atomcontainertest.java

化学图形处理软件

        assertEquals(1.0, acetone.getMinimumBondOrder(c2), 0.0001);
        assertEquals(1.0, acetone.getMinimumBondOrder(c3), 0.0001);
    }

    public void testRemoveElectronContainer_int() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        acetone.addLonePair(2);
        acetone.addLonePair(2);
        IBond b1 = builder.newBond(c1, c2,1);
        IBond b2 = builder.newBond(c1, o, 2);
        IBond b3 = builder.newBond(c1, c3,1);
        acetone.addBond(b1);
        acetone.addBond(b2);
        acetone.addBond(b3);
        
        assertEquals(3, acetone.getBondCount());
        assertEquals(5, acetone.getElectronContainerCount());
        acetone.removeElectronContainer(3);
        assertEquals(3, acetone.getBondCount());
        assertEquals(4, acetone.getElectronContainerCount());
        acetone.removeElectronContainer(0); // first bond now
        assertEquals(2, acetone.getBondCount());
        assertEquals(3, acetone.getElectronContainerCount());
    }

    public void testRemoveElectronContainer_IElectronContainer() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        ILonePair firstLP = builder.newLonePair(o);
        acetone.addElectronContainer(firstLP);
        acetone.addElectronContainer(builder.newLonePair(o));
        IBond b1 = builder.newBond(c1, c2,1);
        IBond b2 = builder.newBond(c1, o, 2);
        IBond b3 = builder.newBond(c1, c3,1);
        acetone.addBond(b1);
        acetone.addBond(b2);
        acetone.addBond(b3);
        
        assertEquals(3, acetone.getBondCount());
        assertEquals(5, acetone.getElectronContainerCount());
        acetone.removeElectronContainer(firstLP);
        assertEquals(3, acetone.getBondCount());
        assertEquals(4, acetone.getElectronContainerCount());
        acetone.removeElectronContainer(b1); // first bond now
        assertEquals(2, acetone.getBondCount());
        assertEquals(3, acetone.getElectronContainerCount());
    }

    public void testAddBond_IBond() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        IBond b1 = builder.newBond(c1, c2,1);
        IBond b2 = builder.newBond(c1, o, 2);
        IBond b3 = builder.newBond(c1, c3,1);
        acetone.addBond(b1);
        acetone.addBond(b2);
        acetone.addBond(b3);
        
        assertEquals(3, acetone.getBondCount());
        Iterator bonds = acetone.bonds();
        while (bonds.hasNext()) assertNotNull(bonds.next());
        assertEquals(b1, acetone.getBond(0));
        assertEquals(b2, acetone.getBond(1));
        assertEquals(b3, acetone.getBond(2));
    }

//    public void testSetElectronContainers_arrayIElectronContainer() {
//        // acetone molecule
//        IMolecule acetone = builder.newMolecule();
//        IAtom c1 = builder.newAtom("C");
//        IAtom c2 = builder.newAtom("C");
//        IAtom o = builder.newAtom("O");
//        IAtom c3 = builder.newAtom("C");
//        acetone.addAtom(c1);
//        acetone.addAtom(c2);
//        acetone.addAtom(c3);
//        acetone.addAtom(o);
//        IElectronContainer[] electronContainers = new IElectronContainer[3];
//        electronContainers[0] = builder.newBond(c1, c2,1);
//        electronContainers[1] = builder.newBond(c1, o, 2);
//        electronContainers[2] = builder.newBond(c1, c3,1);
//        acetone.setElectronContainers(electronContainers);
//        
//        assertEquals(3, acetone.getBondCount());
//        org.openscience.cdk.interfaces.IBond[] bonds = acetone.getBonds();
//        for (int i=0; i<bonds.length; i++) {
//            assertNotNull(bonds[i]);
//        }
//        assertEquals(electronContainers[0], bonds[0]);
//        assertEquals(electronContainers[1], bonds[1]);
//        assertEquals(electronContainers[2], bonds[2]);
//    }

