mmff94atomtypematchertest.java

化学图形处理软件

		haad.addExplicitHydrogensToSatisfyValency(mol);

		String [] testResult={"C","N","HC","HC","HC","HN","HN"};
		AtomTypeTools att=new AtomTypeTools();
        MMFF94AtomTypeMatcher atm= new MMFF94AtomTypeMatcher();
		att.assignAtomTypePropertiesToAtom(mol,false);
        for (int i=0;i<mol.getAtomCount();i++){
        	logger.debug("atomNr:" + mol.getAtom(i).toString());
        	IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
        	assertNotNull(matched);
        	AtomTypeManipulator.configure(mol.getAtom(i), matched);       
        }
        for (int i=0; i<testResult.length;i++){
        	assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
        }
        //System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());    
	}
	/**
	 *  A unit test for JUnit with ethoxyethane
	 */
	public void testFindMatchingAtomType_IAtomContainer_IAtom_Ethoxyethane() throws ClassNotFoundException, CDKException, java.lang.Exception {
		//System.out.println("**** START ATOMTYPE Ethoxyethane TEST ******");	   
		IMolecule mol = builder.newMolecule();
		IAtom carbon = builder.newAtom(Elements.CARBON);
		IAtom oxygen = builder.newAtom(Elements.OXYGEN);
		IAtom carbon2 = builder.newAtom(Elements.CARBON);
		// making sure the order matches the test results
		mol.addAtom(carbon); 
		mol.addAtom(oxygen);
		mol.addAtom(carbon2); 
		mol.addBond(builder.newBond(carbon, oxygen, CDKConstants.BONDORDER_SINGLE));
		mol.addBond(builder.newBond(carbon2, oxygen, CDKConstants.BONDORDER_SINGLE));
		
		haad.addExplicitHydrogensToSatisfyValency(mol);
		
		String [] testResult={"C","O","C","HC","HC","HC","HC","HC","HC"};
		AtomTypeTools att=new AtomTypeTools();
        MMFF94AtomTypeMatcher atm= new MMFF94AtomTypeMatcher();
		att.assignAtomTypePropertiesToAtom(mol,false);
        for (int i=0;i<mol.getAtomCount();i++){
        	logger.debug("atomNr:" + mol.getAtom(i).toString());
        	IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
        	assertNotNull(matched);
        	AtomTypeManipulator.configure(mol.getAtom(i), matched);       
        }
        for (int i=0; i<testResult.length;i++){
        	assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
        }
        //System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());
	}
	/**
	 *  A unit test for JUnit with Methanethiol
	 */
	public void testFindMatchingAtomType_IAtomContainer_IAtom_Methanethiol() throws ClassNotFoundException, CDKException, java.lang.Exception {
		//System.out.println("**** START ATOMTYPE Methanethiol TEST ******");
		IMolecule mol = builder.newMolecule();
		IAtom carbon = builder.newAtom(Elements.CARBON);
		IAtom sulfur = builder.newAtom(Elements.SULFUR);
		// making sure the order matches the test results
		mol.addAtom(carbon); 
		mol.addAtom(sulfur);
		mol.addBond(builder.newBond(carbon, sulfur, CDKConstants.BONDORDER_SINGLE));
		
		haad.addExplicitHydrogensToSatisfyValency(mol);

		String [] testResult={"C","S","HC","HC","HC","HP"};
		AtomTypeTools att=new AtomTypeTools();
        MMFF94AtomTypeMatcher atm= new MMFF94AtomTypeMatcher();
		att.assignAtomTypePropertiesToAtom(mol,false);
        for (int i=0;i<mol.getAtomCount();i++){
        	logger.debug("atomNr:" + mol.getAtom(i).toString());
        	IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
        	assertNotNull(matched);
        	AtomTypeManipulator.configure(mol.getAtom(i), matched);       
        }
        for (int i=0; i<testResult.length;i++){
        	assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
        }
        //System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());		
	}
	/**
	 *  A unit test for JUnit with Chloromethane
	 */
	public void testFindMatchingAtomType_IAtomContainer_IAtom_Chloromethane() throws ClassNotFoundException, CDKException, java.lang.Exception {
		//System.out.println("**** START ATOMTYPE Chlormethane TEST ******");
		IMolecule mol = builder.newMolecule();
		IAtom carbon = builder.newAtom(Elements.CARBON);
		IAtom chlorine = builder.newAtom(Elements.CHLORINE);
		// making sure the order matches the test results
		mol.addAtom(carbon); 
		mol.addAtom(chlorine);
		mol.addBond(builder.newBond(carbon, chlorine, CDKConstants.BONDORDER_SINGLE));
		
		haad.addExplicitHydrogensToSatisfyValency(mol);
		
