structurediagramgeneratortest.java

化学图形处理软件

	public void testDiamantane() throws Exception
	{
		Molecule m = MoleculeFactory.makeDiamantane();
		IAtomContainer ac = generateCoordinates(m);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}
	

	/**
	 *  A unit test for JUnit
	 *
	 *@exception  Exception  thrown if something goes wrong
	 *@cdk.bug 1670871
	 */
	public void xtestBug1670871() throws Exception
	{
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("CC(=O)OC1C=CC(SC23CC4CC(CC(C4)C2)C3)N(C1SC56CC7CC(CC(C7)C5)C6)C(C)=O");
		IAtomContainer ac = generateCoordinates(mol);
		//MoleculeViewer2D.display(new Molecule(ac), false);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}



	/**
	 *  A unit test for JUnit
	 */
	public void testEthylCyclohexane() throws Exception
	{
		Molecule m = MoleculeFactory.makeEthylCyclohexane();
		IAtomContainer ac = generateCoordinates(m);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testBicycloRings() throws Exception
	{
		Molecule m = MoleculeFactory.makeBicycloRings();
		IAtomContainer ac = generateCoordinates(m);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}

	
	/**
	 *  A unit test for JUnit
	 */
	public IMolecule makeJhao3() throws Exception
	{
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("C=C1C2=CC13(CC23)");
		return mol;
	}

	/**
	 *  A unit test for JUnit
	 */
	public IMolecule makeJhao4() throws Exception
	{
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("CCC3C1CC23(CC12)");
		return mol;
	}
	
	/**
	 *  A unit test for JUnit
	 */
	public void testBenzene() throws Exception
	{
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("c1ccccc1");
		IAtomContainer ac = generateCoordinates(mol);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}


	/**
	 * @cdk.bug 780545
	 */
	public void testBug780545() throws Exception
	{
		Molecule mol = new Molecule();
		mol.addAtom(new Atom("C"));
		IAtomContainer ac = generateCoordinates(mol);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}
	
	/**
	 * @cdk.bug 1598409
	 */
	public void testBug1598409() throws Exception
	{
		String smiles = "c1(:c(:c2-C(-c3:c(-C(=O)-c:2:c(:c:1-[H])-[H]):c(:c(:c(:c:3-[H])-[H])-N(-[H])-[H])-[H])=O)-[H])-[H]";
		SmilesParser parser = new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
		IMolecule cdkMol = parser.parseSmiles(smiles);
		HueckelAromaticityDetector.detectAromaticity(cdkMol, false);
		new StructureDiagramGenerator(cdkMol).generateCoordinates();
	}
	
	/**
	 * @cdk.bug 1572062
	 */
	public void testBug1572062() throws Exception {
		String filename = "data/mdl/sdg_test.mol";

//		set up molecule reader
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		IChemObjectReader molReader = new MDLReader(ins);

//		read molecule
		IMolecule molecule = (IMolecule) molReader.read(new
				Molecule());

//		rebuild 2D coordinates
		StructureDiagramGenerator structureDiagramGenerator = 
			new StructureDiagramGenerator();
		for (int i = 0; i < 10; i++) {
			structureDiagramGenerator.setMolecule(molecule);
			structureDiagramGenerator.generateCoordinates();
		}

	}
	
	/**
	 * @cdk.bug 884993
	 */
	public void testBug884993() throws Exception
	{
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule mol = sp.parseSmiles("[N+](=O)([O-])C1=C(O)C(=CC(=C1)[N+](=O)[O-])[N+](=O)[O-].C23N(CCCC2)CCCC3");
		try{
			IAtomContainer ac = generateCoordinates(mol);
            assertTrue(GeometryTools.has2DCoordinates(ac));
            fail("This should have thrown a 'Molecule not connected' exception.");
		} catch(Exception exc) {
			// OK, an exception should have been thrown
			if (!(exc.toString().indexOf("Molecule not connected")>= 0)) fail();
		}
	}
	