//    public void testAddElectronContainers_IAtomContainer() {
//        // acetone molecule
//        IMolecule acetone = builder.newMolecule();
//        IAtom c1 = builder.newAtom("C");
//        IAtom c2 = builder.newAtom("C");
//        IAtom o = builder.newAtom("O");
//        IAtom c3 = builder.newAtom("C");
//        acetone.addAtom(c1);
//        acetone.addAtom(c2);
//        acetone.addAtom(c3);
//        acetone.addAtom(o);
//        IElectronContainer[] electronContainers = new IElectronContainer[3];
//        electronContainers[0] = builder.newBond(c1, c2,1);
//        electronContainers[1] = builder.newBond(c1, o, 2);
//        electronContainers[2] = builder.newBond(c1, c3,1);
//        acetone.setElectronContainers(electronContainers);
//        
//        IAtomContainer tested = builder.newAtomContainer();
//        tested.addBond(builder.newBond(c2, c3));
//        tested.addElectronContainers(acetone);
//        
//        assertEquals(0, tested.getAtomCount());
//        assertEquals(4, tested.getBondCount());
//        org.openscience.cdk.interfaces.IBond[] bonds = tested.getBonds();
//        for (int i=0; i<bonds.length; i++) {
//            assertNotNull(bonds[i]);
//        }
//        assertEquals(electronContainers[0], bonds[1]);
//        assertEquals(electronContainers[1], bonds[2]);
//        assertEquals(electronContainers[2], bonds[3]);
//    }

    public void testAddElectronContainer_IElectronContainer() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        IAtom c = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        acetone.addAtom(c);
        acetone.addAtom(o);
        IBond b1 = builder.newBond(c, o, 2.0);
        acetone.addElectronContainer(b1);
        acetone.addElectronContainer(builder.newLonePair(o));
        acetone.addElectronContainer(builder.newSingleElectron(c));

        assertEquals(3, acetone.getElectronContainerCount());
        assertEquals(1, acetone.getBondCount());
        assertEquals(1, acetone.getLonePairCount());
    }

    public void testGetSingleElectron_IAtom() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        IAtom c = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        acetone.addAtom(c);
        acetone.addAtom(o);
        IBond b1 = builder.newBond(c, o, 2.0);
        acetone.addBond(b1);
        acetone.addLonePair(builder.newLonePair(o));
        ISingleElectron single = builder.newSingleElectron(c);
        acetone.addSingleElectron(single);

        assertEquals(1, acetone.getConnectedSingleElectronsCount(c));
        assertEquals(single, (ISingleElectron)acetone.getConnectedSingleElectronsList(c).get(0));
    }

    public void testRemoveBond_IAtom_IAtom() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        IBond b1 = builder.newBond(c1, c2,1);
        IBond b2 = builder.newBond(c1, o, 2);
        IBond b3 = builder.newBond(c1, c3,1);
        acetone.addBond(b1);
        acetone.addBond(b2);
        acetone.addBond(b3);
        
        assertEquals(3, acetone.getBondCount());
        acetone.removeBond(c1, o);
        assertEquals(2, acetone.getBondCount());
        assertEquals(b1, acetone.getBond(0));
        assertEquals(b3, acetone.getBond(1));
    }

    public void testAddBond_int_int_double() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        acetone.addBond(0, 1, 1);
        acetone.addBond(1, 3, 2);
        acetone.addBond(1, 2, 1);
        
        assertEquals(3, acetone.getBondCount());
        Iterator bonds = acetone.bonds();
        while (bonds.hasNext()) assertNotNull(bonds.next());

