smilesparsertest.java

化学图形处理软件

/* $Revision: 8332 $ $Author: shk3 $ $Date: 2007-05-15 13:25:07 +0000 (Di, 15 Mai 2007) $
 *
 *  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.util.Iterator;
import java.util.List;

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

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.isomorphism.IsomorphismTester;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.test.CDKTestCase;

/**
 * Please see the test.gui package for visual feedback on tests.
 * 
 * @author         steinbeck
 * @cdk.module     test-smiles
 * @cdk.created    2003-09-19
 * 
 * @see org.openscience.cdk.test.gui.SmilesParserTest
 */
public class SmilesParserTest extends CDKTestCase {
	
	private SmilesParser sp;

	/**
	 *  Constructor for the SmilesParserTest object
	 */
	public SmilesParserTest(String name) {
		super(name);
	}

	public void setUp() {
		sp = new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
	}

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

	
	public void testPyridine_N_oxideUncharged() throws Exception {
		String smiles = "O=n1ccccc1";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(7, mol.getAtomCount());
	}
	
	public void testPyridine_N_oxideCharged() throws Exception {
		String smiles = "[O-][n+]1ccccc1";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(7, mol.getAtomCount());
	}

	/*
	 * The next methods tests compounds with several conjugated rings
	 * These compounds would not fail if the Aromaticity Detection was changed
	 * so that a ring is aromatic if all the atoms in a ring have already been flagged
	 * as aromatic from the testing of other rings in the system.
	 */
	public void testUnusualConjugatedRings() throws Exception {		
		//7090-41-7:
		String smiles = "c1(Cl)cc2c3cc(Cl)c(Cl)cc3c2cc1Cl";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(16, mol.getAtomCount());
	}
	
	public void testUnusualConjugatedRings_2() throws Exception {
		//206-44-0:
		String smiles = "c(c(ccc1)ccc2)(c1c(c3ccc4)c4)c23";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(16, mol.getAtomCount());
	}
	
	public void testUnusualConjugatedRings_3() throws Exception {	
		if (!super.runSlowTests()) fail("Skipped time consuming test.");
		
		//207-08-9:
		String smiles = "c2ccc1cc3c(cc1c2)c4cccc5cccc3c45";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(20, mol.getAtomCount());
	}
	
	public void testUnusualConjugatedRings_4() throws Exception {
		//2693-46-1:
		String smiles = "Nc1c(c23)cccc3c4ccccc4c2cc1";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(17, mol.getAtomCount());
	}
	
	public void testUnusualConjugatedRings_5() throws Exception {
		//205-99-2:
		String smiles = "c12ccccc1cc3c4ccccc4c5c3c2ccc5";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(20, mol.getAtomCount());
	}
	
	public void test187_78_0 () throws Exception {
		// are all 4 rings aromatic? Is smiles correct?
		String smiles = "c1c(c23)ccc(c34)ccc4ccc2c1";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(14, mol.getAtomCount());
	}
	
	public void test187_78_0_PubChem() throws Exception {
		// are all 4 rings aromatic? Is smiles correct?
		String smiles = "C1=CC2=C3C(=CC=C4C3=C1C=C4)C=C2";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(14, mol.getAtomCount());
	}

	public void test41814_78_2 () throws Exception {
		String smiles = "Cc1cccc2sc3nncn3c12";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(13, mol.getAtomCount());
	}
	
	public void test239_64_5 () throws Exception {
		String smiles = "c1ccc4c(c1)ccc5c3ccc2ccccc2c3nc45";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(21, mol.getAtomCount());
	}
	
	/*
	 * Compounds like Indolizine (274-40-8) with a fused nitrogen as part of a 6 membered ring
	 * and another ring do not parse
	 */
	public void testIndolizine () throws Exception {
		String smiles = "c2cc1cccn1cc2";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(9, mol.getAtomCount());
	}
	
