Module ImportFrom alias Import alias identifier ImportFrom alias ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam defaults NameLoad kwarg body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr keyword NameLoad NameLoad Expr Call NameLoad keyword NameLoad Expr Call NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad keyword NameLoad Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Num For NameStore Call AttributeLoad NameLoad attr body If CompareEq Call AttributeLoad AttributeLoad NameLoad attr attr Str body AugAssignAdd NameStore Num Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Num For NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str body If CompareEq Call AttributeLoad AttributeLoad NameLoad attr attr Str body AugAssignAdd NameStore Num Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Return SubscriptLoad SubscriptLoad AttributeLoad SubscriptLoad NameLoad Index Str attr Index Call AttributeLoad AttributeLoad NameLoad attr attr Index Str decorator_list FunctionDef arguments args NameParam NameParam defaults Num body Expr Str For NameStore Call AttributeLoad SubscriptLoad NameLoad Index Str attr Call AttributeLoad NameLoad attr keyword NameLoad body If CompareIn Str SubscriptLoad SubscriptLoad NameLoad Index Num Index Str body Expr Yield SubscriptLoad NameLoad Index Num decorator_list FunctionDef arguments args NameParam defaults body Expr 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NameLoad orelse If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr NameLoad For NameStore NameLoad body For NameStore Call AttributeLoad NameLoad attr body Expr Yield NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return ListLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults Str NameLoad vararg kwarg body Expr Str Assign NameStore Call NameLoad Assign SubscriptStore NameLoad Index Str BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr Assign SubscriptStore NameLoad Index Str BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr Assign SubscriptStore NameLoad Index Str BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str If CompareIsNot NameLoad NameLoad body If CompareEq Call AttributeLoad NameLoad attr Str body Assign NameStore Str Assign NameStore BinOpMod Str NameLoad orelse Assign NameStore Str Assign NameStore BinOpMod Str TupleLoad SubscriptLoad NameLoad Index NameLoad NameLoad Assign NameStore Num For NameStore Call AttributeLoad SubscriptLoad AttributeLoad NameLoad attr Index Str attr NameLoad body Assign NameStore SubscriptLoad NameLoad Index Str Return Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults kwarg body Expr Str Assert Call NameLoad NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list FunctionDef arguments args NameParam defaults kwarg body For NameStore AttributeLoad NameLoad attr body For NameStore Call AttributeLoad NameLoad attr NameLoad body Expr Yield NameLoad decorator_list decorator_list
N/A __future__ print_function N/A PyOpenWorm P PyOpenWorm Cell Neuron N/A Cell N/A N/A 
    A neuron.

    See what neurons express some neuropeptide

    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

        >>> aval.name()
        u'AVAL'

        #list all known receptors
        >>> sorted(aval.receptors())
        [u'GGR-3', u'GLR-1', u'GLR-2', u'GLR-4', u'GLR-5', u'NMR-1', u'NMR-2', u'UNC-8']

        #show how many chemical synapses go in and out of AVAL
        >>> aval.Syn_degree()
        90

    Parameters
    ----------
    name : string
        The name of the neuron.

    Attributes
    ----------
    type : DatatypeProperty
        The neuron type (i.e., sensory, interneuron, motor)
    receptor : DatatypeProperty
        The receptor types associated with this neuron
    innexin : DatatypeProperty
        Innexin types associated with this neuron
    neurotransmitter : DatatypeProperty
        Neurotransmitters associated with this neuron
    neuropeptide : DatatypeProperty
        Name of the gene corresponding to the neuropeptide produced by this neuron
    neighbor : Property
        Get neurons connected to this neuron if called with no arguments, or
        with arguments, state that neuronName is a neighbor of this Neuron
    connection : Property
        Get a set of Connection objects describing chemical synapses or gap
        junctions between this neuron and others

     __init__ N/A N/A self name N/A False kwargs N/A N/A N/A N/A N/A super Neuron self __init__ name name kwargs N/A N/A Neighbor owner self N/A N/A Connection owner self N/A N/A N/A Neuron DatatypeProperty type self multiple True N/A N/A N/A Neuron DatatypeProperty receptor self multiple True N/A N/A N/A Neuron DatatypeProperty innexin self multiple True N/A N/A N/A Neuron DatatypeProperty neurotransmitter self multiple True N/A N/A N/A Neuron DatatypeProperty neuropeptide self multiple True N/A N/A self get_neighbors N/A self neighbor N/A N/A self receptors N/A self receptor N/A GJ_degree N/A N/A self N/A N/A N/A Get the degree of this neuron for gap junction edges only

        :returns: total number of incoming and outgoing gap junctions
        :rtype: int
         N/A count 0 N/A c N/A N/A self connection N/A N/A N/A N/A N/A N/A c syntype one gapJunction N/A N/A count 1 N/A count N/A Syn_degree N/A N/A self N/A N/A N/A Get the degree of a this neuron for chemical synapse edges only

        :returns: total number of incoming and outgoing chemical synapses
        :rtype: int
         N/A count 0 N/A c N/A N/A N/A self connection get either N/A N/A N/A N/A N/A N/A c syntype one send N/A N/A count 1 N/A count N/A _type_networkX N/A N/A self N/A N/A N/A Get type of this neuron (motor, interneuron, sensory)

