Enzyme

This class represents enzymes extracted from open databases.

:property go_id: GO term id :type go_id: str :property name: name of the compound :type name: str :property ec: ec accession number :type ec: str :property taxonomy: taxonomy id that gives the organism :type taxonomy: str :property bto: bto id that gives the tissue location :type bto: class:biota.BTO :property uniprot_id: uniprot id of the enzyme :type uniprot_id: str

Uniprot: The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt consortium and host institutions EMBL-EBI, SIB and PIR are committed to the long-term preservation of the UniProt databases.
Brenda: BRENDA is the main collection of enzyme functional data available to the scientific community (https://www.brenda-enzymes.org/). BRENDA data are available under the Creative Commons License (CC BY 4.0), https://creativecommons.org/licenses/by/4.0/.
BKMS: BKMS-react is an integrated and non-redundant biochemical reaction database containing known enzyme-catalyzed and spontaneous reactions. Biochemical reactions collected from BRENDA, KEGG, MetaCyc and SABIO-RK were matched and integrated by aligning substrates and products.

Attributes

created_at: TypedDateTimeUTCdata: dictid: TypedCharFieldlast_modified_at: TypedDateTimeUTC

Functions

__init__

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

as_json

jsonifiable_data_keys : list - ['name', 'description']

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_params

Returns the list of parameters associated with name

name : Any

Name of the parameter

Return type : Params

get_params_as_json

Returns the list of parameters associated with name

name : Any

Name of the parameter

Return type : Params

get_params_by_tax

Returns the list of parameters associated with name

name : Any

Name of the parameter

tax_id : Any

Return type : list

is_alias

is_dirty

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

arg : Any

set_name

Set the name.

name : str

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 enzyme table and related tables.

Extra parameters are passed to :meth:create_table

delete @classmethod

delete_by_id @classmethod

pk : Any

drop_table @classmethod

Drops enzyme 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_name @classmethod

name : Any

page : int - 1

number_of_items_per_page : int - 50

select @classmethod

fields : Any

select_and_follow_if_deprecated @classmethod

Select deprecated enzymes

ec_number : Any

tax_id : Any

select_only_one : bool - False

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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