	/**
	 * @cdk.bug 1714794
	 */
	public void xtestBug1714794() throws Exception {
        String problematicMol2AsSmiles = "N1c2c(c3c(c4c(c(c3O)C)OC(OC=CC(C(C(C(C(C(C(C(C=CC=C(C1=O)C)C)O)C)O)C)OC(=O)C)C)OC)(C4=O)C)c(c2C=NN(C12CC3CC(C1)CC(C2)C3)C)O)O";
        SmilesParser parser = new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
        IMolecule cdkMol = parser.parseSmiles(problematicMol2AsSmiles);
        HueckelAromaticityDetector.detectAromaticity(cdkMol, false);
        new StructureDiagramGenerator(cdkMol).generateCoordinates();
        assertTrue(GeometryTools.has2DCoordinates(cdkMol));
        
        String problematicMol2 = "@<TRIPOS>MOLECULE\n"
            + "mol_197219.smi\n"
            + " 129 135 0 0 0\n"
            + "SMALL\n"
            + "GASTEIGER\n"
            + "Energy = 0\n"
            + "\n"
            + "@<TRIPOS>ATOM\n"
            + "      1 N1          0.0000    0.0000    0.0000 N.am    1  <1>        -0.2782\n"
            + "      2 H1          0.0000    0.0000    0.0000 H       1  <1>         0.1552\n"
            + "      3 C1          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0886\n"
            + "      4 C2          0.0000    0.0000    0.0000 C.ar    1  <1>         0.1500\n"
            + "      5 C3          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0714\n"
            + "      6 C4          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0456\n"
            + "      7 C5          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0788\n"
            + "      8 C6          0.0000    0.0000    0.0000 C.ar    1  <1>         0.1435\n"
            + "      9 C7          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0342\n"
            + "     10 C8          0.0000    0.0000    0.0000 C.ar    1  <1>         0.1346\n"
            + "     11 O1          0.0000    0.0000    0.0000 O.3     1  <1>        -0.5057\n"
            + "     12 H2          0.0000    0.0000    0.0000 H       1  <1>         0.2922\n"
            + "     13 C9          0.0000    0.0000    0.0000 C.3     1  <1>        -0.0327\n"
            + "     14 H3          0.0000    0.0000    0.0000 H       1  <1>         0.0280\n"
            + "     15 H4          0.0000    0.0000    0.0000 H       1  <1>         0.0280\n"
            + "     16 H5          0.0000    0.0000    0.0000 H       1  <1>         0.0280\n"
            + "     17 O2          0.0000    0.0000    0.0000 O.3     1  <1>        -0.4436\n"
            + "     18 C10         0.0000    0.0000    0.0000 C.3     1  <1>         0.3143\n"
            + "     19 O3          0.0000    0.0000    0.0000 O.2     1  <1>        -0.4528\n"
            + "     20 C11         0.0000    0.0000    0.0000 C.2     1  <1>         0.0882\n"
            + "     21 H6          0.0000    0.0000    0.0000 H       1  <1>         0.1022\n"
            + "     22 C12         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0208\n"
            + "     23 H7          0.0000    0.0000    0.0000 H       1  <1>         0.0628\n"
            + "     24 C13         0.0000    0.0000    0.0000 C.3     1  <1>         0.0854\n"
            + "     25 H8          0.0000    0.0000    0.0000 H       1  <1>         0.0645\n"
            + "     26 C14         0.0000    0.0000    0.0000 C.3     1  <1>         0.0236\n"
            + "     27 H9          0.0000    0.0000    0.0000 H       1  <1>         0.0362\n"
            + "     28 C15         0.0000    0.0000    0.0000 C.3     1  <1>         0.1131\n"
            + "     29 H10         0.0000    0.0000    0.0000 H       1  <1>         0.0741\n"
            + "     30 C16         0.0000    0.0000    0.0000 C.3     1  <1>         0.0200\n"
            + "     31 H11         0.0000    0.0000    0.0000 H       1  <1>         0.0359\n"
            + "     32 C17         0.0000    0.0000    0.0000 C.3     1  <1>         0.0661\n"
            + "     33 H12         0.0000    0.0000    0.0000 H       1  <1>         0.0600\n"
            + "     34 C18         0.0000    0.0000    0.0000 C.3     1  <1>         0.0091\n"
            + "     35 H13         0.0000    0.0000    0.0000 H       1  <1>         0.0348\n"
            + "     36 C19         0.0000    0.0000    0.0000 C.3     1  <1>         0.0661\n"
            + "     37 H14         0.0000    0.0000    0.0000 H       1  <1>         0.0602\n"
            + "     38 C20         0.0000    0.0000    0.0000 C.3     1  <1>         0.0009\n"
            + "     39 H15         0.0000    0.0000    0.0000 H       1  <1>         0.0365\n"
            + "     40 C21         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0787\n"
