kabschalignmenttest.java

化学图形处理软件

package org.openscience.cdk.test.geometry.alignment;

import java.io.InputStream;
import java.util.List;

import javax.vecmath.Point3d;

import junit.framework.Test;
import junit.framework.TestSuite;

import org.openscience.cdk.Atom;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.geometry.alignment.KabschAlignment;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.io.HINReader;
import org.openscience.cdk.io.IChemObjectReader;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

/**
 * This class defines regression tests that should ensure that the source code
 * of the org.openscience.cdk.geometry.alignment.KabschAlignment is not broken.
 *
 * @cdk.module test-extra
 *
 * @author     Rajarshi Guha
 * @cdk.created    2004-12-11
 *
 * @see org.openscience.cdk.geometry.alignment.KabschAlignment
 */
public class KabschAlignmentTest extends CDKTestCase {

    public KabschAlignmentTest(String name)
    {
    	super(name);
    }
    /**
     * Defines a set of tests that can be used in automatic regression testing
     * with JUnit.
     */
    public static Test suite() {
        TestSuite suite = new TestSuite(KabschAlignmentTest.class);
        return suite;
    }
    
    public void testAlign() throws ClassNotFoundException, CDKException, java.lang.Exception{
        IAtomContainer ac;
        String filename = "data/hin/gravindex.hin";
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        IChemObjectReader reader = new HINReader(ins);
        ChemFile content = (ChemFile)reader.read((ChemObject)new ChemFile());
        List cList = ChemFileManipulator.getAllAtomContainers(content);
        ac = (IAtomContainer) cList.get(0);

        KabschAlignment ka = new KabschAlignment(ac,ac);
        ka.align();
        double rmsd = ka.getRMSD();
        assertTrue(1e-8 > rmsd);
        assertNotNull(ka.getRotationMatrix());

        double[][] p1 = {
            {16.754  ,20.462  ,45.049  },
            {19.609  ,18.145  ,46.011  },
            {17.101  ,17.256  ,48.707  },
            {13.963  ,18.314  ,46.820  },
            {14.151  ,15.343  ,44.482  },
            {14.959  ,12.459  ,46.880  },
            {11.987  ,13.842  ,48.862  },
            {9.586  ,12.770  ,46.123  },
            {11.006   ,9.245  ,46.116  },
            {10.755   ,9.090  ,49.885  }
        };
        double[][] p2 = {
            {70.246 ,317.510 ,188.263  },
            {73.457 ,317.369 ,190.340  },
            {71.257 ,318.976 ,193.018  },
            {68.053 ,317.543 ,191.651  },
            {68.786 ,313.954 ,192.637  },
            {70.248 ,314.486 ,196.151  },
            {67.115 ,316.584 ,196.561  },
            {64.806 ,313.610 ,196.423  },
            {66.804 ,311.735 ,199.035  },
            {66.863 ,314.832 ,201.113  }
        };
        Atom[] a1 = new Atom[10];
        Atom[] a2 = new Atom[10];
        for (int i = 0; i < 10; i++) {
            a1[i] = new Atom("C");
            Point3d newCoord = new Point3d();
            newCoord.x = p1[i][0];
            newCoord.y = p1[i][1];
            newCoord.z = p1[i][2];
            a1[i].setPoint3d(newCoord);
            a2[i] = new Atom("C");
            newCoord = new Point3d();
            newCoord.x = p2[i][0];
            newCoord.y = p2[i][1];
            newCoord.z = p2[i][2];
            a2[i].setPoint3d(newCoord);
        }
        ka = new KabschAlignment(a1,a2);
        ka.align();
        rmsd = ka.getRMSD();
        assertEquals(0.13479726, rmsd, 0.00000001);
    }
    
}