/**
* 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));
}
/** Tests if the electron count matches the Hückel 4n+2 rule. */
private static boolean isHueckelValid(IAtomContainer singleRing) throws CDKException {
int electronCount = 0;
for (IAtom ringAtom : singleRing.atoms()) {
if (ringAtom.getHybridization() != CDKConstants.UNSET
&& (ringAtom.getHybridization() == Hybridization.SP2)
|| ringAtom.getHybridization() == Hybridization.PLANAR3) {
// for example, a carbon
// note: the double bond is in the ring, that has been tested earlier
// FIXME: this does assume bond orders to be resolved too, when detecting
// sprouting double bonds
if ("N.planar3".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("N.minus.planar3".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("N.amide".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("S.2".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("S.planar3".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("C.minus.planar".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("O.planar3".equals(ringAtom.getAtomTypeName())) {
electronCount += 2;
} else if ("N.sp2.3".equals(ringAtom.getAtomTypeName())) {
electronCount += 1;
} else {
if (factory == null) {
factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/dict/data/cdk-atom-types.owl", ringAtom.getBuilder());
}
IAtomType type = factory.getAtomType(ringAtom.getAtomTypeName());
Object property = type.getProperty(CDKConstants.PI_BOND_COUNT);
if (property != null && property instanceof Integer) {
electronCount += ((Integer) property).intValue();
}
}
} else if (ringAtom.getHybridization() != null
&& ringAtom.getHybridization() == Hybridization.SP3
&& getLonePairCount(ringAtom) > 0) {
// for example, a nitrogen or oxygen
electronCount += 2;
}
}
return (electronCount % 4 == 2) && (electronCount > 2);
}
@Test
public void testGetAtomTypeFromOWL_Sybyl() throws Exception {
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/dict/data/sybyl-atom-types.owl", new ChemObject().getBuilder());
IAtomType atomType = factory.getAtomType("C.3");
Assert.assertNotNull(atomType);
Assert.assertEquals("C", atomType.getSymbol());
Assert.assertEquals("C.3", atomType.getAtomTypeName());
Assert.assertEquals(4, atomType.getFormalNeighbourCount().intValue());
Assert.assertEquals(IAtomType.Hybridization.SP3, atomType.getHybridization());
Assert.assertEquals(0, atomType.getFormalCharge().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());
}