parsertest.java

化学图形处理软件

/* $Revision: 8325 $ $Author: djiao $ $Date: 2007-05-11 18:06:18 +0000 (Fr, 11 Mai 2007) $
 * 
 * Copyright (C) 2004-2007  Egon Willighagen <[e-mail]>
 *
 * 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.smarts;

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

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond;
import org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond;
import org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond;
import org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.smiles.smarts.SMARTSParser;
import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
import org.openscience.cdk.test.CDKTestCase;

/**
 * JUnit test routines for the SMARTS parser.
 *
 * @cdk.module  test-smarts
 * @cdk.require ant1.6
 *
 * @author      Egon Willighagen
 */
public class ParserTest extends CDKTestCase {
    
    public ParserTest() {}

    public ParserTest(String testName) {
        super(testName);
    }
    
    public static Test suite() {
        return new TestSuite(ParserTest.class);
    }
    
    public void parse(String smarts) throws Exception {
    	SMARTSParser.parse(smarts);
    }

    public int match(String smarts, String smiles) throws Exception {
   	 SMARTSQueryTool sqt = new SMARTSQueryTool(smarts);
   	 SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
   	 IAtomContainer atomContainer = sp.parseSmiles(smiles);  
   	 boolean status = sqt.matches(atomContainer);
   	 if (status) {
   		 int nmatch = sqt.countMatches();
   		 return nmatch;
   	 } else {
   		 return 0;
   	 }
   }
    
    public void testQueryAtomCreation() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("*");
    	assertEquals(1, container.getAtomCount());
    	org.openscience.cdk.interfaces.IAtom atom = container.getAtom(0);
    	assertTrue(atom instanceof SMARTSAtom);
    }

    public void testAliphaticAtom() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("A");
    	assertEquals(1, container.getAtomCount());
    	org.openscience.cdk.interfaces.IAtom atom = container.getAtom(0);
    	assertTrue(atom instanceof SMARTSAtom);
    }

    public void testAromaticAtom() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("a");
    	assertEquals(1, container.getAtomCount());
    	org.openscience.cdk.interfaces.IAtom atom = container.getAtom(0);
    	assertTrue(atom instanceof SMARTSAtom);
    }

    public void testDegree() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("[D2]");
    	assertEquals(1, container.getAtomCount());
    	org.openscience.cdk.interfaces.IAtom atom = container.getAtom(0);
    	assertTrue(atom instanceof SMARTSAtom);
    }

    public void testImplicitHCount() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("[h3]");
    	assertEquals(1, container.getAtomCount());
    	org.openscience.cdk.interfaces.IAtom atom = container.getAtom(0);
    	assertTrue(atom instanceof SMARTSAtom);
    }

    public void testTotalHCount() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("[H2]");
    	assertEquals(1, container.getAtomCount());
    	org.openscience.cdk.interfaces.IAtom atom = container.getAtom(0);
    	assertTrue(atom instanceof SMARTSAtom);
    }

    public void testSingleBond() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("C-C");
    	assertEquals(2, container.getAtomCount());
    	assertEquals(1, container.getBondCount());
    	org.openscience.cdk.interfaces.IBond bond = container.getBond(0);
    	assertTrue(bond instanceof OrderQueryBond);
    	OrderQueryBond qBond = (OrderQueryBond)bond;
    	assertEquals(1.0, qBond.getOrder(), 0.001);
    }

    public void testDoubleBond() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("C=C");
    	assertEquals(2, container.getAtomCount());
    	assertEquals(1, container.getBondCount());
    	org.openscience.cdk.interfaces.IBond bond = container.getBond(0);
    	assertTrue(bond instanceof OrderQueryBond);
    	OrderQueryBond qBond = (OrderQueryBond)bond;
    	assertEquals(2.0, qBond.getOrder(), 0.001);
    }

    public void testTripleBond() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("C#C");
    	assertEquals(2, container.getAtomCount());
    	assertEquals(1, container.getBondCount());
    	org.openscience.cdk.interfaces.IBond bond = container.getBond(0);
    	assertTrue(bond instanceof OrderQueryBond);
    	OrderQueryBond qBond = (OrderQueryBond)bond;
    	assertEquals(3.0, qBond.getOrder(), 0.001);
    }

    public void testAromaticBond() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("C:C");
    	assertEquals(2, container.getAtomCount());
    	assertEquals(1, container.getBondCount());
    	org.openscience.cdk.interfaces.IBond bond = container.getBond(0);
    	assertTrue(bond instanceof AromaticQueryBond);
    }

    public void testAnyOrderBond() throws Exception {
    	QueryAtomContainer container = SMARTSParser.parse("C~C");
    	assertEquals(2, container.getAtomCount());
    	assertEquals(1, container.getBondCount());
    	org.openscience.cdk.interfaces.IBond bond = container.getBond(0);
    	assertTrue(bond instanceof AnyOrderQueryBond);
    }

