smartsqueryvisitortest.java

化学图形处理软件

    	assertEquals(2, m);    	
    }
    public void testPropertyAnyAtom1() throws Exception {
    	int m = match("[*]", "C");
    	assertEquals(1, m);    	
    }
    public void testPropertyAnyAtom2() throws Exception {
    	int m = match("[*]", "[2H]C");
    	assertEquals(2, m);    	
    }
    public void testPropertyAnyAtom3() throws Exception {
    	int m = match("[*]", "[H][H]");
    	assertEquals(2, m);    	
    }
    public void testPropertyAnyAtom4() throws Exception {
    	int m = match("[*]", "[1H]C([1H])([1H])[1H]");
    	assertEquals(5, m);    	
    }
    public void testBondSingle1() throws Exception {
    	int m = match("CC", "C=C");
    	assertEquals(0, m);    		
    }
    public void testBondSingle2() throws Exception {
    	int m = match("CC", "C#C");
    	assertEquals(0, m);    		
    }
    public void testBondSingle3() throws Exception {
    	int m = match("CC", "CCO");
    	assertEquals(1, m);    		
    }
    public void testBondSingle4() throws Exception {
    	int m = match("CC", "C1C(C)=C(C=CC(C)=CC=CC(C)=CCO)C(C)(C)C1");
    	assertEquals(14, m);    		
    }
    public void testBondSingle5() throws Exception {
    	int m = match("CC", "CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O");
    	assertEquals(7, m);    		
    }
    public void testBondAny1() throws Exception {
    	int m = match("C~C", "C=C");
    	assertEquals(1, m);
    }
    public void testBondAny2() throws Exception {
    	int m = match("C~C", "C#C");
    	assertEquals(1, m);
    }
    public void testBondAny3() throws Exception {
    	int m = match("C~C", "CCO");
    	assertEquals(1, m);
    }
    public void testBondAny4() throws Exception {
    	int m = match("C~C", "C1C(C)=C(C=CC(C)=CC=CC(C)=CCO)C(C)(C)C1");
    	assertEquals(19, m);
    }    
    public void testBondAny5() throws Exception {
    	int m = match("[C,c]~[C,c]", "CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O");
    	assertEquals(14, m);
    }
    public void testBondRing1() throws Exception {
    	int m = match("C@C", "C=C");
    	assertEquals(0, m);
    }
    public void testBondRing2() throws Exception {
    	int m = match("C@C", "C#C");
    	assertEquals(0, m);
    }
    public void testBondRing3() throws Exception {
    	int m = match("C@C", "C1CCCCC1");
    	assertEquals(6, m);
    }
    public void testBondRing4() throws Exception {
    	int m = match("[C,c]@[C,c]", "c1ccccc1Cc1ccccc1");
    	assertEquals(12, m);
    }
    public void testBondRing5() throws Exception {
    	int m = match("[C,c]@[C,c]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1");
    	assertEquals(15, m);
    }
    public void testBondRing6() throws Exception {
    	int m = match("[C,c]@[C,c]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76");
    	assertEquals(22, m);
    }
    //TODO: Stereo bond not implemented in smiles parser?
    public void testBondStereo1() throws Exception { 
    	int m = match("F/?C=C/Cl", "F/C=C/Cl");
    	assertEquals(1, m);
    }
    public void testBondStereo2() throws Exception {
    	int m = match("F/?C=C/Cl", "FC=C/Cl");
    	assertEquals(1, m);
    }
    public void testBondStereo3() throws Exception {
    	int m = match("F/?C=C/Cl", "FC=CCl");
    	assertEquals(1, m);
    }
    public void testBondStereo4() throws Exception {
    	int m = match("F/?C=C/Cl", "F\\C=C/Cl");
    	assertEquals(0, m);
    }
    public void testLogicalNot1() throws Exception {
    	int m = match("[!c]", "c1cc(C)c(N)cc1");
    	assertEquals(2, m);
    }
    public void testLogicalNot2() throws Exception {
    	int m = match("[!c]", "c1c(C)c(N)cnc1");
    	assertEquals(3, m);
    }
    public void testLogicalNot3() throws Exception {
    	int m = match("[!c]", "c1(C)c(N)cco1");
    	assertEquals(3, m);
    }
    public void testLogicalNot4() throws Exception {
    	int m = match("[!c]", "c1c(C)c(N)c[nH]1");
    	assertEquals(3, m);
    }
