smilesgeneratortest.java

化学图形处理软件

/*  $RCSfile$
 *  $Author: shk3 $
 *  $Date: 2007-05-01 15:50:23 +0000 (Di, 01 Mai 2007) $
 *  $Revision: 8287 $
 *
 *  Copyright (C) 1997-2007  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.smiles;

import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.io.StringWriter;

import javax.vecmath.Point2d;

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

import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.PseudoAtom;
import org.openscience.cdk.Reaction;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.graph.AtomContainerAtomPermutor;
import org.openscience.cdk.graph.AtomContainerBondPermutor;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.CMLReader;
import org.openscience.cdk.io.CMLWriter;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.layout.HydrogenPlacer;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.smiles.SmilesGenerator;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

/**
 * @author         steinbeck
 * @cdk.created    2004-02-09
 * @cdk.module     test-smiles
 */
public class SmilesGeneratorTest extends CDKTestCase {
	
	/**
	 *  Constructor for the SmilesGeneratorTest object
	 *
	 *@param  name  Description of the Parameter
	 */
	public SmilesGeneratorTest(String name)
	{
		super(name);
	}


	/**
	 *  A unit test suite for JUnit
	 *
	 *@return    The test suite
	 */
	public static Test suite()
	{
		return new TestSuite(SmilesGeneratorTest.class);
	}

	/**
	 *  A unit test for JUnit
	 */
	public void testSmilesGenerator()
	{
        Molecule mol2 = MoleculeFactory.makeAlphaPinene();
		SmilesGenerator sg = new SmilesGenerator();
		fixCarbonHCount(mol2);
		String smiles2 = sg.createSMILES(mol2);
		assertNotNull(smiles2);
		assertEquals("C1=C(C)C2CC(C1)C2(C)(C)", smiles2);
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testEthylPropylPhenantren()
	{
		Molecule mol1 = MoleculeFactory.makeEthylPropylPhenantren();
        SmilesGenerator sg = new SmilesGenerator();
		fixCarbonHCount(mol1);
		String smiles1 = sg.createSMILES(mol1);
		assertNotNull(smiles1);
		assertEquals("C=2C=C1C=3C=CC(=CC=3(C=CC1=C(C=2)CC))CCC", smiles1);
	}

	
	
	/**
	 *  A unit test for JUnit
	 */
	public void testPropylCycloPropane()
	{
		Molecule mol1 = MoleculeFactory.makePropylCycloPropane();
        SmilesGenerator sg = new SmilesGenerator();
		fixCarbonHCount(mol1);
		String smiles1 = sg.createSMILES(mol1);
		assertNotNull(smiles1);
		assertEquals("CCCC1CC1", smiles1);
	}
	
	

	/**
	 *  A unit test for JUnit
	 *
	 */
	public void testAlanin() throws Exception
	{
		HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
        Molecule mol1 = new Molecule();
		SmilesGenerator sg = new SmilesGenerator();
		mol1.addAtom(new Atom("N", new Point2d(1, 0)));
		// 1
		mol1.addAtom(new Atom("C", new Point2d(1, 2)));
		// 2
		mol1.addAtom(new Atom("F", new Point2d(1, 2)));
		// 3
		mol1.addAtom(new Atom("C", new Point2d(0, 0)));
		// 4
		mol1.addAtom(new Atom("C", new Point2d(1, 4)));
		// 5
		mol1.addAtom(new Atom("O", new Point2d(1, 5)));
		// 6
		mol1.addAtom(new Atom("O", new Point2d(1, 6)));
		// 7
		mol1.addBond(0, 1, 1);
		// 1
		mol1.addBond(1, 2, 1, CDKConstants.STEREO_BOND_UP);
		// 2
		mol1.addBond(1, 3, 1, CDKConstants.STEREO_BOND_DOWN);
		// 3
		mol1.addBond(1, 4, 1);
		// 4
		mol1.addBond(4, 5, 1);
		// 5
		mol1.addBond(4, 6, 2);
		// 6
		new HydrogenAdder().addHydrogensToSatisfyValency(mol1);
		hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
		IsotopeFactory ifac = IsotopeFactory.getInstance(mol1.getBuilder());
		ifac.configureAtoms(mol1);

		String smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
		assertNotNull(smiles1);
		assertEquals("[H]OC(=O)[C@](F)(N([H])[H])C([H])([H])[H]", smiles1);
		
