smilesgeneratortest.java

化学图形处理软件

		hydroxyl.setHydrogenCount(1);
		hydroxyl.setFormalCharge(-1);
		molecule.addAtom(sodium);
		molecule.addAtom(hydroxyl);
		smiles = sg.createSMILES(molecule);
		assertTrue(smiles.indexOf(".") != -1);
	}


	/**
	 * @cdk.bug 791091
	 */
	public void testBug791091()
	{
		String smiles = "";
		Molecule molecule = new Molecule();
        SmilesGenerator sg = new SmilesGenerator();
		molecule.addAtom(new Atom("C"));
		molecule.addAtom(new Atom("C"));
		molecule.addAtom(new Atom("C"));
		molecule.addAtom(new Atom("C"));
		molecule.addAtom(new Atom("N"));
		molecule.addBond(0, 1, 1.0);
		molecule.addBond(1, 2, 1.0);
		molecule.addBond(2, 4, 1.0);
		molecule.addBond(4, 0, 1.0);
		molecule.addBond(4, 3, 1.0);
		fixCarbonHCount(molecule);
		smiles = sg.createSMILES(molecule);
		assertEquals("N1(C)CCC1", smiles);
	}

	/**
	 * @cdk.bug 590236
	 */
	public void testBug590236()
	{
		String smiles = "";
		Molecule molecule = new Molecule();
        SmilesGenerator sg = new SmilesGenerator();
		molecule.addAtom(new Atom("C"));
		Atom carbon2 = new Atom("C");
		carbon2.setMassNumber(13);
		molecule.addAtom(carbon2);
		molecule.addBond(0, 1, 1.0);
		fixCarbonHCount(molecule);
		smiles = sg.createSMILES(molecule);
		assertEquals("C[13C]", smiles);
	}

	/**
	 * A bug reported for JChemPaint.
	 * 
	 * @cdk.bug 956923
	 */
	public void testSFBug956923() throws Exception 
	{
		String smiles = "";
		Molecule molecule = new Molecule();
        SmilesGenerator sg = new SmilesGenerator();
		Atom sp2CarbonWithOneHydrogen = new Atom("C");
		sp2CarbonWithOneHydrogen.setHybridization(CDKConstants.HYBRIDIZATION_SP2);
		sp2CarbonWithOneHydrogen.setHydrogenCount(1);
		molecule.addAtom(sp2CarbonWithOneHydrogen);
		molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone());
		molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone());
		molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone());
		molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone());
		molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone());
		molecule.addBond(0, 1, 1.0);
		molecule.addBond(1, 2, 1.0);
		molecule.addBond(2, 3, 1.0);
		molecule.addBond(3, 4, 1.0);
		molecule.addBond(4, 5, 1.0);
		molecule.addBond(5, 0, 1.0);
		smiles = sg.createSMILES(molecule);
		assertEquals("c1ccccc1", smiles);
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testAtomPermutation()
	{
		Molecule mol = new Molecule();
		mol.addAtom(new Atom("S"));
		mol.addAtom(new Atom("O"));
		mol.addAtom(new Atom("O"));
		mol.addAtom(new Atom("O"));
		mol.addAtom(new Atom("O"));
		mol.addBond(0, 1, 2.0);
		mol.addBond(0, 2, 2.0);
		mol.addBond(0, 3, 1.0);
		mol.addBond(0, 4, 1.0);
		mol.getAtom(3).setHydrogenCount(1);
		mol.getAtom(4).setHydrogenCount(1);
		AtomContainerAtomPermutor acap = new AtomContainerAtomPermutor(mol);
		SmilesGenerator sg = new SmilesGenerator();
		String smiles = "";
		String oldSmiles = sg.createSMILES(mol);
		while (acap.hasNext())
		{
			smiles = sg.createSMILES(new Molecule((AtomContainer) acap.next()));
			//logger.debug(smiles);
			assertEquals(oldSmiles, smiles);
		}

	}


	/**
	 *  A unit test for JUnit
	 */
	public void testBondPermutation()
	{
		Molecule mol = new Molecule();
		mol.addAtom(new Atom("S"));
		mol.addAtom(new Atom("O"));
		mol.addAtom(new Atom("O"));
		mol.addAtom(new Atom("O"));
		mol.addAtom(new Atom("O"));
		mol.addBond(0, 1, 2.0);
		mol.addBond(0, 2, 2.0);
		mol.addBond(0, 3, 1.0);
		mol.addBond(0, 4, 1.0);
		mol.getAtom(3).setHydrogenCount(1);
		mol.getAtom(4).setHydrogenCount(1);
		AtomContainerBondPermutor acbp = new AtomContainerBondPermutor(mol);
		SmilesGenerator sg = new SmilesGenerator();
		String smiles = "";
		String oldSmiles = sg.createSMILES(mol);
		while (acbp.hasNext())
		{
			smiles = sg.createSMILES(new Molecule((AtomContainer) acbp.next()));
			//logger.debug(smiles);
			assertEquals(oldSmiles, smiles);
		}

