smilesparsertest.java

化学图形处理软件

		IMolecule mol = sp.parseSmiles(sodiumPhenoxide);
		assertEquals(8, mol.getAtomCount());
		assertEquals(7, mol.getBondCount());
		
		IMoleculeSet fragments = ConnectivityChecker.partitionIntoMolecules(mol);
		int fragmentCount = fragments.getMoleculeCount();
		assertEquals(2, fragmentCount);
		org.openscience.cdk.interfaces.IMolecule mol1 = fragments.getMolecule(0);
		org.openscience.cdk.interfaces.IMolecule mol2 = fragments.getMolecule(1);
		// one should have one atom, the other seven atoms
		// in any order, so just test the difference
		assertEquals(6, Math.abs(mol1.getAtomCount() - mol2.getAtomCount()));
	}


	/**
	 *  Example taken from 'Handbook of Chemoinformatics', Gasteiger, 2003, page 89
	 *  (Part I).
	 */
	public void testConnectedByRingClosure() throws Exception {
		String sodiumPhenoxide = "C1.O2.C12";
		IMolecule mol = sp.parseSmiles(sodiumPhenoxide);
		assertEquals(3, mol.getAtomCount());
		assertEquals(2, mol.getBondCount());
		
		IMoleculeSet fragments = ConnectivityChecker.partitionIntoMolecules(mol);
		int fragmentCount = fragments.getMoleculeCount();
		assertEquals(1, fragmentCount);
		org.openscience.cdk.interfaces.IMolecule mol1 = fragments.getMolecule(0);
		assertEquals(3, mol1.getAtomCount());
	}


	/**
	 *  Example taken from 'Handbook of Chemoinformatics', Gasteiger, 2003, page 89
	 *  (Part I).
	 */
	public void testReaction() throws Exception {
		String reactionSmiles = "O>>[H+].[OH-]";
		IReaction reaction = sp.parseReactionSmiles(reactionSmiles);
		assertEquals(1, reaction.getReactantCount());
		assertEquals(2, reaction.getProductCount());
	}


	/**
	 *  Example taken from 'Handbook of Chemoinformatics', Gasteiger, 2003, page 90
	 *  (Part I).
	 */
	public void testReactionWithAgents() throws Exception {
		String reactionSmiles = "CCO.CC(=O)O>[H+]>CC(=O)OCC.O";
		IReaction reaction = sp.parseReactionSmiles(reactionSmiles);
		assertEquals(2, reaction.getReactantCount());
		assertEquals(2, reaction.getProductCount());
		assertEquals(1, reaction.getAgents().getMoleculeCount());
		
		assertEquals(1, reaction.getAgents().getMolecule(0).getAtomCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testImplicitHydrogenCount() throws Exception {
		String smiles = "C";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(1, mol.getAtomCount());
		assertEquals(4, mol.getAtom(0).getHydrogenCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testImplicitHydrogenCount2() throws Exception {
		String smiles = "CC";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(2, mol.getAtomCount());
		assertEquals(3, mol.getAtom(0).getHydrogenCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testImplicitHydrogenCount2b() throws Exception {
		String smiles = "C=C";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(2, mol.getAtomCount());
		assertEquals(2, mol.getAtom(0).getHydrogenCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testImplicitHydrogenCount2c() throws Exception {
		String smiles = "C#C";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(2, mol.getAtomCount());
		assertEquals(1, mol.getAtom(0).getHydrogenCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testImplicitHydrogenCount3() throws Exception {
		String smiles = "CCC";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(3, mol.getAtomCount());
		assertEquals(2, mol.getAtom(1).getHydrogenCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testImplicitHydrogenCount4() throws Exception {
		String smiles = "C1CCCCC1";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(6, mol.getAtomCount());
		assertEquals(2, mol.getAtom(0).getHydrogenCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testImplicitHydrogenCount4a() throws Exception {
		String smiles = "c1=cc=cc=c1";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(6, mol.getAtomCount());
		assertEquals(1, mol.getAtom(0).getHydrogenCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testImplicitHydrogenCount4b() throws Exception {
		String smiles = "c1ccccc1";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(6, mol.getAtomCount());
		assertEquals(1, mol.getAtom(0).getHydrogenCount());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testHOSECodeProblem() throws Exception {
		String smiles = "CC=CBr";
		IMolecule mol = sp.parseSmiles(smiles);
		assertEquals(4, mol.getAtomCount());
		assertEquals("Br", mol.getAtom(3).getSymbol());
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testPyridine() throws Exception {
		IMolecule mol = sp.parseSmiles("c1ccncc1");
		assertEquals(6, mol.getAtomCount());
		// it's a bit hard to detect two double bonds in the pyrrole ring
		// but I do can check the total order in the whole molecule
		double totalBondOrder = 0.0;
		Iterator bonds = mol.bonds();
		while (bonds.hasNext())
			totalBondOrder += ((IBond)bonds.next()).getOrder();
		assertEquals(9.0, totalBondOrder, 0.001);
		// I can also check wether the total neighbor count around the
		// nitrogen is 3, all single bonded
		org.openscience.cdk.interfaces.IAtom nitrogen = mol.getAtom(3);
		// the second atom
		assertEquals("N", nitrogen.getSymbol());
		totalBondOrder = 0.0;
		List bondsList = mol.getConnectedBondsList(nitrogen);
		assertEquals(2, bondsList.size());
		for (int i = 0; i < bondsList.size(); i++)
		{
			totalBondOrder += ((IBond)bondsList.get(i)).getOrder();
		}
		assertEquals(3.0, totalBondOrder, 0.001);
	}