		//by setting additional stereo descriptors, we should get another smiles
		mol1.getBond(1).setStereo(CDKConstants.STEREO_BOND_DOWN);
		mol1.getBond(2).setStereo(CDKConstants.STEREO_BOND_UP);
		smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
		assertNotNull(smiles1);
		assertEquals("[H]OC(=O)[C@](F)(C([H])([H])[H])N([H])[H]", smiles1);
	}


	/**
	 *  A unit test for JUnit
	 *
	 *@exception  Exception  Description of the Exception
	 */
	public void testCisResorcinol() throws Exception
	{
		HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
        Molecule mol1 = new Molecule();
		SmilesGenerator sg = new SmilesGenerator();
		mol1.addAtom(new Atom("O", new Point2d(3, 1)));
		// 1
		mol1.addAtom(new Atom("H", new Point2d(2, 0)));
		// 2
		mol1.addAtom(new Atom("C", new Point2d(2, 1)));
		// 3
		mol1.addAtom(new Atom("C", new Point2d(1, 1)));
		// 4
		mol1.addAtom(new Atom("C", new Point2d(1, 4)));
		// 5
		mol1.addAtom(new Atom("C", new Point2d(1, 5)));
		// 6
		mol1.addAtom(new Atom("C", new Point2d(1, 2)));
		// 7
		mol1.addAtom(new Atom("C", new Point2d(2, 2)));
		// 1
		mol1.addAtom(new Atom("O", new Point2d(3, 2)));
		// 2
		mol1.addAtom(new Atom("H", new Point2d(2, 3)));
		// 3
		mol1.addBond(0, 2, 1, CDKConstants.STEREO_BOND_DOWN);
		// 1
		mol1.addBond(1, 2, 1, CDKConstants.STEREO_BOND_UP);
		// 2
		mol1.addBond(2, 3, 1);
		// 3
		mol1.addBond(3, 4, 1);
		// 4
		mol1.addBond(4, 5, 1);
		// 5
		mol1.addBond(5, 6, 1);
		// 6
		mol1.addBond(6, 7, 1);
		// 3
		mol1.addBond(7, 8, 1, CDKConstants.STEREO_BOND_UP);
		// 4
		mol1.addBond(7, 9, 1, CDKConstants.STEREO_BOND_DOWN);
		// 5
		mol1.addBond(7, 2, 1);
		// 6
		new HydrogenAdder().addHydrogensToSatisfyValency(mol1);
		hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
		IsotopeFactory ifac = IsotopeFactory.getInstance(mol1.getBuilder());
		ifac.configureAtoms(mol1);
		String smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
		assertNotNull(smiles1);
		assertEquals("[H]O[C@]1(C([H])([H])C([H])([H])C([H])([H])C([H])([H])[C@]1(O[H])([H]))([H])", smiles1);
		mol1 = (Molecule) AtomContainerManipulator.removeHydrogens(mol1);
		smiles1 = sg.createSMILES(mol1);
		assertNotNull(smiles1);
		assertEquals("OC1CCCCC1(O)", smiles1);
	}


	/**
	 *  A unit test for JUnit
	 *
	 *@exception  Exception  Description of the Exception
	 */
	public void testCisTransDecalin() throws Exception
	{
		HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
        Molecule mol1 = new Molecule();
		SmilesGenerator sg = new SmilesGenerator();
		mol1.addAtom(new Atom("H", new Point2d(1, 0)));
		// 1
		mol1.addAtom(new Atom("C", new Point2d(1, 2)));
		// 2
		mol1.addAtom(new Atom("C", new Point2d(1, 2)));
		// 3
		mol1.addAtom(new Atom("C", new Point2d(0, 0)));
		// 4
		mol1.addAtom(new Atom("C", new Point2d(1, 4)));
		// 5
		mol1.addAtom(new Atom("C", new Point2d(1, 5)));
		// 6
		mol1.addAtom(new Atom("C", new Point2d(1, 6)));
		// 7
		mol1.addAtom(new Atom("H", new Point2d(1, 0)));
		// 1
		mol1.addAtom(new Atom("C", new Point2d(1, 2)));
		// 2
		mol1.addAtom(new Atom("C", new Point2d(1, 2)));
		// 3
		mol1.addAtom(new Atom("C", new Point2d(1, 2)));
		// 2
		mol1.addAtom(new Atom("C", new Point2d(1, 2)));
		// 3
		mol1.addBond(0, 1, 1, CDKConstants.STEREO_BOND_DOWN);
		// 1
		mol1.addBond(1, 2, 1);
		// 2
		mol1.addBond(2, 3, 1);
		// 3
		mol1.addBond(3, 4, 1);
		// 4
		mol1.addBond(4, 5, 1);
		// 5
		mol1.addBond(5, 6, 1);
		// 6
		mol1.addBond(6, 7, 1, CDKConstants.STEREO_BOND_DOWN);
		// 3
		mol1.addBond(6, 8, 1);
		// 4
		mol1.addBond(8, 9, 1);
		// 5
		mol1.addBond(9, 10, 1);
		// 6
		mol1.addBond(10, 11, 1);
		// 6
		mol1.addBond(11, 1, 1);
		// 6
		mol1.addBond(1, 6, 1);
		// 6

