smilesgeneratortest.java

化学图形处理软件

		try
		{
			smiles1 = sg.createSMILES(mol1, true, bool);
		} catch (Exception exc)
		{
			System.out.println(exc);
			if (!standAlone)
			{
				fail();
			}
		}
		if (standAlone)
		{
			System.err.println("SMILES 1: " + smiles1);
		}
		assertNotNull(smiles1);
		assertTrue(smiles1.equals("F/C(=C/(F)S)S"));
		mol1.getAtom(4).setPoint2d(new Point2d(0, 3));
		mol1.getAtom(5).setPoint2d(new Point2d(2, 3));
		try
		{
			smiles1 = sg.createSMILES(mol1, true, bool);
		} catch (Exception exc)
		{
			System.out.println(exc);
			if (!standAlone)
			{
				fail();
			}
		}
		if (standAlone)
		{
			System.err.println("SMILES 1: " + smiles1);
		}
		assertNotNull(smiles1);
		assertTrue(smiles1.equals("F/C(=C\\(F)S)S"));
		try
		{
			new HydrogenAdder().addHydrogensToSatisfyValency(mol1);
			hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
		} catch (IOException ex)
		{
		} catch (ClassNotFoundException ex)
		{
		}
		bool = new boolean[mol1.getBondCount()];
		bool[2] = true;
		try
		{
			smiles1 = sg.createSMILES(mol1, true, bool);
		} catch (Exception exc)
		{
			System.out.println(exc);
			if (!standAlone)
			{
				fail();
			}
		}
		assertTrue(smiles1.equals("[H]S/C(F)=C/(F)S[H]"));
		mol1.getAtom(5).setPoint2d(new Point2d(0, 3));
		mol1.getAtom(4).setPoint2d(new Point2d(2, 3));
		try
		{
			smiles1 = sg.createSMILES(mol1, true, bool);
		} catch (Exception exc)
		{
			System.out.println(exc);
			if (!standAlone)
			{
				fail();
			}
		}
		assertTrue(smiles1.equals("[H]S/C(F)=C\\(F)S[H]"));
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testPartitioning()
	{
		String smiles = "";
		Molecule molecule = new Molecule();
        SmilesGenerator sg = new SmilesGenerator();
		Atom sodium = new Atom("Na");
		sodium.setFormalCharge(+1);
		Atom hydroxyl = new Atom("O");
		hydroxyl.setHydrogenCount(1);
		hydroxyl.setFormalCharge(-1);
		molecule.addAtom(sodium);
		molecule.addAtom(hydroxyl);
		try
		{
			smiles = sg.createSMILES(molecule);
		} catch (Exception exc)
		{
			System.out.println(exc);
			if (!standAlone)
			{
				fail();
			}
		}
		if (standAlone)
		{
			System.err.println("SMILES: " + smiles);
		}
		assertTrue(smiles.indexOf(".") != -1);
	}


	/**
	 *  A unit test for JUnit
	 */
	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);
		try
		{
			smiles = sg.createSMILES(molecule);
		} catch (Exception exc)
		{
			System.out.println(exc);
			if (!standAlone)
			{
				fail();
			}
		}
		if (standAlone)
		{
			System.err.println("SMILES: " + smiles);
		}
		assertEquals("N1(C)CCC1", smiles);
	}


	/**
	 *  A bug reported for JChemPaint.
	 */
	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);
		try
		{
			smiles = sg.createSMILES(molecule);
		} catch (Exception exc)
		{
			fail(exc.getMessage());
		}
		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());
			}
			if (standAlone)
			{
				System.out.println("Hydrogen count for atom " + f + ": " + atom.getHydrogenCount());
			}
		}
	}


	/**
	 *  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);
		try
		{
			smiles = sg.createSMILES(molecule);
		} catch (Exception exc)
		{
			System.out.println(exc);
			if (!standAlone)
			{
				fail();
			}
		}
		if (standAlone)
		{
			System.err.println("SMILES: " + smiles);
		}
		assertEquals("[*]", smiles);

	}


	/**
	 *  Test generation of a reaction SMILES. I know, it's a stupid alchemic
	 *  reaction, but it serves its purpose.
	 */
	public void testReactionSMILES()
	{
		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();
		try
		{
			String smiles = sg.createSMILES(reaction);
			//logger.debug("Generated SMILES: " + smiles);
			assertEquals("C>[*]>[Au]", smiles);
		} catch (Exception exc)
		{
			System.out.println(exc);
		}
	}


	/**
	 *  Test generation of a d and l alanin
	 */
	public void testAlaSMILES()
	{
		try
		{
			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]);
			assertFalse(smiles1.equals(smiles2));
		} catch (Exception exc)
		{
			System.out.println(exc);
		}
	}


	/**
	 *  Test some sugars
	 */
	public void testSugarSMILES()
	{
		try
		{
			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 HydrogenAdder().addExplicitHydrogensToSatisfyValency(mol1);
			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 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]);
			assertFalse(smiles1.equals(smiles2));
		} catch (Exception exc)
		{
			System.out.println(exc);
		}
	}

	private void display(Molecule molecule)
	{
		StructureDiagramGenerator sdg = new StructureDiagramGenerator();
		MoleculeViewer2D mv = new MoleculeViewer2D();
		Renderer2DModel r2dm = mv.getRenderer2DModel();
		r2dm.setDrawNumbers(true);

		try
		{
			sdg.setMolecule((Molecule) molecule.clone());
			sdg.generateCoordinates(new Vector2d(0, 1));
			mv.setAtomContainer(sdg.getMolecule());
			mv.display();
		} catch (Exception exc)
		{
			System.out.println("*** Exit due to an unexpected error during coordinate generation ***");
			exc.printStackTrace();
		}
	}


	/**
	 *  Test for some rings where the double bond is broken
	 */
	public void testCycloOctan()
	{
		try
		{
			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");
		} catch (Exception exc)
		{
			exc.printStackTrace();
			System.out.println(exc);
			fail(exc.getMessage());
		}
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testCycloOcten()
	{
		try
		{
			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");
		} catch (Exception exc)
		{
			exc.printStackTrace();
			System.out.println(exc);
			fail(exc.getMessage());
		}
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testCycloOctadien()
	{
		try
		{
			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");
		} catch (Exception exc)
		{
			exc.printStackTrace();
			System.out.println(exc);
			fail(exc.getMessage());
		}
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testSFBug1089770_1()
	{
		try
		{
			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)");
		} catch (Exception exc)
		{
			exc.printStackTrace();
			System.out.println(exc);
			fail(exc.getMessage());
		}
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testSFBug1089770_2()
	{
		try
		{
			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");
		} catch (Exception exc)
		{
			exc.printStackTrace();
			System.out.println(exc);
			fail(exc.getMessage());
		}
	}

}