		String [] testResult={"C","CL","HC","HC","HC"};
		AtomTypeTools att=new AtomTypeTools();
        MMFF94AtomTypeMatcher atm= new MMFF94AtomTypeMatcher();
		att.assignAtomTypePropertiesToAtom(mol,false);
        for (int i=0;i<mol.getAtomCount();i++){
        	logger.debug("atomNr:" + mol.getAtom(i).toString());
        	IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
        	assertNotNull(matched);
        	AtomTypeManipulator.configure(mol.getAtom(i), matched);       
        }
        for (int i=0; i<testResult.length;i++){
        	assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
        }
       //System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());			
	}
	/**
	 *  A unit test for JUnit with Benzene
	 */
	public void testFindMatchingAtomType_IAtomContainer_IAtom_Benzene() throws ClassNotFoundException, CDKException, java.lang.Exception {
		//System.out.println("**** START ATOMTYPE Benzene TEST ******");
		IMolecule mol = builder.newMolecule();
		for (int i=0; i<6; i++) {
			IAtom carbon = builder.newAtom(Elements.CARBON);
			carbon.setFlag(CDKConstants.ISAROMATIC, true);
			// making sure the order matches the test results
			mol.addAtom(carbon);			
		}
		IBond ringBond = builder.newBond(mol.getAtom(0), mol.getAtom(1), CDKConstants.BONDORDER_DOUBLE);
		ringBond.setFlag(CDKConstants.ISAROMATIC, true);
		mol.addBond(ringBond);
		ringBond = builder.newBond(mol.getAtom(1), mol.getAtom(2), CDKConstants.BONDORDER_SINGLE);
		ringBond.setFlag(CDKConstants.ISAROMATIC, true);
		mol.addBond(ringBond);
		ringBond = builder.newBond(mol.getAtom(2), mol.getAtom(3), CDKConstants.BONDORDER_DOUBLE);
		ringBond.setFlag(CDKConstants.ISAROMATIC, true);
		mol.addBond(ringBond);
		ringBond = builder.newBond(mol.getAtom(3), mol.getAtom(4), CDKConstants.BONDORDER_SINGLE);
		ringBond.setFlag(CDKConstants.ISAROMATIC, true);
		mol.addBond(ringBond);
		ringBond = builder.newBond(mol.getAtom(4), mol.getAtom(5), CDKConstants.BONDORDER_DOUBLE);
		ringBond.setFlag(CDKConstants.ISAROMATIC, true);
		mol.addBond(ringBond);
		ringBond = builder.newBond(mol.getAtom(5), mol.getAtom(0), CDKConstants.BONDORDER_SINGLE);
		ringBond.setFlag(CDKConstants.ISAROMATIC, true);
		mol.addBond(ringBond);
			
		haad.addExplicitHydrogensToSatisfyValency(mol);		
		
		String [] testResult={"Car","Car","Car","Car","Car","Car","HC","HC","HC","HC","HC","HC"};
		AtomTypeTools att=new AtomTypeTools();
        MMFF94AtomTypeMatcher atm= new MMFF94AtomTypeMatcher();
        att.assignAtomTypePropertiesToAtom(mol,false);
        for (int i=0;i<mol.getAtomCount();i++){
        	logger.debug("atomNr:" + mol.getAtom(i).toString());
        	IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
        	assertNotNull(matched);
        	//System.out.println("MatchedTypeID:"+matched.getID()+" "+matched.getSymbol()+" "+matched.getAtomTypeName());
        	AtomTypeManipulator.configure(mol.getAtom(i), matched);       
        }
        for (int i=0; i<testResult.length;i++){
        	assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
        }
        
        //System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());
        //System.out.println(mol.toString());
	}
	/**
	 *  A unit test for JUnit with Water
	 */
	public void testFindMatchingAtomType_IAtomContainer_IAtom_Water() throws ClassNotFoundException, CDKException, java.lang.Exception {
		//System.out.println("**** START ATOMTYPE Water TEST ******");
		IMolecule mol = builder.newMolecule();
		IAtom oxygen = builder.newAtom(Elements.OXYGEN);
		// making sure the order matches the test results
		mol.addAtom(oxygen);
		haad.addExplicitHydrogensToSatisfyValency(mol);

		String [] testResult={"OH2","HO","HO"};
		AtomTypeTools att=new AtomTypeTools();
        MMFF94AtomTypeMatcher atm= new MMFF94AtomTypeMatcher();
		att.assignAtomTypePropertiesToAtom(mol,false);
        for (int i=0;i<mol.getAtomCount();i++){
        	logger.debug("atomNr:" + mol.getAtom(i).toString());
        	IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
        	assertNotNull(matched);
        	AtomTypeManipulator.configure(mol.getAtom(i), matched);       
        }
        for (int i=0; i<testResult.length;i++){
        	assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
        }
        //System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());		
	}
}