		new HydrogenAdder().addHydrogensToSatisfyValency(mol1);
		hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
		IsotopeFactory ifac = IsotopeFactory.getInstance(mol1.getBuilder());
		ifac.configureAtoms(mol1);
		String smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
		assertNotNull(smiles1);
		assertEquals("[H]C1([H])(C([H])([H])C([H])([H])C\\2([H])(C([H])([H])C([H])([H])C([H])([H])C([H])([H])C\\2([H])(C1([H])([H]))))", smiles1);
		mol1.getBond(6).setStereo(CDKConstants.STEREO_BOND_UP);
		String smiles3 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
		assertNotSame(smiles1, smiles3);
	}


	/**
	 *  A unit test for JUnit
	 *
	 *@exception  Exception  Description of the Exception
	 */
	public void testDoubleBondConfiguration() throws Exception
	{
		HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
		Molecule mol1 = new Molecule();
        SmilesGenerator sg = new SmilesGenerator();
		mol1.addAtom(new Atom("S", new Point2d(0, 0)));
		// 1
		mol1.addAtom(new Atom("C", new Point2d(1, 1)));
		// 2
		mol1.addAtom(new Atom("F", new Point2d(2, 0)));
		// 3
		mol1.addAtom(new Atom("C", new Point2d(1, 2)));
		// 4
		mol1.addAtom(new Atom("F", new Point2d(2, 3)));
		// 5
		mol1.addAtom(new Atom("S", new Point2d(0, 3)));
		// 1

		mol1.addBond(0, 1, 1);
		// 1
		mol1.addBond(1, 2, 1);
		// 2
		mol1.addBond(1, 3, 2);
		// 3
		mol1.addBond(3, 4, 1);
		// 4
		mol1.addBond(3, 5, 1);
		// 4
		IsotopeFactory ifac = IsotopeFactory.getInstance(mol1.getBuilder());
		ifac.configureAtoms(mol1);
		boolean[] bool = new boolean[mol1.getBondCount()];
		bool[2] = true;
		String smiles1 = sg.createSMILES(mol1, true, bool);
		assertNotNull(smiles1);
		assertTrue(smiles1.equals("F/C(=C/(F)S)S"));
		mol1.getAtom(4).setPoint2d(new Point2d(0, 3));
		mol1.getAtom(5).setPoint2d(new Point2d(2, 3));
		
		smiles1 = sg.createSMILES(mol1, true, bool);
		assertNotNull(smiles1);
		assertTrue(smiles1.equals("F/C(=C\\(F)S)S"));

		new HydrogenAdder().addHydrogensToSatisfyValency(mol1);
		hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
		bool = new boolean[mol1.getBondCount()];
		bool[2] = true;
		smiles1 = sg.createSMILES(mol1, true, bool);
		assertTrue(smiles1.equals("[H]S/C(F)=C/(F)S[H]"));
		
		mol1.getAtom(5).setPoint2d(new Point2d(0, 3));
		mol1.getAtom(4).setPoint2d(new Point2d(2, 3));
		smiles1 = sg.createSMILES(mol1, true, bool);
		assertTrue(smiles1.equals("[H]S/C(F)=C\\(F)S[H]"));
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testPartitioning()
	{
		String smiles = "";
		Molecule molecule = new Molecule();
        SmilesGenerator sg = new SmilesGenerator();
		Atom sodium = new Atom("Na");
		sodium.setFormalCharge(+1);
		Atom hydroxyl = new Atom("O");