    public void testLogicalNot5() throws Exception {
    	int m = match("[!c]", "O=n1ccccc1");
    	assertEquals(2, m);
    }
    public void testLogicalNot6() throws Exception {
    	int m = match("[!c]", "[O-][n+]1ccccc1");
    	assertEquals(2, m);
    }
    public void testLogicalNot7() throws Exception {
    	int m = match("[!c]", "c1ncccc1C1CCCN1C");
    	assertEquals(7, m);
    }
    public void testLogicalNot8() throws Exception {
    	int m = match("[!c]", "c1ccccc1C(=O)OC2CC(N3C)CCC3C2C(=O)OC");
    	assertEquals(16, m);
    }
    public void testLogicalOr1() throws Exception {
    	int m = match("[N,O,o]", "c1cc(C)c(N)cc1");
    	assertEquals(1, m);
    }
    public void testLogicalOr2() throws Exception {
    	int m = match("[N,O,o]", "c1c(C)c(N)cnc1");
    	assertEquals(1, m);
    }
    public void testLogicalOr3() throws Exception {
    	int m = match("[N,O,o]", "c1(C)c(N)cco1");
    	assertEquals(2, m);
    }
    public void testLogicalOr4() throws Exception {
    	int m = match("[N,O,o]", "c1c(C)c(N)c[nH]1");
    	assertEquals(1, m);
    }
    public void testLogicalOr5() throws Exception {
    	int m = match("[N,O,o]", "O=n1ccccc1");
    	assertEquals(1, m);
    }
    public void testLogicalOr6() throws Exception {
    	int m = match("[N,O,o]", "[O-][n+]1ccccc1");
    	assertEquals(1, m);
    }
    public void testLogicalOr7() throws Exception {
    	int m = match("[N,O,o]", "c1ncccc1C1CCCN1C");
    	assertEquals(1, m);
    }
    public void testLogicalOr8() throws Exception {
    	int m = match("[N,O,o]", "c1ccccc1C(=O)OC2CC(N3C)CCC3C2C(=O)OC");
    	assertEquals(5, m);
    }
    public void testLogicalOrHighAnd1() throws Exception {
    	int m = match("[N,#6&+1,+0]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1");
    	assertEquals(24, m);
    }
    public void testLogicalOrHighAnd2() throws Exception {
    	int m = match("[N,#6&+1,+0]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76");
    	assertEquals(25, m);
    }
    public void testLogicalOrHighAnd3() throws Exception {
    	int m = match("[N,#6&+1,+0]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34");
    	assertEquals(24, m);
    }
    public void testLogicalOrHighAnd4() throws Exception {
    	int m = match("[N,#6&+1,+0]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5");
    	assertEquals(21, m);
    }
    public void testLogicalOrHighAnd5() throws Exception {
    	int m = match("[N,#6&+1,+0]", "N1N([Hg-][O+]=C1N=Nc2ccccc2)c3ccccc3");
    	assertEquals(17, m);
    }
    /*
    public void testLogicalOrHighAnd6() throws Exception { 
    	//TODO: This takes a long time to match
    	long start = Calendar.getInstance().getTimeInMillis();
    	//int m = match("[N,#6&+1,+0]", "[Na+].[Na+].[O-]C(=O)c1ccccc1c2c3ccc([O-])cc3oc4cc(=O)ccc24");
    	new SmilesParser(DefaultChemObjectBuilder.getInstance());
    	SMARTSParser.parse("[N,#6&+1,+0]");
    	long end = Calendar.getInstance().getTimeInMillis();
    	System.out.println( (end - start) );
    	//assertEquals(23, m);
    }
    */
    public void testLogicalOrHighAnd7() throws Exception {
    	int m = match("[N,#6&+1,+0]", "[Cl-].Clc1ccc([I+]c2cccs2)cc1");
    	assertEquals(12, m);
    }
    public void testLogicalOrLowAnd1() throws Exception {
    	int m = match("[#7,C;+0,+1]", "CCN(CC)C(=O)C1CN(C)C2CC3=CNc(ccc4)c3c4C2=C1");
    	assertEquals(15, m);    	
    }
    public void testLogicalOrLowAnd2() throws Exception {
    	int m = match("[#7,C;+0,+1]", "N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76");
    	assertEquals(17, m);    	
    }
    public void testLogicalOrLowAnd3() throws Exception {
    	int m = match("[#7,C;+0,+1]", "COc1cc2c(ccnc2cc1)C(O)C4CC(CC3)C(C=C)CN34");
    	assertEquals(13, m);    	
    }
    public void testLogicalOrLowAnd4() throws Exception {
    	int m = match("[#7,C;+0,+1]", "C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5");
    	assertEquals(12, m);    	
    }
    
