com.actelion.research.chem.coords.FragmentAssociation Maven / Gradle / Ivy

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There is a newer version: 2024.12.1

package com.actelion.research.chem.coords;

/**
 * Created by thomas on 9/23/16.
 */
public class FragmentAssociation {
	private InventorFragment[] mFragment;
	private double[] mX,mY;
	private int[] mCount;

	public FragmentAssociation(InventorFragment f1, InventorFragment f2, int atomIndex1, int atomIndex2) {
		mFragment = new InventorFragment[2];
		mFragment[0] = f1;
		mFragment[1] = f2;
		mX = new double[2];
		mY = new double[2];
		mX[0] = mFragment[0].getAtomX(atomIndex1);
		mY[0] = mFragment[0].getAtomY(atomIndex1);
		mX[1] = mFragment[1].getAtomX(atomIndex2);
		mY[1] = mFragment[1].getAtomY(atomIndex2);
		mCount = new int[2];
		mCount[0] = 1;
		mCount[1] = 1;
		}

	/**
	 * Uses center of gravity of the fragments as anchor points
	 * @param f1
	 * @param f2
	 */
	public FragmentAssociation(InventorFragment f1, InventorFragment f2) {
		mFragment = new InventorFragment[2];
		mFragment[0] = f1;
		mFragment[1] = f2;
		mX = new double[2];
		mY = new double[2];
		mCount = new int[2];
		for (int i=0; i<2; i++) {
			for (int j=0; j mFragment[1].mAtomY[i])
				yMin = mFragment[1].mAtomY[i];
			if (yMax < mFragment[1].mAtomY[i])
				yMax = mFragment[1].mAtomY[i];
			}

		double range = yMax - yMin + 2*minDistance;
		int binCount = (int)Math.ceil(range);
		yMin += (range - binCount) / 2 - minDistance;
		double[] leftX = new double[binCount];
		for (int i=0; i mFragment[1].mAtomX[i])
					leftX[j] = mFragment[1].mAtomX[i];
				}
			}

		for (int i=0; i= 0 && index < leftX.length
			 && dx < mFragment[0].mAtomX[i] - leftX[index])
				dx = mFragment[0].mAtomX[i] - leftX[index];
			}

		for (int i=0; i