hydrogenaddertest.java

化学图形处理软件

        mol.addBond(b1);
        mol.addBond(b2);
        mol.addBond(b3);
 
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(6, mol.getAtomCount());
        assertEquals(5, mol.getBondCount());
        assertEquals(2, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(3, mol.getConnectedBondsCount(s));
    }
    
    public void testAceticAcid() throws Exception {
        Molecule mol = new Molecule();
        Atom carbonylOxygen = new Atom("O");
        Atom hydroxylOxygen = new Atom("O");
        Atom methylCarbon = new Atom("C");
        Atom carbonylCarbon = new Atom("C");
        mol.addAtom(carbonylOxygen);
        mol.addAtom(hydroxylOxygen);
        mol.addAtom(methylCarbon);
        mol.addAtom(carbonylCarbon);
        Bond b1 = new Bond(methylCarbon, carbonylCarbon, 1.0);
        Bond b2 = new Bond(carbonylOxygen, carbonylCarbon, 2.0);
        Bond b3 = new Bond(hydroxylOxygen, carbonylCarbon, 1.0);
        mol.addBond(b1);
        mol.addBond(b2);
        mol.addBond(b3);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(8, mol.getAtomCount());
        assertEquals(7, mol.getBondCount());
        assertEquals(4, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(1, mol.getConnectedBondsCount(carbonylOxygen));
        assertEquals(2, mol.getConnectedBondsCount(hydroxylOxygen));
        assertEquals(4, mol.getConnectedBondsCount(methylCarbon));
        assertEquals(3, mol.getConnectedBondsCount(carbonylCarbon));
    }
    
    public void testEthane() throws Exception {
        Molecule mol = new Molecule();
        Atom carbon1 = new Atom("C");
        Atom carbon2 = new Atom("C");
        Bond b = new Bond(carbon1, carbon2, 1.0);
        mol.addAtom(carbon1);
        mol.addAtom(carbon2);
        mol.addBond(b);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(8, mol.getAtomCount());
        assertEquals(7, mol.getBondCount());
        assertEquals(6, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(4, mol.getConnectedBondsCount(carbon1));
        assertEquals(4, mol.getConnectedBondsCount(carbon2));
    }

    public void testEthene() throws Exception {
        Molecule mol = new Molecule();
        Atom carbon1 = new Atom("C");
        Atom carbon2 = new Atom("C");
        Bond b = new Bond(carbon1, carbon2, 2.0);
        mol.addAtom(carbon1);
        mol.addAtom(carbon2);
        mol.addBond(b);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(6, mol.getAtomCount());
        assertEquals(5, mol.getBondCount());
        assertEquals(4, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(3, mol.getConnectedBondsCount(carbon1));
        assertEquals(3, mol.getConnectedBondsCount(carbon2));
    }

    public void testEthyne() throws Exception {
        Molecule mol = new Molecule();
        Atom carbon1 = new Atom("C");
        Atom carbon2 = new Atom("C");
        Bond b = new Bond(carbon1, carbon2, 3.0);
        mol.addAtom(carbon1);
        mol.addAtom(carbon2);
        mol.addBond(b);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(4, mol.getAtomCount());
        assertEquals(3, mol.getBondCount());
        assertEquals(2, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(2, mol.getConnectedBondsCount(carbon1));
        assertEquals(2, mol.getConnectedBondsCount(carbon2));
    }

    public void testAromaticSaturation() throws Exception {
        Molecule mol = new Molecule();
        mol.addAtom(new Atom("C")); // 0
        mol.addAtom(new Atom("C")); // 1
        mol.addAtom(new Atom("C")); // 2
        mol.addAtom(new Atom("C")); // 3
        mol.addAtom(new Atom("C")); // 4
        mol.addAtom(new Atom("C")); // 5
        mol.addAtom(new Atom("C")); // 6
        mol.addAtom(new Atom("C")); // 7
        
        
        mol.addBond(0, 1, 1.0); // 1
        mol.addBond(1, 2, 1.0); // 2
        mol.addBond(2, 3, 1.0); // 3
        mol.addBond(3, 4, 1.0); // 4
        mol.addBond(4, 5, 1.0); // 5
        mol.addBond(5, 0, 1.0); // 6
        mol.addBond(0, 6, 1.0); // 7
        mol.addBond(6, 7, 3.0); // 8
        
        for (int f = 0; f < 6; f++) {
            mol.getAtom(f).setFlag(CDKConstants.ISAROMATIC, true);
            mol.getAtom(f).setHybridization(CDKConstants.HYBRIDIZATION_SP2);
            mol.getBond(f).setFlag(CDKConstants.ISAROMATIC, true);
        }
        adder.addHydrogensToSatisfyValency(mol);
        new SaturationChecker().saturate(mol);
        MFAnalyser mfa = new MFAnalyser(mol);
        assertEquals(6, mfa.getAtomCount("H"));
    }
    
    public void testAddImplicitHydrogens() throws Exception {
        Molecule molecule = null;
        String filename = "data/mdl/saturationcheckertest.mol";
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLReader reader = new MDLReader(ins);
        molecule = (Molecule)reader.read((ChemObject)new Molecule());
        adder.addHydrogensToSatisfyValency(molecule);
    }
    
