atomcontainertest.java

化学图形处理软件

        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(0, acetone.getBondNumber(b1));
        assertEquals(1, acetone.getBondNumber(b2));
        assertEquals(2, acetone.getBondNumber(b3));
        
        // test the default return value
        assertEquals(-1, acetone.getBondNumber(builder.newBond()));
    }
    
    public void testGetBondNumber_IAtom_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);
        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(0, acetone.getBondNumber(c1, c2));
        assertEquals(1, acetone.getBondNumber(c1, o));
        assertEquals(2, acetone.getBondNumber(c1, c3));
    }
    
    public void testGetBond_IAtom_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);
        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);
        
        assertTrue(b1.equals(acetone.getBond(c1, c2)));        
        assertTrue(b2.equals(acetone.getBond(c1, o)));        
        assertTrue(b3.equals(acetone.getBond(c1, c3)));
        
        // test the default return value
        assertNull(acetone.getBond(builder.newAtom(), builder.newAtom()));
    }
    
//    public void testGetConnectedAtoms_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);
//        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.getConnectedAtomsList(c1).length);
//        assertEquals(1, acetone.getConnectedAtoms(c2).length);
//        assertEquals(1, acetone.getConnectedAtoms(c3).length);
//        assertEquals(1, acetone.getConnectedAtoms(o).length);
//    }
    
    public void testGetConnectedAtomsList_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);
        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.getConnectedAtomsList(c1).size());
        assertEquals(1, acetone.getConnectedAtomsList(c2).size());
        assertEquals(1, acetone.getConnectedAtomsList(c3).size());
        assertEquals(1, acetone.getConnectedAtomsList(o).size());
    }
    
    public void testGetConnectedAtomsCount_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);
        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.getConnectedAtomsCount(c1));
        assertEquals(1, acetone.getConnectedAtomsCount(c2));
        assertEquals(1, acetone.getConnectedAtomsCount(c3));
        assertEquals(1, acetone.getConnectedAtomsCount(o));
    }
    
    public void testGetLonePairCount() {
        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);
        
        // add lone pairs on oxygen
        ILonePair lp1 = builder.newLonePair(o);
        ILonePair lp2 = builder.newLonePair(o);
        acetone.addLonePair(lp1);
        acetone.addLonePair(lp2);
        
        assertEquals(2, acetone.getLonePairCount());
    }

    public void testGetConnectedLonePairsCount_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);
        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);
        
        // add lone pairs on oxygen
        ILonePair lp1 = builder.newLonePair(o);
        ILonePair lp2 = builder.newLonePair(o);
        acetone.addLonePair(lp1);
        acetone.addLonePair(lp2);
        
        assertEquals(2, acetone.getConnectedLonePairsCount(o));
        assertEquals(0, acetone.getConnectedLonePairsCount(c2));
        assertEquals(0, acetone.getConnectedLonePairsCount(c3));
        assertEquals(0, acetone.getConnectedLonePairsCount(c1));
    }

    public void testGetBondOrderSum_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);
        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);
        
        // add lone pairs on oxygen
        ILonePair lp1 = builder.newLonePair(o);
        ILonePair lp2 = builder.newLonePair(o);
        acetone.addLonePair(lp1);
        acetone.addLonePair(lp2);
        
        assertEquals(4.0, acetone.getBondOrderSum(c1), 0.00001);
        assertEquals(1.0, acetone.getBondOrderSum(c2), 0.00001);
        assertEquals(1.0, acetone.getBondOrderSum(c3), 0.00001);
        assertEquals(2.0, acetone.getBondOrderSum(o), 0.00001);
    }
    
    public void testGetBondCount_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);
        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);
        
        // add lone pairs on oxygen
        ILonePair lp1 = builder.newLonePair(o);
        ILonePair lp2 = builder.newLonePair(o);
        acetone.addLonePair(lp1);
        acetone.addLonePair(lp2);
        
        assertEquals(3, acetone.getConnectedBondsCount(c1));
        assertEquals(1, acetone.getConnectedBondsCount(c2));
        assertEquals(1, acetone.getConnectedBondsCount(c3));
        assertEquals(1, acetone.getConnectedBondsCount(o));
    }
    
    public void testGetBondCount_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);
        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);
        
        // add lone pairs on oxygen
        ILonePair lp1 = builder.newLonePair(o);
        ILonePair lp2 = builder.newLonePair(o);
        acetone.addLonePair(lp1);
        acetone.addLonePair(lp2);
        
        assertEquals(3, acetone.getConnectedBondsCount(0));
        assertEquals(1, acetone.getConnectedBondsCount(1));
        assertEquals(1, acetone.getConnectedBondsCount(2));
        assertEquals(1, acetone.getConnectedBondsCount(3));
    }
    
    public void testGetAtomParity_IAtom() {
        IAtom carbon = builder.newAtom("C");
        carbon.setID("central");
        IAtom carbon1 = builder.newAtom("C");
        carbon1.setID("c1");
        IAtom carbon2 = builder.newAtom("C");
        carbon2.setID("c2");
        IAtom carbon3 = builder.newAtom("C");
        carbon3.setID("c3");
        IAtom carbon4 = builder.newAtom("C");
        carbon4.setID("c4");
        int parityInt = 1;
        IAtomParity parity = builder.newAtomParity(carbon, carbon1, carbon2, carbon3, carbon4, parityInt);
        IAtomContainer container = builder.newAtomContainer();
        container.addAtomParity(parity);
        org.openscience.cdk.interfaces.IAtomParity copy = container.getAtomParity(carbon);
        assertNotNull(copy);
        assertEquals(parity, copy);
    }

    /** Test for RFC #9 */
    public void testToString() {
        IAtomContainer container = builder.newAtomContainer();
        String description = container.toString();
        for (int i=0; i< description.length(); i++) {
            assertTrue(description.charAt(i) != '\n');
            assertTrue(description.charAt(i) != '\r');
        }
    }

    public void testStateChanged_IChemObjectChangeEvent() {
        ChemObjectListenerImpl listener = new ChemObjectListenerImpl();
        IAtomContainer chemObject = builder.newAtomContainer();
        chemObject.addListener(listener);
        
        chemObject.addAtom(builder.newAtom());
        assertTrue(listener.changed);
        
        listener.reset();
        assertFalse(listener.changed);
        chemObject.addBond(builder.newBond(builder.newAtom(), builder.newAtom()));
        assertTrue(listener.changed);
    }

    private class ChemObjectListenerImpl implements IChemObjectListener {
        private boolean changed;
        
        private ChemObjectListenerImpl() {
            changed = false;
        }
        
        public void stateChanged(IChemObjectChangeEvent e) {
            changed = true;
        }
        
        public void reset() {
            changed = false;
        }
    }
    
    public void testAddAtomParity_IAtomParity() {
        testGetAtomParity_IAtom();
    }
    
    public void testGetConnectedSingleElectronsCount_IAtom() {
        // another rather artifial example
        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);
        ISingleElectron single1 = builder.newSingleElectron(c);
        ISingleElectron single2 = builder.newSingleElectron(c);
        ISingleElectron single3 = builder.newSingleElectron(o);
        acetone.addSingleElectron(single1);
        acetone.addSingleElectron(single2);
        acetone.addSingleElectron(single3);

        assertEquals(2, aceton