	}

	private void fixCarbonHCount(Molecule mol) {
		/*
		 *  the following line are just a quick fix for this
		 *  particluar carbon-only molecule until we have a proper
		 *  hydrogen count configurator
		 */
		double bondCount = 0;
		org.openscience.cdk.interfaces.IAtom atom;
		for (int f = 0; f < mol.getAtomCount(); f++)
		{
			atom = mol.getAtom(f);
			bondCount = mol.getBondOrderSum(atom);
			if (atom.getSymbol().equals("C"))
			{
				atom.setHydrogenCount(4 - (int) bondCount - (int) atom.getCharge());
			}
			if (atom.getSymbol().equals("N"))
			{
				atom.setHydrogenCount(3 - (int) bondCount - (int) atom.getCharge());
			}
		}
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testPseudoAtom()
	{
		Atom atom = new PseudoAtom("Star");
		SmilesGenerator sg = new SmilesGenerator();
		String smiles = "";
		Molecule molecule = new Molecule();
		molecule.addAtom(atom);
		smiles = sg.createSMILES(molecule);
		assertEquals("[*]", smiles);
	}


	/**
	 *  Test generation of a reaction SMILES. I know, it's a stupid alchemic
	 *  reaction, but it serves its purpose.
	 */
	public void testReactionSMILES() throws Exception {
		Reaction reaction = new Reaction();
		Molecule methane = new Molecule();
		methane.addAtom(new Atom("C"));
		reaction.addReactant(methane);
		Molecule magic = new Molecule();
		magic.addAtom(new PseudoAtom("magic"));
		reaction.addAgent(magic);
		Molecule gold = new Molecule();
		gold.addAtom(new Atom("Au"));
		reaction.addProduct(gold);

		SmilesGenerator sg = new SmilesGenerator();
		String smiles = sg.createSMILES(reaction);
		//logger.debug("Generated SMILES: " + smiles);
		assertEquals("C>[*]>[Au]", smiles);
	}


	/**
	 *  Test generation of a D and L alanin.
	 */
	public void testAlaSMILES() throws Exception {
		String filename = "data/mdl/l-ala.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		Molecule mol1 = (Molecule) reader.read(new Molecule());
		new HydrogenAdder().addExplicitHydrogensToSatisfyValency(mol1);
		new HydrogenPlacer().placeHydrogens2D(mol1, 1.0);
		filename = "data/mdl/d-ala.mol";
		ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		reader = new MDLReader(ins);
		Molecule mol2 = (Molecule) reader.read(new Molecule());
		new HydrogenAdder().addExplicitHydrogensToSatisfyValency(mol2);
		new HydrogenPlacer().placeHydrogens2D(mol2, 1.0);
		SmilesGenerator sg = new SmilesGenerator();
		String smiles1 = sg.createChiralSMILES(mol1, new boolean[20]);
		String smiles2 = sg.createChiralSMILES(mol2, new boolean[20]);
		assertNotSame(smiles1, smiles2);
	}


	/**
	 *  Test some sugars
	 */
	public void testSugarSMILES() throws Exception {
		String filename = "data/mdl/D-mannose.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		Molecule mol1 = (Molecule) reader.read(new Molecule());
		new HydrogenPlacer().placeHydrogens2D(mol1, 1.0);
		filename = "data/mdl/D+-glucose.mol";
		ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		reader = new MDLReader(ins);
		Molecule mol2 = (Molecule) reader.read(new Molecule());
		new HydrogenPlacer().placeHydrogens2D(mol2, 1.0);
		SmilesGenerator sg = new SmilesGenerator();
		String smiles1 = sg.createChiralSMILES(mol1, new boolean[20]);
		String smiles2 = sg.createChiralSMILES(mol2, new boolean[20]);
		assertNotSame(smiles1, smiles2);
	}

	/**
	 *  Test for some rings where the double bond is broken
	 */
	public void testCycloOctan() throws Exception {
		String filename = "data/mdl/cyclooctan.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		Molecule mol1 = (Molecule) reader.read(new Molecule());
		SmilesGenerator sg = new SmilesGenerator();
		String moleculeSmile = sg.createSMILES(mol1);
		assertEquals(moleculeSmile, "C1=CCCCCCC1");
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testCycloOcten() throws Exception {
		String filename = "data/mdl/cycloocten.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		Molecule mol1 = (Molecule) reader.read(new Molecule());
		SmilesGenerator sg = new SmilesGenerator();
		String moleculeSmile = sg.createSMILES(mol1);
		assertEquals(moleculeSmile, "C1C=CCCCCC1");
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testCycloOctadien() throws Exception {
		String filename = "data/mdl/cyclooctadien.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		Molecule mol1 = (Molecule) reader.read(new Molecule());
		SmilesGenerator sg = new SmilesGenerator();
		String moleculeSmile = sg.createSMILES(mol1);
		assertEquals(moleculeSmile, "C=1CCC=CCCC=1");
	}