	/**
	 * @cdk.bug 1306780
	 */
	public void testParseK() throws CDKException {
		IMolecule mol = sp.parseSmiles("C=CCC(=NOS(=O)(=O)[O-])SC1OC(CO)C(O)C(O)C1(O).[Na+]");
		assertNotNull(mol);
		assertEquals(23, mol.getAtomCount());
		mol = sp.parseSmiles("C=CCC(=NOS(=O)(=O)[O-])SC1OC(CO)C(O)C(O)C1(O).[K]");
		assertNotNull(mol);
		assertEquals(23, mol.getAtomCount());
		mol = sp.parseSmiles("C=CCC(=NOS(=O)(=O)[O-])SC1OC(CO)C(O)C(O)C1(O).[K+]");
		assertNotNull(mol);
		assertEquals(23, mol.getAtomCount());
	}
	
	
	/**
	 * @cdk.bug 1459299
	 */
	public void testBug1459299() throws Exception {
		IMolecule mol = sp.parseSmiles("Cc1nn(C)cc1[C@H]2[C@H](C(=O)N)C(=O)C[C@@](C)(O)[C@@H]2C(=O)N");
		assertNotNull(mol);
		assertEquals(22, mol.getAtomCount());
	}
	
	/**
	 * @cdk.bug 1365547
	 */
	public void testBug1365547() throws Exception {
		IMolecule mol = sp.parseSmiles("c2ccc1[nH]ccc1c2");
		assertNotNull(mol);
		assertEquals(9, mol.getAtomCount());
		assertTrue(mol.getBond(0).getFlag(CDKConstants.ISAROMATIC));
	}
	
	/**
	 * @cdk.bug 1365547
	 */
	public void testBug1365547_2() throws Exception {
		IMolecule mol = sp.parseSmiles("[H]c1c([H])c(c([H])c2c([H])c([H])n([H])c12)Br");
		assertNotNull(mol);
		assertEquals(16, mol.getAtomCount());
		assertEquals(17, mol.getBondCount());
		for (int i=0; i<17; i++) {
			IBond bond = mol.getBond(i);
			if (bond.getAtom(0).getSymbol().equals("H") ||
					bond.getAtom(0).getSymbol().equals("Br") ||
					bond.getAtom(1).getSymbol().equals("H") ||
					bond.getAtom(1).getSymbol().equals("Br")) {
				assertFalse(bond.getFlag(CDKConstants.ISAROMATIC));
			} else {
				assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
			}
		}
	}
	
