smartsqueryvisitortest.java

化学图形处理软件

package org.openscience.cdk.test.smiles.smarts.parser.visitor;

import java.io.StringReader;

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

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
import org.openscience.cdk.smiles.smarts.parser.ASTStart;
import org.openscience.cdk.smiles.smarts.parser.SMARTSParser;
import org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor;
import org.openscience.cdk.test.CDKTestCase;

/**
 * JUnit testing routine for SmartsQueryVisitor
 *
 * @author Dazhi Jiao
 * @cdk.created 2007-05-10
 * @cdk.module test-smarts
 * @cdk.keyword SMARTS 
 */
public class SmartsQueryVisitorTest extends CDKTestCase {
    public SmartsQueryVisitorTest() {}

    public SmartsQueryVisitorTest(String testName) {
        super(testName);
    }
    
    public static Test suite() {
        return new TestSuite(SmartsQueryVisitorTest.class);
    }
    
    public void visit(String smarts) throws Exception {
    	SMARTSParser parser = new SMARTSParser(new StringReader(smarts));
    	ASTStart start = parser.Start();
    	SmartsQueryVisitor visitor = new SmartsQueryVisitor();
    	visitor.visit(start, null);
    }
    
    public int match(String smarts, String smiles) throws Exception {
    	 SMARTSQueryTool sqt = new SMARTSQueryTool(smarts, true);
    	 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 testPattern1() throws Exception {
        visit("[CX4]");
    }
    public void testPattern2() throws Exception {
        visit("[$([CX2](=C)=C)]");
    }
    public void testPattern3() throws Exception {
        visit("[$([CX3]=[CX3])]");
    }
    public void testPattern4() throws Exception {
        visit("[$([CX2]#C)]");
    }
    public void testPattern5() throws Exception {
        visit("[CX3]=[OX1]");
    }
    public void testPattern6() throws Exception {
        visit("[$([CX3]=[OX1]),$([CX3+]-[OX1-])]");
    }
    public void testPattern7() throws Exception {
        visit("[CX3](=[OX1])C");
    }
    public void testPattern8() throws Exception {
        visit("[OX1]=CN");
    }
    public void testPattern9() throws Exception {
        visit("[CX3](=[OX1])O");
    }
    public void testPattern10() throws Exception {
        visit("[CX3](=[OX1])[F,Cl,Br,I]");
    }
    public void testPattern11() throws Exception {
        visit("[CX3H1](=O)[#6]");
    }
    public void testPattern12() throws Exception {
        visit("[CX3](=[OX1])[OX2][CX3](=[OX1])");
    }
    public void testPattern13() throws Exception {
        visit("[NX3][CX3](=[OX1])[#6]");
    }
    public void testPattern14() throws Exception {
        visit("[NX3][CX3]=[NX3+]");
    }
    public void testPattern15() throws Exception {
        visit("[NX3,NX4+][CX3](=[OX1])[OX2,OX1-]");
    }
    public void testPattern16() throws Exception {
        visit("[NX3][CX3](=[OX1])[OX2H0]");
    }
    public void testPattern17() throws Exception {
        visit("[NX3,NX4+][CX3](=[OX1])[OX2H,OX1-]");
    }
    public void testPattern18() throws Exception {
        visit("[CX3](=O)[O-]");
    }
    public void testPattern19() throws Exception {
        visit("[CX3](=[OX1])(O)O");
    }
    public void testPattern20() throws Exception {
        visit("[CX3](=[OX1])([OX2])[OX2H,OX1H0-1]");
    }
    public void testPattern21() throws Exception {
        visit("[CX3](=O)[OX2H1]");
    }
    public void testPattern22() throws Exception {
        visit("[CX3](=O)[OX1H0-,OX2H1]");
    }
    public void testPattern23() throws Exception {
        visit("[NX3][CX2]#[NX1]");
    }
    public void testPattern24() throws Exception {
        visit("[#6][CX3](=O)[OX2H0][#6]");
    }
    public void testPattern25() throws Exception {
        visit("[#6][CX3](=O)[#6]");
    }
    public void testPattern26() throws Exception {
        visit("[OD2]([#6])[#6]");
    }
    public void testPattern27() throws Exception {
        visit("[H]");
    }
    public void testPattern28() throws Exception {
        visit("[!#1]");
    }
    public void testPattern29() throws Exception {
