get_neuron_generic_gate_hje: Get a generic neuron gate with n inputs and 1 output

In DanielKneipp/DNAr: Simulates chemical reaction networks constructed with DNA

Get a generic neuron gate with n inputs and 1 output

Description

This function returns a generic neuron gate. Generic because the number of inputs of this gate will be specified as an argument (length of input_neuron_names).

Usage

get_neuron_generic_gate_hje(gate_name, input_neuron_names, output_neuron_name,
  input_neuron_cis, binding_enzyme_configs, binding_cis,
  binding_inhibit = NULL)

Arguments

gate_name	String specifying the gate name. Used for identification purpose.
output_neuron_name	A string being the output neuron name
input_neuron_cis	A vector of number representing the initial concentration of each neuron
binding_enzyme_configs	A list where each element represents a enzyme configuration. Each configuration is a list with the following parameters: ci: Initial concentration of the enzyme k: Vector with the rate constants of forward and backward reactions, respectively.
binding_cis	Numeric vector with the initial concentration of the bindings
binding_inhibit	Boolean vector where each elements specifies whether the binding with the same index will be an inhibitory binding or not. If no vector is passed, no binding will be inhibited.
input_neuron_name	A list of string. Each string specifies

Details

A neuron gate is a gate made with neurons, more specifically, 1 + n neurons, where n is the number of inputs. Each input is a binary neuron that passes its output to the last neuron, the output neuron. This neuron has as input the sum of the output of all input neurons.

Value

A list representing the gate. This list comes with three parameters:

• output_neuron_crn: A neuron CRN returned by get_neuron_hje();

• input_neuron_crns: A list of neuron CRNs also returned by get_neuron_hje();

• binding_crns: A list of binding CRNs returned by get_neuron_binding_hje(), which are the binding of each input neuron with the output neuron.

See Also

react() for more about the neuron behavior.

DanielKneipp/DNAr documentation built on Jan. 7, 2023, 12:42 p.m.