            + "     41 H16         0.0000    0.0000    0.0000 H       1  <1>         0.0576\n"
            + "     42 C22         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0649\n"
            + "     43 H17         0.0000    0.0000    0.0000 H       1  <1>         0.0615\n"
            + "     44 C23         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0542\n"
            + "     45 H18         0.0000    0.0000    0.0000 H       1  <1>         0.0622\n"
            + "     46 C24         0.0000    0.0000    0.0000 C.2     1  <1>         0.0115\n"
            + "     47 C25         0.0000    0.0000    0.0000 C.2     1  <1>         0.2441\n"
            + "     48 O4          0.0000    0.0000    0.0000 O.2     1  <1>        -0.2702\n"
            + "     49 C26         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0348\n"
            + "     50 H19         0.0000    0.0000    0.0000 H       1  <1>         0.0279\n"
            + "     51 H20         0.0000    0.0000    0.0000 H       1  <1>         0.0279\n"
            + "     52 H21         0.0000    0.0000    0.0000 H       1  <1>         0.0279\n"
            + "     53 C27         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0566\n"
            + "     54 H22         0.0000    0.0000    0.0000 H       1  <1>         0.0236\n"
            + "     55 H23         0.0000    0.0000    0.0000 H       1  <1>         0.0236\n"
            + "     56 H24         0.0000    0.0000    0.0000 H       1  <1>         0.0236\n"
            + "     57 O5          0.0000    0.0000    0.0000 O.3     1  <1>        -0.3909\n"
            + "     58 H25         0.0000    0.0000    0.0000 H       1  <1>         0.2098\n"
            + "     59 C28         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0577\n"
            + "     60 H26         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     61 H27         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     62 H28         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     63 O6          0.0000    0.0000    0.0000 O.3     1  <1>        -0.3910\n"
            + "     64 H29         0.0000    0.0000    0.0000 H       1  <1>         0.2098\n"
            + "     65 C29         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0567\n"
            + "     66 H30         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     67 H31         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     68 H32         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     69 O7          0.0000    0.0000    0.0000 O.3     1  <1>        -0.4608\n"
            + "     70 C30         0.0000    0.0000    0.0000 C.2     1  <1>         0.3042\n"
            + "     71 O8          0.0000    0.0000    0.0000 O.2     1  <1>        -0.2512\n"
            + "     72 C31         0.0000    0.0000    0.0000 C.3     1  <1>         0.0332\n"
            + "     73 H33         0.0000    0.0000    0.0000 H       1  <1>         0.0342\n"
            + "     74 H34         0.0000    0.0000    0.0000 H       1  <1>         0.0342\n"
            + "     75 H35         0.0000    0.0000    0.0000 H       1  <1>         0.0342\n"
            + "     76 C32         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0564\n"
            + "     77 H36         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     78 H37         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     79 H38         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     80 O9          0.0000    0.0000    0.0000 O.3     1  <1>        -0.3753\n"
            + "     81 C33         0.0000    0.0000    0.0000 C.3     1  <1>         0.0372\n"
            + "     82 H39         0.0000    0.0000    0.0000 H       1  <1>         0.0524\n"
            + "     83 H40         0.0000    0.0000    0.0000 H       1  <1>         0.0524\n"
            + "     84 H41         0.0000    0.0000    0.0000 H       1  <1>         0.0524\n"
            + "     85 C34         0.0000    0.0000    0.0000 C.2     1  <1>         0.2505\n"
            + "     86 O10         0.0000    0.0000    0.0000 O.2     1  <1>        -0.2836\n"
            + "     87 C35         0.0000    0.0000    0.0000 C.3     1  <1>         0.0210\n"
            + "     88 H42         0.0000    0.0000    0.0000 H       1  <1>         0.0309\n"
            + "     89 H43         0.0000    0.0000    0.0000 H       1  <1>         0.0309\n"
            + "     90 H44         0.0000    0.0000    0.0000 H       1  <1>         0.0309\n"
            + "     91 C36         0.0000    0.0000    0.0000 C.ar    1  <1>         0.1361\n"