        visit("[H+]");
    }
    public void testPattern30() throws Exception {
        visit("[+H]");
    }
    public void testPattern31() throws Exception {
        visit("[NX3;H2,H1;!$(NC=O)]");
    }
    public void testPattern32() throws Exception {
        visit("[NX3][CX3]=[CX3]");
    }
    public void testPattern33() throws Exception {
        visit("[NX3;H2,H1;!$(NC=O)].[NX3;H2,H1;!$(NC=O)]");
    }
    public void testPattern34() throws Exception {
        visit("[NX3][$(C=C),$(cc)]");
    }
    public void testPattern35() throws Exception {
        visit("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]");
    }
    public void testPattern36() throws Exception {
        visit("[NX3H2,NH3X4+][CX4H]([*])[CX3](=[OX1])[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-]");
    }
    public void testPattern37() throws Exception {
        visit("[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N]");
    }
    public void testPattern38() throws Exception {
        visit("[CH3X4]");
    }
    public void testPattern39() throws Exception {
        visit("[CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]");
    }
    public void testPattern40() throws Exception {
        visit("[CH2X4][CX3](=[OX1])[NX3H2]");
    }
    public void testPattern41() throws Exception {
        visit("[CH2X4][CX3](=[OX1])[OH0-,OH]");
    }
    public void testPattern42() throws Exception {
        visit("[CH2X4][SX2H,SX1H0-]");
    }
    public void testPattern43() throws Exception {
        visit("[CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]");
    }
    public void testPattern44() throws Exception {
        visit("[$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N])]");
    }
    public void testPattern45() throws Exception {
        visit("[CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1");
    }
    public void testPattern47() throws Exception {
        visit("[CHX4]([CH3X4])[CH2X4][CH3X4]");
    }
    public void testPattern48() throws Exception {
        visit("[CH2X4][CHX4]([CH3X4])[CH3X4]");
    }
    public void testPattern49() throws Exception {
        visit("[CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]");
    }
    public void testPattern50() throws Exception {
        visit("[CH2X4][CH2X4][SX2][CH3X4]");
    }
    public void testPattern51() throws Exception {
        visit("[CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1");
    }
    public void testPattern52() throws Exception {
        visit("[$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]");
    }
    public void testPattern53() throws Exception {
        visit("[CH2X4][OX2H]");
    }
    public void testPattern54() throws Exception {
        visit("[NX3][CX3]=[SX1]");
    }
    public void testPattern55() throws Exception {
        visit("[CHX4]([CH3X4])[OX2H]");
    }
    public void testPattern56() throws Exception {
        visit("[CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12");
    }
    public void testPattern57() throws Exception {
        visit("[CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1");
    }
    public void testPattern58() throws Exception {
        visit("[CHX4]([CH3X4])[CH3X4]");
    }
    public void testPattern59() throws Exception {
        visit("[CH3X4]");
    }
    public void testPattern60() throws Exception {
        visit("[CH2X4][CH2X4][CH2X4][NHX3][CH0X3](=[NH2X3+,NHX2+0])[NH2X3]");
    }
    public void testPattern61() throws Exception {
        visit("[CH2X4][CX3](=[OX1])[NX3H2]");
    }
    public void testPattern62() throws Exception {
        visit("[CH2X4][CX3](=[OX1])[OH0-,OH]");
    }
    public void testPattern63() throws Exception {
        visit("[CH2X4][SX2H,SX1H0-]");
    }
    public void testPattern64() throws Exception {
        visit("[CH2X4][CH2X4][CX3](=[OX1])[OH0-,OH]");
    }
    public void testPattern65() throws Exception {
        visit("[CH2X4][#6X3]1:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]:[$([#7X3H+,#7X2H0+0]:[#6X3H]:[#7X3H]),$([#7X3H])]:[#6X3H]1");
    }