        assertEquals(c1, acetone.getBond(0).getAtom(0));
        assertEquals(c2, acetone.getBond(0).getAtom(1));
        assertEquals(1.0, acetone.getBond(0).getOrder(), 0.001);
        assertEquals(c2, acetone.getBond(1).getAtom(0));
        assertEquals(o, acetone.getBond(1).getAtom(1));
        assertEquals(2.0, acetone.getBond(1).getOrder(), 0.001);
        assertEquals(c2, acetone.getBond(2).getAtom(0));
        assertEquals(c3, acetone.getBond(2).getAtom(1));
        assertEquals(1.0, acetone.getBond(2).getOrder(), 0.001);
    }

    public void testAddBond_int_int_double_int() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        acetone.addBond(0, 1, 1, CDKConstants.STEREO_BOND_UP); // yes this is crap
        acetone.addBond(1, 3, 2, CDKConstants.STEREO_BOND_DOWN);
        acetone.addBond(1, 2, 1, CDKConstants.STEREO_BOND_NONE);
        
        assertEquals(3, acetone.getBondCount());
        Iterator bonds = acetone.bonds();
        while (bonds.hasNext()) assertNotNull(bonds.next());

        assertEquals(c1, acetone.getBond(0).getAtom(0));
        assertEquals(c2, acetone.getBond(0).getAtom(1));
        assertEquals(1.0, acetone.getBond(0).getOrder(), 0.001);
        assertEquals(CDKConstants.STEREO_BOND_UP, acetone.getBond(0).getStereo());
        assertEquals(c2, acetone.getBond(1).getAtom(0));
        assertEquals(o, acetone.getBond(1).getAtom(1));
        assertEquals(2.0, acetone.getBond(1).getOrder(), 0.001);
        assertEquals(CDKConstants.STEREO_BOND_DOWN, acetone.getBond(1).getStereo());
        assertEquals(c2, acetone.getBond(2).getAtom(0));
        assertEquals(c3, acetone.getBond(2).getAtom(1));
        assertEquals(1.0, acetone.getBond(2).getOrder(), 0.001);
        assertEquals(CDKConstants.STEREO_BOND_NONE, acetone.getBond(2).getStereo());
    }

    public void testContains_IElectronContainer() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        IBond b1 = builder.newBond(c1, c2,1);
        IBond b2 = builder.newBond(c1, o, 2);
        IBond b3 = builder.newBond(c1, c3,1);
        acetone.addBond(b1);
        acetone.addBond(b2);
        acetone.addBond(b3);
        ILonePair lp1 = builder.newLonePair(o);
        ILonePair lp2 = builder.newLonePair(o);
        acetone.addLonePair(lp1);
        acetone.addLonePair(lp2);
        
        assertTrue(acetone.contains(b1));
        assertTrue(acetone.contains(b2));
        assertTrue(acetone.contains(b3));
        assertTrue(acetone.contains(lp1));
        assertTrue(acetone.contains(lp2));
    }
    
    public void testGetFirstAtom() {
        IAtomContainer container = builder.newAtomContainer();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("O");
        IAtom o = builder.newAtom("H");
        container.addAtom(c1);
        container.addAtom(c2);
        container.addAtom(o);
        
        assertNotNull(container.getFirstAtom());
        assertEquals("C", container.getFirstAtom().getSymbol());
    }

    public void testGetLastAtom() {
        IAtomContainer container = builder.newAtomContainer();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("O");
        IAtom o = builder.newAtom("H");
        container.addAtom(c1);
        container.addAtom(c2);
        container.addAtom(o);
        
        assertNotNull(container.getLastAtom());
        assertEquals("H", container.getLastAtom().getSymbol());
    }
    
    public void testGetAtomNumber_IAtom() {
        IMolecule acetone = builder.newMolecule();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        
        assertEquals(0, acetone.getAtomNumber(c1));
        assertEquals(1, acetone.getAtomNumber(c2));
        assertEquals(2, acetone.getAtomNumber(c3));
        assertEquals(3, acetone.getAtomNumber(o));
    }
    
    public void testGetBondNumber_IBond() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);