	
	/**
	 *  A unit test for JUnit
	 */
	public void testSmiles1() throws Exception {
		String smiles = "C1c2c(c3c(c(O)cnc3)cc2)CC(=O)C1";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertEquals(16, molecule.getAtomCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testSmiles2() throws Exception {
		String smiles = "O=C(O3)C1=COC(OC4OC(CO)C(O)C(O)C4O)C2C1C3C=C2COC(C)=O";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertEquals(29, molecule.getAtomCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testSmiles3() throws Exception
	{
		String smiles = "CN1C=NC2=C1C(N(C)C(N2C)=O)=O";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertEquals(14, molecule.getAtomCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testSmiles4() throws Exception {
		String smiles = "CN(C)CCC2=CNC1=CC=CC(OP(O)(O)=O)=C12";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertEquals(19, molecule.getAtomCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testSmiles5() throws Exception {
		String smiles = "O=C(O)C1C(OC(C3=CC=CC=C3)=O)CC2N(C)C1CC2";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertEquals(21, molecule.getAtomCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testSmiles6() throws Exception {
		String smiles = "C1(C2(C)(C))C(C)=CCC2C1";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertEquals(10, molecule.getAtomCount());
	}

	public void testSmiles7() throws Exception {
		String smiles = "C1(C=C(C=C(C=C(C=C(C=CC%35=C%36)C%31=C%35C%32=C%33C%36=C%34)C%22=C%31C%23=C%32C%24=C%25C%33=C%26C%34=CC%27=CC%28=CC=C%29)C%14=C%22C%15=C%23C%16=C%24C%17=C%18C%25=C%19C%26=C%27C%20=C%28C%29=C%21)C6=C%14C7=C%15C8=C%16C9=C%17C%12=C%11C%18=C%10C%19=C%20C%21=CC%10=CC%11=CC(C=C%30)=C%12%13)=C(C6=C(C7=C(C8=C(C9=C%13C%30=C5)C5=C4)C4=C3)C3=C2)C2=CC=C1";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertNotNull(molecule);
	}

	public void testSmiles8() throws Exception {
		String smiles = "CC1(C(=C(CC(C1)O)C)C=CC(=CC=CC(=CC=CC=C(C=CC=C(C=CC1=C(CC(CC1(C)C)O)C)C)C)C)C)C";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertNotNull(molecule);
	}

	public void testSmiles9() throws Exception {
		String smiles = "NC(C(C)C)C(NC(C(C)O)C(NC(C(C)C)C(NC(CCC(N)=O)C(NC(CC([O-])[O-])C(NCC(NC(CC(N)=O)C(NC(Cc1ccccc1)C(NC(CO)C(NC(Cc2ccccc2)C(NC(CO)C(NC(CC(C)C)C(NC(CCC([O-])[O-])C(NC(CO)C(NC(C(C)C)C(NC(CCCC[N+])C(NC(CCCC[N+])C(NC(CC(C)C)C(NC(CCCC[N+])C(NC(CC([O-])[O-])C(NC(CC(C)C)C(NC(CCC(N)=O)C(NC(CCC([O-])[O-])C(N3CCCC3C(NC(CCC(N)=O)C(NC(CCC([O-])[O-])C(N4CCCC4C(NC(CCCNC([N+])[N+])C(NC(C(C)C)C(NCC(NC(CCCC[N+])C(NC(CC(C)C)C(NC(CCCNC([N+])[N+])C(NC(CC(N)=O)C(NC(Cc5ccccc5)C(NC(C)C(N6CCCC6C(NC(C(C)CC)C(N7CCCC7C(NCC(NC(CCC([O-])[O-])C(N8CCCC8C(NC(C(C)C)C(NC(C(C)C)C(N9CCCC9C(NC(C(C)CC)C(NC(CC(C)C)C(NC%19C[S][S]CC(C(NC(CCCC[N+])C(NC(CCC([O-])[O-])C(N%10CCCC%10C(NC(CC(N)=O)C(NC(C)C(NC(CCC(N)=O)C(NC(CCC([O-])[O-])C(NC(C(C)CC)C(NC(CC(C)C)C(NC(CCC(N)=O)C(NC(CCCNC([N+])[N+])C(NC(CC(C)C)C(NC(CCC([O-])[O-])C(NC(CCC([O-])[O-])C(NC(C(C)CC)C(NC(C)C(NC(CCC([O-])[O-])C(NC(CC([O-])[O-])C(N%11CCCC%11C(NCC(NC(C(C)O)C(NC%14C[S][S]CC%13C(NC(C(C)O)C(NCC(NC(C[S][S]CC(C(NC(C)C(NC(Cc%12ccc(O)cc%12)C(NC(C)C(NC(C)C(N%13)=O)=O)=O)=O)=O)NC(=O)C(C(C)CC)NC(=O)C(CCC([O-])[O-])NC%14=O)C(O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)NC(=O)C(CC(C)C)NC(=O)C%15CCCN%15C(=O)C(CCCC[N+])NC(=O)C(CC(C)C)NC(=O)C(CCC([O-])[O-])NC(=O)C(CCC([O-])[O-])NC(=O)C%16CCCN%16C(=O)C(Cc%17ccccc%17)NC(=O)C(CC(N)=O)NC(=O)C%18CCCN%18C(=O)C(CC(N)=O)NC(=O)C(CO)NC%19=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertNotNull(molecule);
	}