    public void testLogicalOrLowAnd5() throws Exception {
    	int m = match("[#7,C;+0,+1]", "N1N([Hg-][O+]=C1N=Nc2ccccc2)c3ccccc3");
    	assertEquals(5, m);    	
    }
    /*
    public void testLogicalOrLowAnd6() throws Exception { //TODO: this takes very long
    	int m = match("[#7,C;+0,+1]", "[Na+].[Na+].[O-]C(=O)c1ccccc1c2c3ccc([O-])cc3oc4cc(=O)ccc24");
    	assertEquals(1, m);    	
    }
    */
    public void testLogicalOrLowAnd7() throws Exception {
    	int m = match("[#7,C;+0,+1]", "[Cl-].Clc1ccc([I+]c2cccs2)cc1");
    	assertEquals(0, m);    	
    }
    
    public void testRing1() throws Exception {
    	int m = match("C1CCCCC1", "C1CCCCC1CCCC");
    	assertEquals(12, m);     	
    }
    public void testRing2() throws Exception {
    	int m = match("C1CCCCC1", "C1CCCCC1C1CCCCC1");
    	assertEquals(24, m);     	
    }
    public void testRing3() throws Exception {
    	int m = match("C1CCCCC1", "C1CCCC12CCCCC2");
    	assertEquals(12, m);     	
    }
    public void testRing4() throws Exception {
    	int m = match("C1CCCCC1", "c1ccccc1O");
    	assertEquals(0, m);     	
    }
    public void testRing5() throws Exception {
    	int m = match("C1CCCCC1", "c1ccccc1CCCCCC");
    	assertEquals(0, m);     	
    }
    public void testRing6() throws Exception {
    	int m = match("C1CCCCC1", "CCCCCC");
    	assertEquals(0, m);     	
    }
    public void testAromaticRing1() throws Exception {
    	int m = match("c1ccccc1", "c1ccccc1");
    	assertEquals(12, m);
    }    
    public void testAromaticRing2() throws Exception {
    	int m = match("c1ccccc1", "c1cccc2c1cccc2");
    	assertEquals(24, m);
    }
    public void testAromaticRing3() throws Exception {
    	int m = match("c1ccccn1", "c1cccc2c1cccc2");
    	assertEquals(0, m);
    }
    public void testAromaticRing4() throws Exception {
    	int m = match("c1ccccn1", "c1cccc2c1cccn2");
    	assertEquals(2, m);
    }    
    
    /*
     * Testing amino acides matching. AA smarts from Daylight smarts example page
     */
    public void testAminoAcid1() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid2() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCCNC(N)=N)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid3() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC(N)=O)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid4() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC(O)=O)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid5() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CS)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid6() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCC(N)=O)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid7() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCC(O)=O)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid8() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC([H])C(O)=O");
    	assertEquals(0, m);
    }
    public void testAminoAcid9() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CNC=N1)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid10() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C(CC)C)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid11() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC(C)C)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid12() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCCCN)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid13() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CCSC)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid14() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CC=CC=C1)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid15() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "OC(C1CCCN1)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid16() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CO)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid17() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C(C)O)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid18() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CNC2=C1C=CC=C2)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid19() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(CC1=CC=C(O)C=C1)C(O)=O");
    	assertEquals(1, m);
    }
    public void testAminoAcid20() throws Exception {
    	int m = match("[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", "NC(C(C)C)C(O)=O");
    	assertEquals(1, m);
    }    
}