def create_synapse(self, pre_neuron, post_neuron,
transporter=Transporters.GLUTAMATE, receptor=Receptors.AMPA,
enzyme_concentration=1.0, axon_delay=0, dendrite_strength=25):
# If single molecule is true, the synapse will save time and space by
# assuming that only one molecule will move through it. This means
# that the proteins must use the same native molecule, and no
# exogenous molecules can be admitted into the synapse.
# First, we must validate that the proteins use the same molecule.
# Then we ensure that the molecule is in active_molecules.
if transporter.native_mol_id != receptor.native_mol_id:
raise ValueError
# Create synapse.
synapse = Neuron.create_synapse(pre_neuron, post_neuron,
transporter=transporter, receptor=receptor,
enzyme_concentration=enzyme_concentration,
axon_delay=axon_delay, dendrite_strength=dendrite_strength)
self.synapses.append(synapse)
return synapse
def create_synapse(self, pre_neuron, post_neuron,
transporter=Transporters.GLUTAMATE, receptor=Receptors.AMPA,
enzyme_concentration=1.0,
axon_delay=None, dendrite_strength=0.05, active_molecules=[Molecule_IDs.GLUTAMATE],
axon_probe_name=None, cleft_probe_name=None, dendrite_probe_name=None):
# If single molecule is true, the synapse will save time and space by
# assuming that only one molecule will move through it. This means
# that the proteins must use the same native molecule, and no
# exogenous molecules can be admitted into the synapse.
# First, we must validate that the proteins use the same molecule.
# Then we ensure that the molecule is in active_molecules.
if transporter.native_mol_id != receptor.native_mol_id:
raise ValueError
if transporter.native_mol_id not in active_molecules:
active_molecules.append(transporter.native_mol_id)
# Create synapse.
synapse = Neuron.create_synapse(pre_neuron, post_neuron,
transporter=transporter, receptor=receptor,
active_molecules = active_molecules, enzyme_concentration=enzyme_concentration,
axon_delay=axon_delay, dendrite_strength=dendrite_strength)
self.synapses.append(synapse)
# Set up probes.
if axon_probe_name:
axon = synapse.axon
probe = ConcentrationProbe(axon.native_mol_id)
self.concentration_probes[axon] = probe
self.probes[axon_probe_name] = probe
if cleft_probe_name:
cleft = synapse.synaptic_cleft
probe = ConcentrationProbe(synapse.axon.native_mol_id)
self.concentration_probes[cleft] = probe
self.probes[cleft_probe_name] = probe
if dendrite_probe_name:
dendrite = synapse.dendrites[0]
probe = ConcentrationProbe(dendrite.native_mol_id)
self.concentration_probes[dendrite] = probe
self.probes[dendrite_probe_name] = probe
return synapse
def create_synapse(self, pre_neuron, post_neuron,
receptor=epsp, delay=0, strength=1):
synapse = Neuron.create_synapse(pre_neuron, post_neuron,
receptor=receptor, delay=delay, strength=strength)
self.synapses.append(synapse)
return synapse
