aminoacidcountdescriptortest.java

化学图形处理软件

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-06-26 09:17:24 +0000 (Di, 26 Jun 2007) $
 * $Revision: 8424 $
 * 
 * Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
 * 
 * Contact: [e-mail]
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. 
 */
package org.openscience.cdk.test.qsar.descriptors.molecular;

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

import org.openscience.cdk.BioPolymer;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.qsar.result.IntegerArrayResult;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.ProteinBuilderTool;

/**
 * TestSuite that runs a test for the AtomCountDescriptor.
 *
 * @cdk.module test-qsar
 */
 
public class AminoAcidCountDescriptorTest extends CDKTestCase {
	
	public  AminoAcidCountDescriptorTest() {}
    
	public static Test suite() {
		return new TestSuite(AminoAcidCountDescriptorTest.class);
	}
    
	public void testAACount() throws CDKException {
        IMolecularDescriptor descriptor = new AminoAcidCountDescriptor();
        
        BioPolymer protein = ProteinBuilderTool.createProtein("ARNDCFQEGHIPLKMSTYVW");
        IDescriptorResult result = descriptor.calculate(protein).getValue();
        assertTrue(result instanceof IntegerArrayResult);
        IntegerArrayResult iaResult = (IntegerArrayResult)result;
        for (int i=0; i<iaResult.length(); i++) {
        	assertTrue(iaResult.get(i) >= 1); // all AAs are found at least once
        }
        assertEquals(20, iaResult.get(8)); // glycine is in all of them, so 20 times
	}

	public void testFCount() throws CDKException {
        IMolecularDescriptor descriptor = new AminoAcidCountDescriptor();
        
        BioPolymer protein = ProteinBuilderTool.createProtein("FF");
        IDescriptorResult result = descriptor.calculate(protein).getValue();
        assertTrue(result instanceof IntegerArrayResult);
        IntegerArrayResult iaResult = (IntegerArrayResult)result;
        assertEquals(2, iaResult.get(8));
        assertEquals(4, iaResult.get(5)); // thingy is symmetrical, so two mappings at each AA position possible
	}

	public void testTCount() throws CDKException {
        IMolecularDescriptor descriptor = new AminoAcidCountDescriptor();
        
        BioPolymer protein = ProteinBuilderTool.createProtein("TT");
        IDescriptorResult result = descriptor.calculate(protein).getValue();
        assertTrue(result instanceof IntegerArrayResult);
        IntegerArrayResult iaResult = (IntegerArrayResult)result;
        assertEquals(2, iaResult.get(8));
        assertEquals(2, iaResult.get(16));
	}
}