    /**
     * From http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=parsertest.java.
     */
    public void testPattern1() throws Exception {
        parse("[CX4]");
    }
    public void testPattern2() throws Exception {
        parse("[$([CX2](=C)=C)]");
    }
    public void testPattern3() throws Exception {
        parse("[$([CX3]=[CX3])]");
    }
    public void testPattern4() throws Exception {
        parse("[$([CX2]#C)]");
    }
    public void testPattern5() throws Exception {
        parse("[CX3]=[OX1]");
    }
    public void testPattern6() throws Exception {
        parse("[$([CX3]=[OX1]),$([CX3+]-[OX1-])]");
    }
    public void testPattern7() throws Exception {
        parse("[CX3](=[OX1])C");
    }
    public void testPattern8() throws Exception {
        parse("[OX1]=CN");
    }
    public void testPattern9() throws Exception {
        parse("[CX3](=[OX1])O");
    }
    public void testPattern10() throws Exception {
        parse("[CX3](=[OX1])[F,Cl,Br,I]");
    }
    public void testPattern11() throws Exception {
        parse("[CX3H1](=O)[#6]");
    }
    public void testPattern12() throws Exception {
        parse("[CX3](=[OX1])[OX2][CX3](=[OX1])");
    }
    public void testPattern13() throws Exception {
        parse("[NX3][CX3](=[OX1])[#6]");
    }
    public void testPattern14() throws Exception {
        parse("[NX3][CX3]=[NX3+]");
    }
    public void testPattern15() throws Exception {
        parse("[NX3,NX4+][CX3](=[OX1])[OX2,OX1-]");
    }
    public void testPattern16() throws Exception {
        parse("[NX3][CX3](=[OX1])[OX2H0]");
    }
    public void testPattern17() throws Exception {
        parse("[NX3,NX4+][CX3](=[OX1])[OX2H,OX1-]");
    }
    public void testPattern18() throws Exception {
        parse("[CX3](=O)[O-]");
    }
    public void testPattern19() throws Exception {
        parse("[CX3](=[OX1])(O)O");
    }
    public void testPattern20() throws Exception {
        parse("[CX3](=[OX1])([OX2])[OX2H,OX1H0-1]");
    }
    public void testPattern21() throws Exception {
        parse("[CX3](=O)[OX2H1]");
    }
    public void testPattern22() throws Exception {
        parse("[CX3](=O)[OX1H0-,OX2H1]");
    }
    public void testPattern23() throws Exception {
        parse("[NX3][CX2]#[NX1]");
    }
    public void testPattern24() throws Exception {
        parse("[#6][CX3](=O)[OX2H0][#6]");
    }
    public void testPattern25() throws Exception {
        parse("[#6][CX3](=O)[#6]");
    }
    public void testPattern26() throws Exception {
        parse("[OD2]([#6])[#6]");
    }
    public void testPattern27() throws Exception {
        parse("[H]");
    }
    public void testPattern28() throws Exception {
        parse("[!#1]");
    }
    public void testPattern29() throws Exception {
        parse("[H+]");
    }
    public void testPattern30() throws Exception {
        parse("[+H]");
    }
    public void testPattern31() throws Exception {
        parse("[NX3;H2,H1;!$(NC=O)]");
    }
    public void testPattern32() throws Exception {
        parse("[NX3][CX3]=[CX3]");
    }
    public void testPattern33() throws Exception {
        parse("[NX3;H2,H1;!$(NC=O)].[NX3;H2,H1;!$(NC=O)]");
    }
    public void testPattern34() throws Exception {
        parse("[NX3][$(C=C),$(cc)]");
    }
    public void testPattern35() throws Exception {
        parse("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]");
    }
    public void testPattern36() throws Exception {
        parse("[NX3H2,NH3X4+][CX4H]([*])[CX3](=[OX1])[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-]");
    }
    public void testPattern37() throws Exception {
        parse("[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N]");
    }
    public void testPattern38() throws Exception {
        parse("[CH3X4]");
    }
    public void testPattern39() throws Exception {
        parse("[CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]");
    }
    public void testPattern40() throws Exception {
        parse("[CH2X4][CX3](=[OX1])[NX3H2]");
    }
    public void testPattern41() throws Exception {
        parse("[CH2X4][CX3](=[OX1])[OH0-,OH]");
    }
    public void testPattern42() throws Exception {
        parse("[CH2X4][SX2H,SX1H0-]");
    }
    public void testPattern43() throws Exception {
        parse("[CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]");
    }
    public void testPattern44() throws Exception {
        parse("[$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N])]");
    }
    public void testPattern45() throws Exception {
        parse("[CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1");
    }
    public void testPattern47() throws Exception {
        parse("[CHX4]([CH3X4])[CH2X4][CH3X4]");
    }
    public void testPattern48() throws Exception {
        parse("[CH2X4][CHX4]([CH3X4])[CH3X4]");
    }
    public void testPattern49() throws Exception {
        parse("[CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]");
    }
    public void testPattern50() throws Exception {
        parse("[CH2X4][CH2X4][SX2][CH3X4]");
    }
    public void testPattern51() throws Exception {
        parse("[CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1");
    }
    public void testPattern52() throws Exception {
        parse("[$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]");
    }
    public void testPattern53() throws Exception {
        parse("[CH2X4][OX2H]");
    }
    public void testPattern54() throws Exception {
        parse("[NX3][CX3]=[SX1]");
    }
    public void testPattern55() throws Exception {
        parse("[CHX4]([CH3X4])[OX2H]");
    }
    public void testPattern56() throws Exception {
        parse("[CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12");
    }
    public void testPattern57() throws Exception {
        parse("[CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1");
    }
    public void testPattern58() throws Exception {
        parse("[CHX4]([CH3X4])[CH3X4]");
    }
    public void testPattern59() throws Exception {
        parse("[CH3X4]");
    }
    public void testPattern60() throws Exception {
        parse("[CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]");
    }
    public void testPattern61() throws Exception {
        parse("[CH2X4][CX3](=[OX1])[NX3H2]");
    }
    public void testPattern62() throws Exception {
        parse("[CH2X4][CX3](=[OX1])[OH0-,OH]");
    }
    public void testPattern63() throws Exception {
        parse("[CH2X4][SX2H,SX1H0-]");
    }
    public void testPattern64() throws Exception {
        parse("[CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]");