    /**
     * Tests wether the it actually resets an old value if zero missing hydrogens
     * were calculated (bug found 2004-01-09 by egonw).
     */
    public void testaddImplicitHydrogensToSatisfyValency_OldValue() throws Exception {
        Molecule mol = new Molecule();
        mol.addAtom(new Atom("C"));
        Atom oxygen = new Atom("O");
        mol.addAtom(oxygen);
        mol.addAtom(new Atom("C"));
        
        mol.addBond(0, 1, 1.0);
        mol.addBond(1, 2, 1.0);
        
        oxygen.setHydrogenCount(2); /* e.g. caused by the fact that the element symbol
                                       was changed from C to O (=actual bug) */
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(0, oxygen.getHydrogenCount());
    }

    public void testRadical() throws Exception 
    {
    	Molecule mol = new Molecule();
    	mol.addAtom(new Atom("C"));
    	mol.addAtom(new Atom("C"));
    	mol.addSingleElectron(mol.getBuilder().newSingleElectron(mol.getAtom(0)));
    	mol.addBond(0,1,1);
    	adder.addImplicitHydrogensToSatisfyValency(mol);
    	assertEquals(3, mol.getAtom(1).getHydrogenCount());
    	assertEquals(2, mol.getAtom(0).getHydrogenCount());
    	
    }
    /**
     * @cdk.bug 1575269
     *
     */
    public void testAdenine() throws Exception 
    {
    	IMolecule mol = new Molecule(); // Adenine
    	IAtom a1 = mol.getBuilder().newAtom("C");
    	a1.setPoint2d(new Point2d(21.0223, -17.2946));  mol.addAtom(a1);
    	IAtom a2 = mol.getBuilder().newAtom("C");
    	a2.setPoint2d(new Point2d(21.0223, -18.8093));  mol.addAtom(a2);
    	IAtom a3 = mol.getBuilder().newAtom("C");
    	a3.setPoint2d(new Point2d(22.1861, -16.6103));  mol.addAtom(a3);
    	IAtom a4 = mol.getBuilder().newAtom("N");
    	a4.setPoint2d(new Point2d(19.8294, -16.8677));  mol.addAtom(a4);
    	IAtom a5 = mol.getBuilder().newAtom("N");
    	a5.setPoint2d(new Point2d(22.2212, -19.5285));  mol.addAtom(a5);
    	IAtom a6 = mol.getBuilder().newAtom("N");
    	a6.setPoint2d(new Point2d(19.8177, -19.2187));  mol.addAtom(a6);
    	IAtom a7 = mol.getBuilder().newAtom("N");
    	a7.setPoint2d(new Point2d(23.4669, -17.3531));  mol.addAtom(a7);
    	IAtom a8 = mol.getBuilder().newAtom("N");
    	a8.setPoint2d(new Point2d(22.1861, -15.2769));  mol.addAtom(a8);
    	IAtom a9 = mol.getBuilder().newAtom("C");
    	a9.setPoint2d(new Point2d(18.9871, -18.0139));  mol.addAtom(a9);
    	IAtom a10 = mol.getBuilder().newAtom("C");
    	a10.setPoint2d(new Point2d(23.4609, -18.8267));  mol.addAtom(a10);
    	IBond b1 = mol.getBuilder().newBond(a1, a2, 2.0);
    	mol.addBond(b1);
    	IBond b2 = mol.getBuilder().newBond(a1, a3, 1.0);
    	mol.addBond(b2);
    	IBond b3 = mol.getBuilder().newBond(a1, a4, 1.0);
    	mol.addBond(b3);
    	IBond b4 = mol.getBuilder().newBond(a2, a5, 1.0);
    	mol.addBond(b4);
    	IBond b5 = mol.getBuilder().newBond(a2, a6, 1.0);
    	mol.addBond(b5);
    	IBond b6 = mol.getBuilder().newBond(a3, a7, 2.0);
    	mol.addBond(b6);
    	IBond b7 = mol.getBuilder().newBond(a3, a8, 1.0);
    	mol.addBond(b7);
    	IBond b8 = mol.getBuilder().newBond(a4, a9, 2.0);
    	mol.addBond(b8);
    	IBond b9 = mol.getBuilder().newBond(a5, a10, 2.0);
    	mol.addBond(b9);
    	IBond b10 = mol.getBuilder().newBond(a6, a9, 1.0);
    	mol.addBond(b10);
    	IBond b11 = mol.getBuilder().newBond(a7, a10, 1.0);
    	mol.addBond(b11);
    	HydrogenAdder ha = new HydrogenAdder();
    	HueckelAromaticityDetector.detectAromaticity(mol);
    	ha.addExplicitHydrogensToSatisfyValency(mol);
    	MFAnalyser mfa1 = new MFAnalyser(mol);
    	assertEquals(5, mfa1.getAtomCount("H"));
    	
    }
    
    /**
     * @cdk.bug 1727373
     *
     */
    public void testBug1727373() throws Exception {
        Molecule molecule = null;
        String filename = "data/mdl/carbocations.mol";
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLReader reader = new MDLReader(ins);
        molecule = (Molecule)reader.read((ChemObject)new Molecule());
        adder.addImplicitHydrogensToSatisfyValency(molecule);
        assertEquals(2,molecule.getAtom(0).getHydrogenCount());
        assertEquals(0,molecule.getAtom(1).getHydrogenCount());
        assertEquals(1,molecule.getAtom(2).getHydrogenCount());
        assertEquals(2,molecule.getAtom(3).getHydrogenCount());
    }
    
}