PyOpenWorm.worm module

class PyOpenWorm.worm.Worm(scientific_name=False, **kwargs)

Bases: PyOpenWorm.biology.BiologyType

A representation of the whole worm.

All worms with the same name are considered to be the same object.

Attributes:

neuron_network : ObjectProperty

The neuron network of the worm

muscle : ObjectProperty

Muscles of the worm

defined_augment()

This fuction must return False if identifier_augment() would raise an IdentifierMissingException. Override it when defining a non-standard identifier for subclasses of DataObjects.

get_neuron_network()

Return the neuron network of the worm.

Example:

# Grabs the representation of the neuronal network
>>> net = P.Worm().get_neuron_network()

# Grab a specific neuron
>>> aval = net.aneuron('AVAL')

>>> aval.type()
set([u'interneuron'])

#show how many connections go out of AVAL
>>> aval.connection.count('pre')
77

Returns:An object to work with the network of the worm Return type:PyOpenWorm.Network

get_semantic_net()

Get the underlying semantic network as an RDFLib Graph

Returns:A semantic network containing information about the worm Return type:rdflib.ConjunctiveGraph

identifier_augment(*args, **kwargs)

Override this method to define an identifier in lieu of one explicity set.

One must also override defined_augment() to return True whenever this method could return a valid identifier. IdentifierMissingException should be raised if an identifier cannot be generated by this method.

Raises:

IdentifierMissingException

muscles()

Get all Muscle objects attached to the Worm.

Example:

>>> muscles = P.Worm().muscles()
>>> len(muscles)
96

Returns:A set of all muscles Return type:set