        Use the networkX representation as the source

        :returns: the type
        :rtype: str
         N/A N/A N/A N/A N/A self N/A nx node N/A N/A N/A N/A self name one N/A ntype N/A get_incidents N/A N/A self type N/A 0 N/A N/A  Get neurons which synapse at this neuron  N/A item N/A N/A N/A self N/A nx in_edges_iter N/A N/A self name data True N/A N/A N/A GapJunction N/A N/A item N/A 2 N/A synapse N/A N/A N/A N/A item N/A 0 N/A _as_neuroml N/A N/A self N/A N/A N/A Return this neuron as a NeuroML representation

          :rtype: libNeuroML.Neuron
        N/A N/A Neighbor N/A N/A P Property N/A N/A multiple True __init__ N/A N/A self N/A kwargs N/A N/A N/A N/A N/A P Property __init__ self neighbor kwargs N/A N/A self _conns N/A N/A get N/A N/A self N/A kwargs N/A N/A Get a list of neighboring neurons.

           Parameters
           ----------
           See parameters for PyOpenWorm.connection.Connection

           Returns
           -------
           list of Neuron
         N/A N/A N/A len N/A self _conns 0 N/A N/A c N/A self _conns N/A N/A N/A N/A N/A c post_cell N/A N/A c N/A N/A P Connection pre_cell N/A self owner kwargs N/A r N/A N/A c load N/A N/A N/A N/A N/A r post_cell N/A values N/A N/A self N/A N/A N/A N/A N/A property set N/A N/A self other N/A kwargs N/A N/A c N/A N/A P Connection pre_cell N/A self owner post_cell other kwargs N/A N/A N/A N/A self _conns append c N/A c N/A triples N/A N/A self N/A kwargs N/A N/A c N/A self _conns N/A N/A x N/A N/A c triples kwargs N/A N/A N/A x N/A N/A Connection N/A N/A P Property N/A N/A A representation of the connection between neurons. Either a gap junction
    or a chemical synapse

    TODO: Add neurotransmitter type.
    TODO: Add connection strength
     N/A multiple True __init__ N/A N/A self N/A kwargs N/A N/A N/A N/A N/A P Property __init__ self connection kwargs N/A N/A self _conns N/A N/A get N/A N/A self pre_post_or_either N/A pre kwargs N/A N/A Get a list of connections associated with the owning neuron.

           Parameters
           ----------
           type: What kind of junction to look for.
                        0=all, 1=gap junctions only, 2=all chemical synapses
                        3=incoming chemical synapses, 4=outgoing chemical synapses
           Returns
           -------
           list of Connection
         N/A c N/A N/A N/A pre_post_or_either pre N/A N/A N/A N/A c append N/A N/A P Connection pre_cell N/A self owner kwargs N/A N/A N/A pre_post_or_either post N/A N/A N/A N/A c append N/A N/A P Connection post_cell N/A self owner kwargs N/A N/A N/A pre_post_or_either either N/A N/A N/A N/A c append N/A N/A P Connection pre_cell N/A self owner kwargs N/A N/A N/A c append N/A N/A P Connection post_cell N/A self owner kwargs N/A x c N/A N/A r N/A N/A x load N/A N/A N/A r N/A values N/A N/A self N/A N/A N/A N/A N/A property count N/A N/A self pre_post_or_either syntype N/A pre None args kwargs N/A N/A Get a list of connections associated with the owning neuron.

           Parameters
           ----------
           See parameters for PyOpenWorm.connection.Connection

           Returns
           -------
           int
               The number of connections matching the paramters given
         N/A options N/A dict N/A N/A options N/A pre N/A 
                     ?x c:pre_cell ?z .
                     ?z sp:value <%s> .
                      N/A N/A N/A self owner identifier N/A N/A options N/A post N/A 
                      ?x c:post_cell ?z .
                      ?z sp:value <%s> .
                       N/A N/A N/A self owner identifier N/A N/A options N/A either N/A  { %s } UNION { %s } .  N/A N/A options N/A post N/A options N/A pre N/A N/A syntype None N/A N/A N/A N/A N/A syntype lower gapjunction N/A N/A syntype gapJunction N/A syntype_pattern N/A FILTER( EXISTS { ?x c:syntype ?v . ?v sp:value "%s" . }) . syntype N/A N/A syntype_pattern N/A q N/A 
        prefix ow: <http://openworm.org/entities/>
        prefix c: <http://openworm.org/entities/Connection/>
        prefix sp: <http://openworm.org/entities/SimpleProperty/>
        prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
        SELECT (COUNT(?x) as ?count) WHERE {
         %s
         %s
        }
         N/A N/A options N/A pre_post_or_either syntype_pattern N/A res 0 N/A x N/A N/A N/A N/A self conf N/A rdf.graph query q N/A N/A res N/A x N/A count N/A N/A int res N/A set N/A N/A self conn N/A kwargs N/A N/A Add a connection associated with the owner Neuron

           Parameters
           ----------
           conn : PyOpenWorm.connection.Connection
               connection associated with the owner neuron

           Returns
           -------
           A PyOpenWorm.neuron.Connection
         N/A N/A isinstance conn N/A P Connection N/A N/A N/A N/A self _conns append conn N/A triples N/A N/A self N/A kwargs N/A N/A c N/A self _conns N/A N/A x N/A N/A c triples kwargs N/A N/A N/A x N/A N/A