    public void testPattern67() throws Exception {
        visit("[CHX4]([CH3X4])[CH2X4][CH3X4]");
    }
    public void testPattern68() throws Exception {
        visit("[CH2X4][CHX4]([CH3X4])[CH3X4]");
    }
    public void testPattern69() throws Exception {
        visit("[CH2X4][CH2X4][CH2X4][CH2X4][NX4+,NX3+0]");
    }
    public void testPattern70() throws Exception {
        visit("[CH2X4][CH2X4][SX2][CH3X4]");
    }
    public void testPattern71() throws Exception {
        visit("[CH2X4][cX3]1[cX3H][cX3H][cX3H][cX3H][cX3H]1");
    }
    public void testPattern72() throws Exception {
        visit("[CH2X4][OX2H]");
    }
    public void testPattern73() throws Exception {
        visit("[CHX4]([CH3X4])[OX2H]");
    }
    public void testPattern74() throws Exception {
        visit("[CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12");
    }
    public void testPattern75() throws Exception {
        visit("[CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1");
    }
    public void testPattern76() throws Exception {
        visit("[CHX4]([CH3X4])[CH3X4]");
    }
    public void testPattern77() throws Exception {
        visit("[$(*-[NX2-]-[NX2+]#[NX1]),$(*-[NX2]=[NX2+]=[NX1-])]");
    }
    public void testPattern78() throws Exception {
        visit("[$([NX1-]=[NX2+]=[NX1-]),$([NX1]#[NX2+]-[NX1-2])]");
    }
    public void testPattern79() throws Exception {
        visit("[#7]");
    }
    public void testPattern80() throws Exception {
        visit("[NX2]=N");
    }
    public void testPattern81() throws Exception {
        visit("[NX2]=[NX2]");
    }
    public void testPattern82() throws Exception {
        visit("[$([NX2]=[NX3+]([O-])[#6]),$([NX2]=[NX3+0](=[O])[#6])]");
    }
    public void testPattern83() throws Exception {
        visit("[$([#6]=[N+]=[N-]),$([#6-]-[N+]#[N])]");
    }
    public void testPattern84() throws Exception {
        visit("[$([nr5]:[nr5,or5,sr5]),$([nr5]:[cr5]:[nr5,or5,sr5])]");
    }
    public void testPattern85() throws Exception {
        visit("[NX3][NX3]");
    }
    public void testPattern86() throws Exception {
        visit("[NX3][NX2]=[*]");
    }
    public void testPattern87() throws Exception {
        visit("[CX3;$([C]([#6])[#6]),$([CH][#6])]=[NX2][#6]");
    }
    public void testPattern88() throws Exception {
        visit("[$([CX3]([#6])[#6]),$([CX3H][#6])]=[$([NX2][#6]),$([NX2H])]");
    }
    public void testPattern89() throws Exception {
        visit("[NX3+]=[CX3]");
    }
    public void testPattern90() throws Exception {
        visit("[CX3](=[OX1])[NX3H][CX3](=[OX1])");
    }
    public void testPattern91() throws Exception {
        visit("[CX3](=[OX1])[NX3H0]([#6])[CX3](=[OX1])");
    }
    public void testPattern92() throws Exception {
        visit("[CX3](=[OX1])[NX3H0]([NX3H0]([CX3](=[OX1]))[CX3](=[OX1]))[CX3](=[OX1])");
    }
    public void testPattern93() throws Exception {
        visit("[$([NX3](=[OX1])(=[OX1])O),$([NX3+]([OX1-])(=[OX1])O)]");
    }
    public void testPattern94() throws Exception {
        visit("[$([OX1]=[NX3](=[OX1])[OX1-]),$([OX1]=[NX3+]([OX1-])[OX1-])]");
    }
    public void testPattern95() throws Exception {
        visit("[NX1]#[CX2]");
    }
    public void testPattern96() throws Exception {
        visit("[CX1-]#[NX2+]");
    }
    public void testPattern97() throws Exception {
        visit("[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]");
    }
    public void testPattern98() throws Exception {
        visit("[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8].[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]");
    }
    public void testPattern99() throws Exception {
        visit("[NX2]=[OX1]");
    }
    public void testPattern101() throws Exception {
        visit("[$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]");
    }
    public void testPattern102() throws Exception {
        visit("[OX2H]");
    }
    public void testPattern103() throws Exception {
        visit("[#6][OX2H]");
    }
    public void testPattern104() throws Exception {