	/**
	 * @cdk.bug 1089770
	 */
	public void testSFBug1089770_1() throws Exception {
		String filename = "data/mdl/bug1089770-1.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		Molecule mol1 = (Molecule) reader.read(new Molecule());
		SmilesGenerator sg = new SmilesGenerator();
		String moleculeSmile = sg.createSMILES(mol1);
		//logger.debug(filename + " -> " + moleculeSmile);
		assertEquals(moleculeSmile, "C1CCC=2CCCC=2(C1)");
	}

	/**
	 * @cdk.bug 1089770
	 */
	public void testSFBug1089770_2() throws Exception {
		String filename = "data/mdl/bug1089770-2.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		Molecule mol1 = (Molecule) reader.read(new Molecule());
		SmilesGenerator sg = new SmilesGenerator();
		String moleculeSmile = sg.createSMILES(mol1);
		//logger.debug(filename + " -> " + moleculeSmile);
		assertEquals(moleculeSmile, "C=1CCC=CCCC=1");
	}
	
	/**
	 * @cdk.bug 1014344
	 */
	public void testSFBug1014344() throws Exception {
		String filename = "data/mdl/bug1014344-1.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		Molecule mol1 = (Molecule) reader.read(new Molecule());
		new HydrogenAdder().addImplicitHydrogensToSatisfyValency(mol1);
		SmilesGenerator sg = new SmilesGenerator();
		String molSmiles = sg.createSMILES(mol1);
		StringWriter output=new StringWriter();
		CMLWriter cmlWriter = new CMLWriter(output);
        cmlWriter.write(mol1);
        CMLReader cmlreader=new CMLReader(new ByteArrayInputStream(output.toString().getBytes()));
        IAtomContainer mol2=((IChemFile)cmlreader.read(new ChemFile())).getChemSequence(0).getChemModel(0).getMoleculeSet().getAtomContainer(0);
        new HydrogenAdder().addImplicitHydrogensToSatisfyValency(mol2);
        String cmlSmiles = sg.createSMILES(new Molecule(mol2));
        assertEquals(molSmiles,cmlSmiles);        
	}

	/**
	 * @cdk.bug 1014344
	 */
	public void testTest() throws Exception {
		String filename_cml = "data/mdl/9554.mol";
		String filename_mol = "data/mdl/9553.mol";
		InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(filename_cml);
		InputStream ins2 = this.getClass().getClassLoader().getResourceAsStream(filename_mol);
		MDLReader reader1 = new MDLReader(ins1);
        Molecule mol1 = (Molecule) reader1.read(new Molecule());
        new HydrogenAdder().addExplicitHydrogensToSatisfyValency(mol1);
        StructureDiagramGenerator sdg=new StructureDiagramGenerator(mol1);
        sdg.generateCoordinates();
		
		MDLReader reader2 = new MDLReader(ins2);		
		Molecule mol2 = (Molecule) reader2.read(new Molecule());
		new HydrogenAdder().addExplicitHydrogensToSatisfyValency(mol2);
        sdg=new StructureDiagramGenerator(mol2);
        sdg.generateCoordinates();
		
		SmilesGenerator sg = new SmilesGenerator();
		
		String moleculeSmile1 = sg.createChiralSMILES(mol1, new boolean[mol1.getBondCount()]);
		String moleculeSmile2 = sg.createChiralSMILES(mol2, new boolean[mol2.getBondCount()]);
		assertFalse(moleculeSmile1.equals(moleculeSmile2));
	}
	
	
	/**
	 * @cdk.bug 1014344
	 */
	public void testSFBug1014344_1() throws Exception {
		String filename_cml = "data/cml/bug1014344-1.cml";
		String filename_mol = "data/mdl/bug1014344-1.mol";
		InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(filename_cml);
		InputStream ins2 = this.getClass().getClassLoader().getResourceAsStream(filename_mol);
		CMLReader reader1 = new CMLReader(ins1);
        IChemFile chemFile = (IChemFile)reader1.read(new ChemFile());
        IChemSequence seq = chemFile.getChemSequence(0);
        IChemModel model = seq.getChemModel(0);
        IMolecule mol1 = model.getMoleculeSet().getMolecule(0);
		
		MDLReader reader2 = new MDLReader(ins2);		
		Molecule mol2 = (Molecule) reader2.read(new Molecule());
		
		SmilesGenerator sg = new SmilesGenerator();
		
		String moleculeSmile1 = sg.createSMILES(mol1);
//		logger.debug(filename_cml + " -> " + moleculeSmile1);
		String moleculeSmile2 = sg.createSMILES(mol2);
//		logger.debug(filename_mol + " -> " + moleculeSmile2);
		assertEquals(moleculeSmile1, moleculeSmile2);
	}

}