/**
* Test reading from a XML config file with content like:
*
* <pre>
* <atomType id="C">
* <!-- for example in CC-->
* <atom elementType="C" formalCharge="0">
* <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
* <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
* <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
* <scalar dataType="xsd:integer" dictRef="cdk:valency">4</scalar>
* </atom>
* <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
* <scalar dataType="xsd:string" dictRef="cdk:DA">-</scalar>
* <scalar dataType="xsd:string" dictRef="cdk:sphericalMatcher">[CSP]-[0-4][-]?+;[A-Za-z\+\-&&[^=%]]{0,6}[(].*+</scalar>
* </atomType>
* </pre>
*
* @throws Exception if the atom typ info cannot be loaded
*/
@Test
public void testGetAtomTypeFromMM2() throws Exception {
AtomTypeFactory factory;
factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/mm2_atomtypes.xml", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("C");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C", atomType.getAtomTypeName());
Assert.assertEquals(
"[CSP]-[0-4][-]?+;[A-Za-z\\+\\-&&[^=%]]{0,6}[(].*+",
atomType.getProperty(CDKConstants.SPHERICAL_MATCHER));
Assert.assertEquals(Hybridization.SP3, atomType.getHybridization());
atomType = factory.getAtomType("Sthi");
Assert.assertNotNull(atomType);
Assert.assertEquals("S", atomType.getSymbol());
Assert.assertEquals("Sthi", atomType.getAtomTypeName());
Assert.assertEquals(
"S-[2];[H]{0,3}+=C.*+", atomType.getProperty(CDKConstants.SPHERICAL_MATCHER));
Assert.assertEquals(Hybridization.SP2, atomType.getHybridization());
Assert.assertTrue(atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR));
Assert.assertEquals(5, atomType.getProperty(CDKConstants.PART_OF_RING_OF_SIZE));
}
@Test
public void testGetAtomTypeFromOWL() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/dict/data/cdk-atom-types.owl", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("C.sp3");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C.sp3", atomType.getAtomTypeName());
Assert.assertEquals(IAtomType.Hybridization.SP3, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertEquals(4, atomType.getFormalNeighbourCount().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
0, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(0, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
atomType = factory.getAtomType("N.sp2.radical");
Assert.assertNotNull(atomType);
Assert.assertEquals("N", atomType.getSymbol());
Assert.assertEquals("N.sp2.radical", atomType.getAtomTypeName());
Assert.assertEquals(IAtomType.Hybridization.SP2, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertEquals(1, atomType.getFormalNeighbourCount().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
1, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(1, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
atomType = factory.getAtomType("N.planar3");
Assert.assertNotNull(atomType);
Assert.assertEquals("N", atomType.getSymbol());
Assert.assertEquals("N.planar3", atomType.getAtomTypeName());
Assert.assertEquals(IAtomType.Hybridization.PLANAR3, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().intValue());
Assert.assertEquals(3, atomType.getFormalNeighbourCount().intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.LONE_PAIR_COUNT) instanceof Integer);
Assert.assertEquals(
1, ((Integer) atomType.getProperty(CDKConstants.LONE_PAIR_COUNT)).intValue());
Assert.assertNotNull(atomType.getProperty(CDKConstants.PI_BOND_COUNT));
Assert.assertTrue(atomType.getProperty(CDKConstants.PI_BOND_COUNT) instanceof Integer);
Assert.assertEquals(0, ((Integer) atomType.getProperty(CDKConstants.PI_BOND_COUNT)).intValue());
}
public String perceiveCDKAtomTypes(IMolecule mol)
throws InvocationTargetException {
ICDKMolecule cdkmol;
try {
cdkmol = cdk.asCDKMolecule(mol);
}
catch ( BioclipseException e ) {
e.printStackTrace();
throw new InvocationTargetException(
e, "Error while creating a ICDKMolecule" );
}
IAtomContainer ac = cdkmol.getAtomContainer();
CDKAtomTypeMatcher cdkMatcher
= CDKAtomTypeMatcher.getInstance(ac.getBuilder());
StringBuffer result = new StringBuffer();
int i = 1;
for (IAtom atom : ac.atoms()) {
IAtomType type = null;
try {
type = cdkMatcher.findMatchingAtomType(ac, atom);
}
catch ( CDKException e ) {}
result.append(i).append(':').append(
type != null ? type.getAtomTypeName() : "null"
).append('\n'); // FIXME: should use NEWLINE here
i++;
}
return result.toString();
}
@Test
public void testGetAtomType_String() throws Exception {
IAtomType atomType = atf.getAtomType("C4");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C4", atomType.getAtomTypeName());
Assert.assertEquals(4.0, atomType.getBondOrderSum(), 0.001);
Assert.assertEquals(IBond.Order.TRIPLE, atomType.getMaxBondOrder());
}
@Test
public void testGetAtomTypeFromJmol() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/jmol_atomtypes.txt", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("H");
Assert.assertNotNull(atomType);
Assert.assertEquals("H", atomType.getSymbol());
Assert.assertEquals("H", atomType.getAtomTypeName());
}