pypath.core.entity.Entity

class pypath.core.entity.Entity(identifier, entity_type=None, id_type=None, taxon=9606, attrs=None)

Bases: Logger, AttributeHandler

Represents a molecular entity such as protein, miRNA, lncRNA or small molecule.

Parameters:

• identifier (str) – An identifier from the reference database e.g. UniProt ID for proteins.

• entity_type (str) – The type of the molecular entity, defaults to 'protein'.

• id_type (str) – The type of the identifier (the reference database), default is 'uniprot'.

• taxon (int) – The NCBI Taxonomy Identifier of the molecular entity, e.g. 9606 for human. Use 0 for non taxon specific molecules e.g. metabolites or drug compounds.

• attrs (NoneType,dict) – A dictionary of additional attributes.

__init__(identifier, entity_type=None, id_type=None, taxon=9606, attrs=None)

Make this instance a logger.

Parameters:

• name – The label of this instance that will be prepended to all messages it sends to the logger.

• module – Send the messages by the logger of this module.

Methods

__init__(identifier[, entity_type, id_type, ...])	Make this instance a logger.
count_entity_type(entities, entity_type)	Counts elements in an iterable of entities or identifiers of type(s) in entity_type.
entity_info(identifier)
entity_name_str(entity)
filter_entity_type(entities, entity_type)	Filters an iterable of entities or identifiers keeping only the ones of type(s) in entity_type.
get_entity_type()
igraph_vertex_label(igraph_v)
igraph_vertex_name(igraph_v)
igraph_vertex_name_label(igraph_v)
info()
is_complex()
is_mirna()
is_protein()
is_small_molecule()
only_complexes(entities)
only_mirnas(entities)
only_proteins(entities)
reload()
serialize(**kwargs)	Generates a JSON string with the full contents of the attributes, without any whitespace or line break.
set_label()
update_attrs([attrs])	Updates the attributes stored here.

Attributes

identifier
entity_type
id_type
taxon
label
key
attrs

classmethod count_entity_type(entities, entity_type)

Counts elements in an iterable of entities or identifiers of type(s) in entity_type.

Parameters:

• entities (iterable) – A list, set, tuple or other iterable yielding entities or identifiers.

• entity_type (str,set) – One or more entity types e.g. {'protein', 'mirna'}.

Returns:

int

classmethod filter_entity_type(entities, entity_type)

Filters an iterable of entities or identifiers keeping only the ones of type(s) in entity_type.

Parameters:

• entities (iterable) – A list, set, tuple or other iterable yielding entities or identifiers.

• entity_type (str,set) – One or more entity types e.g. {'protein', 'mirna'}.

Returns:

Same type of object as entities if the type of the object is list, set or tuple, otherwise a generator.

serialize(**kwargs)

Generates a JSON string with the full contents of the attributes, without any whitespace or line break.

Returns

(str): The attributes JSON serialized.

update_attrs(attrs=None, **kwargs)

Updates the attributes stored here. The attributes with identical keys are merged using the pypath.share.common.combine_attrs() function.

The new attributes can be provided three ways: an object with an attribute called attrs; a dictionary of attributes; or the attributes as keyword arguments.