ModelSelect

search_by_ec_numbers @classmethod

ec_numbers : list | str

Return type : ModelSelect

search_by_name @classmethod

name : Any

page : int - 1

number_of_items_per_page : int - 50

search_by_tax_ids @classmethod

tax_ids : list | str

Return type : ModelSelect

select @classmethod

fields : Any

set_by_id @classmethod

key : Any

value : Any

table_exists @classmethod

truncate_table @classmethod

options : Any

update @classmethod

_Model__data : Any

update : Any

update_all @classmethod

Automically and safely save a list of models in the database. If an error occurs during the operation, the whole transactions is rolled back (if use_transaction=True).

model_list : list

List of models

fields : list

batch_size : int - 10000

use_transaction : bool - True

If True, wraps bulk_update in a transaction. If False, bulk_update handles its own transactions (for MariaDB timeout issues)

Return type : list

validate_model @classmethod

copy @staticmethod

method : Any

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