package affectors;

import main.Node;
import main.Globals;

/**
 * <p>This is one half of an affector that converts a single node into another
 * based on some enzymatic activity.  Use this affector in the substrate.  Use
 * {@link EnzymeConversionEC_Pro_Aff} in the product.  For cases in which the
 * enzyme, product and the substrate are all on the membrane.
 *
 * <p> <b>Formula</b>
 * <br>dSUBSTRATE/dt = -max * SUBSTRATE Phi(ENZYME,K_enzyme,nu_enzyme)
 *
 * <p> <b>Parameters</b>
 * <table width="500" border="1">
 * <tr><td width="150">Substrate [SUBSTRATE]</td><td> The substrate Node</td></tr>
 * <tr><td width="150">Enzyme [ENZYME]</td><td> The enzyme Node</td></tr>
 * <tr><td>max [max]</td><td> Maximal rate of reaction.</td></tr>
 * <tr><td>k_enzyme [K_Enzyme]</td><td> Concentration of enzyme where activity is half maximal.</td></tr>
 * <tr><td>nu_enzyme [nu_Enzyme]</td><td> Apparent cooperativity of enzyme activity.</td></tr>
 * </table>
 *
 * <p><b>Usage</b>
 * <code><font size = "3"><br>&SUBSTRATE
 * <blockquote>
 * 		&EnzymeConversionEC_Sub_Aff 	SUBSTRATE	ENZYME	max 	K_enzyme 	nu_enzyme
 * </blockquote>
 * &endNodep</code></font>
 *
 * @author Josselin Milloz
 * @see EnzymeConversionEC_Pro_Aff
 */


public class EnzymeConversionEC_Sub_Aff extends Affector {
	int		max;
	int		k_enzyme;
	int 	nu_enzyme;
	static final String		affectorDescription = "Enzymatic conversion.  Use EnzymeConversionEC_Pro_Aff on product";
	static final String	[]	nodeDescriptions = {"Substrate", "Enzyme"};
	static final String	[]	paramDescriptions = {"Maximal rate of reaction",
												 "half maximal enzyme concentration",
												 "Cooperativity of enzyme"};
	static final int	[]	whichSides = { -1,-1 };

	public EnzymeConversionEC_Sub_Aff()	{}

	protected void setLabelsAndTypes()	{
		setDescriptions(affectorDescription, nodeDescriptions, paramDescriptions);
		setContainsTarget(true);
		setSided(true, whichSides);

		this.Type[GUI_CAPABLE] = 1;
		this.Type[CERTIFICATION] = Affector.RETURNS_DERIV;
		this.Type[MATHTYPE] = Affector.GG;
		this.Type[TERMTYPE] = Affector.CONVERSION;
	}
	
	public void setParameterNumbers(int [] param_nums)
	{
		max = param_nums[0];
		k_enzyme = param_nums[1];
		nu_enzyme = param_nums[2];
	}
	
	public float getValue(Node which_node)	{
		float total_kinase = Nodes[1].getIntegrationValue(side);
		float source = Nodes[0].getIntegrationValue(side);
		float theTerm = params[max] * source *
					Phi(total_kinase, params[k_enzyme], params[nu_enzyme]);

		return -Globals.characteristicTime * theTerm;
	}

	public float getNCValue(Node which_node)  {
		float total_kinase = Nodes[1].getIntegrationValue(side);
		float theTerm = params[max] *
					Phi(total_kinase, params[k_enzyme], params[nu_enzyme]);

		return -Globals.characteristicTime * theTerm;
	}
}