	/**
	 * @cdk.bug 1296113
	 */
	public void testSFBug1296113() throws Exception {
		String smiles = "S(=O)(=O)(-O)-c1c2c(c(ccc2-N-c2ccccc2)-N=N-c2c3c(c(cc2)-N=N-c2c4c(c(ccc4)-S(=O)(=O)-O)ccc2)cccc3)ccc1";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertNotNull(molecule);
	}

    /**
     * @cdk.bug 1324105
     */
    public void testAromaticSmiles2() throws Exception {
    	String smiles = "n12:n:n:n:c:2:c:c:c:c:1";
    	IMolecule molecule = sp.parseSmiles(smiles);
    	Iterator bonds = molecule.bonds();
    	while (bonds.hasNext()) assertTrue(((IBond)bonds.next()).getFlag(CDKConstants.ISAROMATIC));
    }

	/**
	 *  A unit test for JUnit
	 */
	public void testAromaticSmilesWithCharge() throws Exception {
		String smiles = "c1cc[c-]cc1";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertTrue(molecule.getAtom(0).getFlag(CDKConstants.ISAROMATIC));
		assertTrue(molecule.getBond(0).getFlag(CDKConstants.ISAROMATIC));
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testAromaticSmiles() throws Exception {
		String smiles = "c1ccccc1";
		IMolecule molecule = sp.parseSmiles(smiles);
		assertTrue(molecule.getAtom(0).getFlag(CDKConstants.ISAROMATIC));
		assertTrue(molecule.getBond(0).getFlag(CDKConstants.ISAROMATIC));
	}
	
	
	/**
	 * @cdk.bug 630475
	 */
	public void testSFBug630475() throws Exception {
		String smiles = "CC1(C(=C(CC(C1)O)C)C=CC(=CC=CC(=CC=CC=C(C=CC=C(C=CC1=C(CC(CC1(C)C)O)C)C)C)C)C)C";
		IMolecule mol = sp.parseSmiles(smiles);
		assertTrue(mol.getAtomCount() > 0);
	}


	/**
	 * @cdk.bug 585811
	 */
	public void testSFBug585811() throws Exception {
		String smiles = "CC(C(C8CCC(CC8)=O)C3C4C(CC5(CCC(C9=CC(C=CN%10)=C%10C=C9)CCCC5)C4)C2CCC1CCC7(CCC7)C6(CC6)C1C2C3)=O";
		IMolecule mol = sp.parseSmiles(smiles);
		assertTrue(mol.getAtomCount() > 0);
	}


	/**
	 * @cdk.bug 593648
	 */
	public void testSFBug593648() throws Exception {
		String smiles = "CC1=CCC2CC1C(C)2C";
		IMolecule mol = sp.parseSmiles(smiles);
		
		IMolecule apinene = mol.getBuilder().newMolecule();
		apinene.addAtom(mol.getBuilder().newAtom("C"));
		// 1
		apinene.addAtom(mol.getBuilder().newAtom("C"));
		// 2
		apinene.addAtom(mol.getBuilder().newAtom("C"));
		// 3
		apinene.addAtom(mol.getBuilder().newAtom("C"));
		// 4
		apinene.addAtom(mol.getBuilder().newAtom("C"));
		// 5
		apinene.addAtom(mol.getBuilder().newAtom("C"));
		// 6
		apinene.addAtom(mol.getBuilder().newAtom("C"));
		// 7
		apinene.addAtom(mol.getBuilder().newAtom("C"));
		// 8
		apinene.addAtom(mol.getBuilder().newAtom("C"));
		// 9
		apinene.addAtom(mol.getBuilder().newAtom("C"));
		// 10
		
		apinene.addBond(0, 1, 2.0);
		// 1
		apinene.addBond(1, 2, 1.0);
		// 2
		apinene.addBond(2, 3, 1.0);
		// 3
		apinene.addBond(3, 4, 1.0);
		// 4
		apinene.addBond(4, 5, 1.0);
		// 5
		apinene.addBond(5, 0, 1.0);
		// 6