package affectors; import main.Node; import main.Globals; /** This is similar to the Psi function except the inhibitor is in a neighboring cell from the one that contains the target Node. The input node used is from the neighboring cells. Use this version only for membrane-bound components, and only when the interaction in which it takes part is an interaction across a membrane (i.e. I have used it to repress heterodimerizations between ligand and receptor).

Formula
dnodex/dt = 1 - (NODEY ^ nu) / (K ^ nu + NODEY ^ nu)

Parameters

Affecting Node [NODEY] Usually an inhibitor Node. Will come from the face of a cell opposite to nodex's cell.

Half-maximal inhibition level [K_NODEYnodex] The concentration of inhibitor at which transcription is reduced by half.

Cooperativity [nu_NODEYnodex] The non-linearity of the inhibiting function. The higher the value, the sharper the curves in the S-shaped inhibition function.

Usage &nodex

&PsiECAff NODEY K_NODEYnodex nu_NODEYnodex


			&endProductAff

&endnodex/code>

*/
public class PsiECAff extends Affector	{
	/** The half-maximal coefficient. */
	int		kParam;
	/** The "cooperativity" exponent. */
	int		nuParam;
	
	static final String		desc = "Sigmoid turn-off formula";
	static final String	[]	nodeDescriptions = {"Inhibitor"};
	static final String	[]	paramDescriptions = {"Kappa: half-maximal coefficient",
												"nu: cooperativity"};
	static final int	[]	whichSides = {-1};
	
	public PsiECAff()	{}
	
	protected void setLabelsAndTypes()	{
		setDescriptions(this.desc, nodeDescriptions, paramDescriptions);
		setSided(true, whichSides);

		this.Type[GUI_CAPABLE] = 1;
		this.Type[CERTIFICATION] = Affector.RETURNS_DERIV;
	}
	
	public void setParameterNumbers(int [] param_nums)
	{
		kParam = param_nums[0];
		nuParam = param_nums[1];
	}
	
	public float getValue(Node which_node)	{
		return (Globals.characteristicTime * Psi(Nodes[0].getIntegrationValue(otherSide),params[kParam],params[nuParam]));
	}

}

Affecting Node [NODEY]	Usually an inhibitor Node. Will come from the face of a cell opposite to nodex's cell.
Half-maximal inhibition level [K_NODEYnodex]	The concentration of inhibitor at which transcription is reduced by half.
Cooperativity [nu_NODEYnodex]	The non-linearity of the inhibiting function. The higher the value, the sharper the curves in the S-shaped inhibition function.