	/**
	 * @cdk.bug 1235852
	 */
	public void testBug1235852() throws Exception {
		//                             0 1 234 56 7 890 12 3456 78
		IMolecule mol = sp.parseSmiles("O=C(CCS)CC(C)CCC2Cc1ccsc1CC2");
		assertNotNull(mol);
		assertEquals(19, mol.getAtomCount());
		assertEquals(20, mol.getBondCount());
		// test only option for delocalized bond system
		assertEquals(4.0, mol.getBondOrderSum(mol.getAtom(12)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(13)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(14)), 0.001);
		assertEquals(2.0, mol.getBondOrderSum(mol.getAtom(15)), 0.001);
		assertEquals(4.0, mol.getBondOrderSum(mol.getAtom(16)), 0.001);
	}
	
	/**
	 * @cdk.bug 1519183
	 */
	public void testBug1519183() throws Exception {
		//                             0    12345  6
		IMolecule mol = sp.parseSmiles("c%101ccccc1.O%10"); // phenol
		assertNotNull(mol);
		assertEquals(7, mol.getAtomCount());
		assertEquals(7, mol.getBondCount());
	}
	
	/**
	 * @cdk.bug 1530926
	 */
	public void testBug1530926() throws Exception {
		//                              0      12345   6
		IMolecule mol = sp.parseSmiles("[n+]%101ccccc1.[O-]%10");
		assertNotNull(mol);
		assertEquals(7, mol.getAtomCount());
		assertEquals(7, mol.getBondCount());
		for (int i=0; i<7; i++) {
			IBond bond = mol.getBond(i);
			if (bond.getAtom(0).getSymbol().equals("O") ||
					bond.getAtom(1).getSymbol().equals("O")) {
				assertFalse(bond.getFlag(CDKConstants.ISAROMATIC));
			} else {
				assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
			}
		}
	}

	/**
	 * @cdk.bug 1541333
	 */
	public void testBug1541333() throws Exception {
		//                              01  2 345  67  8 9 0 12 3 4  5 67 89  0  1 2
		IMolecule mol1 = sp.parseSmiles("OC(=O)CSC1=NC=2C=C(C=CC2N1C=3C=CC=CC3)N(=O)O");
		assertNotNull(mol1);
		assertEquals(23, mol1.getAtomCount());
		assertEquals(25, mol1.getBondCount());
		IMolecule mol2 = sp.parseSmiles("OC(=O)CSc1nc2cc(ccc2n1c3ccccc3)N(=O)O");
		assertNotNull(mol2);
		assertEquals(23, mol2.getAtomCount());
		assertEquals(25, mol2.getBondCount());
		// do some checking
		assertEquals(2.0, mol1.getBond(1).getOrder(), 0.0001);
		assertEquals(2.0, mol2.getBond(1).getOrder(), 0.0001);
		assertTrue(mol1.getBond(7).getFlag(CDKConstants.ISAROMATIC));
		assertTrue(mol2.getBond(7).getFlag(CDKConstants.ISAROMATIC));
	}
	/**
	 * @cdk.bug 1719287
	 */
	public void testBug1719287() throws Exception {
		//                             0  1 23 45
		IMolecule mol = sp.parseSmiles("OC(=O)[C@@H](N)CC[S+1](C)C[C@@H](O1)[C@@H](O)[C@@H](O)[C@@H]1n(c3)c(n2)c(n3)c(N)nc2");
		assertNotNull(mol);
		assertEquals(6, mol.getAtomCount());
		assertEquals(6, mol.getBondCount());
		// test only option for delocalized bond system
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(0)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(1)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(2)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(3)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(4)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(5)), 0.001);			
	}
	
	/**
	 * @cdk.bug 1503541
	 */
	public void testBug1503541() throws Exception {
		//                             0  1 23 45
		IMolecule mol = sp.parseSmiles("C=1C=CC=CC=1"); // phenol
		assertNotNull(mol);
		assertEquals(6, mol.getAtomCount());
		assertEquals(6, mol.getBondCount());
		// test only option for delocalized bond system
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(0)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(1)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(2)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(3)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(4)), 0.001);
		assertEquals(3.0, mol.getBondOrderSum(mol.getAtom(5)), 0.001);			
	}
	
}