pypath.internals.intera.Complex

class pypath.internals.intera.Complex(components, ncbi_tax_id=9606, name=None, ids=None, sources=None, interactions=None, references=None, proteins=None, attrs=None)

Bases: object

__init__(components, ncbi_tax_id=9606, name=None, ids=None, sources=None, interactions=None, references=None, proteins=None, attrs=None)

Represents a molecular complex.

componentslist,dict

Either a list of identifiers or a dict with identifiers as keys and stoichiometric coefficients as values. List of identifiers also assumed to represent stoichiometry by repetition of identifiers.

ncbi_tax_idint

NCBI taxonomy identifier of the complex. It implies all members of the complex belong to the same organism. Support for multi- organism complexes will be implemented in the future.

namestr

A custom name or identifier of the complex.

idsdict

Identifiers. If sources is a set, list or tuple it should be a dict with database names as keys and set of identifiers as values. If sources is a string, it can be a set of identifiers or a single identifier.

sourcesset,str

Database(s) the complex has been defined in.

interactionslist,dict

Interactions between the components of the complex. Either a list of tuples of component IDs or a dict with tuples as keys and custom interaction properties as values.

proteinslist,dict

Synonym for components, kept for compatibility.

Methods

__init__(components[, ncbi_tax_id, name, ...])	Represents a molecular complex.
add_attr(source, attr)	Attributes can store annotations for complexes.
add_ids(ids[, source])
add_source(source)
get_interaction(component1, component2)
has_interaction(component1, component2)
iter_proteins()
merge(other)	Adds the annotations (sources, references, attrs) of the other Complex instance to this one.
reload()
set_interaction(component1, component2, ...)

Attributes

genesymbol_str
genesymbols
have_stoichiometry
stoichiometry
stoichiometry_str
stoichiometry_str_genesymbols

add_attr(source, attr)

Attributes can store annotations for complexes.

merge(other)

Adds the annotations (sources, references, attrs) of the other Complex instance to this one. If the other Complex has different components it does nothing.