atomcontainertest.java

化学图形处理软件

        ILonePair lp1 = builder.newLonePair(o);
        ILonePair lp2 = builder.newLonePair(o);
        acetone.addLonePair(lp1);
        acetone.addLonePair(lp2);
        
        // remove the oxygen
        acetone.removeAtomAndConnectedElectronContainers(o);
        assertEquals(3, acetone.getAtomCount());
        assertEquals(2, acetone.getBondCount());
        assertEquals(0, acetone.getLonePairCount());
    }

    public void testGetAtomCount() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        assertEquals(0, acetone.getAtomCount());
        
        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(4, acetone.getAtomCount());
    }
    
    public void testGetBondCount() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        assertEquals(0, acetone.getBondCount());
        
        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());
    }
    
    public void testAtomContainer_int_int_int_int() {
        // create an empty container with predefined
        // array lengths
        IAtomContainer ac = new org.openscience.cdk.AtomContainer(5,6,1,2);
        
        assertEquals(0, ac.getAtomCount());
        assertEquals(0, ac.getElectronContainerCount());
        
        
        // test wether the ElectronContainer is correctly initialized
        ac.addBond(builder.newBond(builder.newAtom("C"), builder.newAtom("C"), 2));
        ac.addLonePair(builder.newLonePair(builder.newAtom("N")));
    }

    public void testAtomContainer() {
        // create an empty container with in the constructor defined array lengths
        IAtomContainer container = builder.newAtomContainer();
        
        assertEquals(0, container.getAtomCount());
        assertEquals(0, container.getBondCount());
        
        // test wether the ElectronContainer is correctly initialized
        container.addBond(builder.newBond(builder.newAtom("C"), builder.newAtom("C"), 2));
        container.addLonePair(builder.newLonePair(builder.newAtom("N")));
    }

    public void testAtomContainer_IAtomContainer() {
        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);
        
        IAtomContainer container = builder.newAtomContainer(acetone);
        assertEquals(4, container.getAtomCount());
        assertEquals(3, container.getBondCount());
    }
    
    public void testAdd_IAtomContainer() {
        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);
        
        IAtomContainer container = builder.newAtomContainer();
        container.add(acetone);
        assertEquals(4, container.getAtomCount());
        assertEquals(3, container.getBondCount());
    }
    
    public void testRemove_IAtomContainer() throws Exception {
        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);
        
        IAtomContainer container = builder.newAtomContainer();
        container.add(acetone);
        assertEquals(4, container.getAtomCount());
        assertEquals(3, container.getBondCount());
        container.remove((IAtomContainer)acetone.clone());
        assertEquals(4, container.getAtomCount());
        assertEquals(3, container.getBondCount());
        container.remove(acetone);
        assertEquals(0, container.getAtomCount());
        assertEquals(0, container.getBondCount());
    }
    
    public void testRemoveAllElements() {
        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);
        
        IAtomContainer container = builder.newAtomContainer();
        container.add(acetone);
        assertEquals(4, container.getAtomCount());
        assertEquals(3, container.getBondCount());
        container.removeAllElements();
        assertEquals(0, container.getAtomCount());
        assertEquals(0, container.getBondCount());
    }
    
    public void testRemoveAtom_int() {
        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(4, acetone.getAtomCount());
        acetone.removeAtom(1);
        assertEquals(3, acetone.getAtomCount());
        assertEquals(c1, acetone.getAtom(0));
        assertEquals(c3, acetone.getAtom(1));
        assertEquals(o, acetone.getAtom(2));
    }
    
    public void testRemoveAtom_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(4, acetone.getAtomCount());
        acetone.removeAtom(c3);
        assertEquals(3, acetone.getAtomCount());
        assertEquals(c1, acetone.getAtom(0));
        assertEquals(c2, acetone.getAtom(1));
        assertEquals(o, acetone.getAtom(2));
    }
    
    public void testSetAtom_int_IAtom() {
        IAtomContainer container = builder.newAtomContainer();
        IAtom c = builder.newAtom("C");
        container.setAtom(0, c);
        
        assertNotNull(container.getAtom(0));
        assertEquals("C", container.getAtom(0).getSymbol());
    }
    
    public void testGetAtom_int() {
        IAtomContainer acetone = builder.newAtomContainer();
        
        IAtom c = builder.newAtom("C");
        IAtom n = builder.newAtom("N");
        IAtom o = builder.newAtom("O");
        IAtom s = builder.newAtom("S");
        acetone.addAtom(c);
        acetone.addAtom(n);
        acetone.addAtom(o);
        acetone.addAtom(s);
        
        org.openscience.cdk.interfaces.IAtom a1 = acetone.getAtom(0);
        assertNotNull(a1);
        assertEquals("C", a1.getSymbol());
        org.openscience.cdk.interfaces.IAtom a2 = acetone.getAtom(1);
        assertNotNull(a2);
        assertEquals("N", a2.getSymbol());
        org.openscience.cdk.interfaces.IAtom a3 = acetone.getAtom(2);
        assertNotNull(a3);
        assertEquals("O", a3.getSymbol());
        org.openscience.cdk.interfaces.IAtom a4 = acetone.getAtom(3);
        assertNotNull(a4);
        assertEquals("S", a4.getSymbol());
    }
    
    public void testGetBond_int() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        assertEquals(0, acetone.getBondCount());
        
        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, c2,3.0);
        IBond b2 = builder.newBond(c1, o, 2.0);
        IBond b3 = builder.newBond(c1, c3,1.0);
        acetone.addBond(b1);
        acetone.addBond(b2);
        acetone.addBond(b3);
        
        assertEquals(3.0, acetone.getBond(0).getOrder(), 0.00001);
        assertEquals(2.0, acetone.getBond(1).getOrder(), 0.00001);
        assertEquals(1.0, acetone.getBond(2).getOrder(), 0.00001);
    }
    
//    public void testSetElectronContainer_int_IElectronContainer() {
//        IAtomContainer container = builder.newAtomContainer();
//        IAtom c1 = builder.newAtom("C");
//        IAtom c2 = builder.newAtom("C");
//        container.addAtom(c1);
//        container.addAtom(c2);
//        IBond b = builder.newBond(c1, c2, 3);
//        container.setElectronContainer(3, b);
//        
//        assertTrue(container.getElectronContainer(3) instanceof org.openscience.cdk.interfaces.IBond);
//        IBond bond = (IBond)container.getElectronContainer(3);
//        assertEquals(3.0, bond.getOrder(), 0.00001);
//    }
    
    public void testGetElectronContainerCount() {
        // 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);
        
        assertEquals(3, acetone.getBondCount());
        assertEquals(2, acetone.getLonePairCount());
        assertEquals(5, acetone.getElectronContainerCount());
    }
    
    public void testRemoveAllBonds() {
        // 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.removeAllBonds();
	assertEquals(0, acetone.getBondCount());
    }
    
    public void testRemoveAllElectronContainers() {
        // 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);