class RSphaeroides(Chemotaxis):
# Define the structure of the cell in terms of connections.
# TODO: How do we specify initial values for proteins where there are more
# than one of the same?
def __init__(self, values={}):
Chemotaxis.__init__(self)
self.proteinMCP = GreenProtein("MCP")
self._ligandEdges.append(self.proteinMCP)
self.proteinW2 = GreenProtein("W2")
self.proteinW3 = GreenProtein("W3")
self.proteinA2_0 = GreenProtein("A2")
self.proteinA2_1 = GreenProtein("A2")
self.proteinR2 = RedProtein("R2")
self.proteinR2.addEdge(self.proteinMCP, EdgeType.Methylation)
self.proteinP_0 = Protein("P")
self.proteinA2_1.addEdge(self.proteinP_0, EdgeType.PhosphoTransfer)
self.proteinTlp = GreenProtein("Tlp")
self._ligandEdges.append(self.proteinMCP)
self.proteinW4 = GreenProtein("R4")
self.proteinA4 = GreenProtein("A4")
self.proteinA3 = GreenProtein("A3")
self.proteinR3 = RedProtein("R3")
self.proteinR3.addEdge(self.proteinTlp, EdgeType.Methylation)
self.proteinP_1 = Protein("P")
self.proteinA4.addEdge(self.proteinP_1, EdgeType.PhosphoTransfer)
self.proteinB1_0 = YellowProtein("B1")
self.proteinB1_1 = YellowProtein("B1")
self.proteinB1_0.addEdge(self.proteinB1_1, EdgeType.FlagellumControl)
self.proteinB1_1.addEdge(self.proteinB1_0, EdgeType.FlagellumControl)
self.proteinP_2 = Protein("P")
# TODO: How to add a phosphotransfer with an edge?
self.proteinY6_1 = BlueProtein("Y6")
self.proteinY6_1.addEdge(self._flagellumOut, EdgeType.FlagellumControl)
self.proteins = [ self.proteinMCP, self.proteinW2, self.proteinW3
, self.proteinA2_0, self.proteinA2_1, self.proteinR2
, self.proteinP_0, self.proteinTlp, self.proteinA4
, self.proteinA3, self.proteinR3, self.proteinP_1
, self.proteinB1_0, self.proteinB1_1, self.proteinP_2 ]
def __init__(self, values={}):
Chemotaxis.__init__(self)
self.proteinMCP = GreenProtein("MCP")
self._ligandEdges.append(self.proteinMCP)
self.proteinW2 = GreenProtein("W2")
self.proteinW3 = GreenProtein("W3")
self.proteinA2_0 = GreenProtein("A2")
self.proteinA2_1 = GreenProtein("A2")
self.proteinR2 = RedProtein("R2")
self.proteinR2.addEdge(self.proteinMCP, EdgeType.Methylation)
self.proteinP_0 = Protein("P")
self.proteinA2_1.addEdge(self.proteinP_0, EdgeType.PhosphoTransfer)
self.proteinTlp = GreenProtein("Tlp")
self._ligandEdges.append(self.proteinMCP)
self.proteinW4 = GreenProtein("R4")
self.proteinA4 = GreenProtein("A4")
self.proteinA3 = GreenProtein("A3")
self.proteinR3 = RedProtein("R3")
self.proteinR3.addEdge(self.proteinTlp, EdgeType.Methylation)
self.proteinP_1 = Protein("P")
self.proteinA4.addEdge(self.proteinP_1, EdgeType.PhosphoTransfer)
self.proteinB1_0 = YellowProtein("B1")
self.proteinB1_1 = YellowProtein("B1")
self.proteinB1_0.addEdge(self.proteinB1_1, EdgeType.FlagellumControl)
self.proteinB1_1.addEdge(self.proteinB1_0, EdgeType.FlagellumControl)
self.proteinP_2 = Protein("P")
# TODO: How to add a phosphotransfer with an edge?
self.proteinY6_1 = BlueProtein("Y6")
self.proteinY6_1.addEdge(self._flagellumOut, EdgeType.FlagellumControl)
self.proteins = [ self.proteinMCP, self.proteinW2, self.proteinW3
, self.proteinA2_0, self.proteinA2_1, self.proteinR2
, self.proteinP_0, self.proteinTlp, self.proteinA4
, self.proteinA3, self.proteinR3, self.proteinP_1
, self.proteinB1_0, self.proteinB1_1, self.proteinP_2 ]