/** 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);
}
/**
* This method calculates the hybridization of an atom.
*
* @param atom The IAtom for which the DescriptorValue is requested
* @param container Parameter is the atom container.
* @return The hybridization
*/
@TestMethod(value = "testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom, IAtomContainer container) {
IAtomType atomType;
try {
atomType =
CDKAtomTypeMatcher.getInstance(atom.getBuilder()).findMatchingAtomType(container, atom);
} catch (CDKException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult((int) Double.NaN), // does that work??
getDescriptorNames(),
new CDKException("Atom type was null"));
}
if (atomType == null) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult((int) Double.NaN), // does that work??
getDescriptorNames(),
new CDKException("Atom type was null"));
}
if (atomType.getHybridization() == null) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult((int) Double.NaN), // does that work??
getDescriptorNames(),
new CDKException("Hybridization was null"));
}
int hybridizationCDK = atomType.getHybridization().ordinal();
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult(hybridizationCDK),
getDescriptorNames());
}
public String perceiveSybylAtomTypes(IMolecule mol)
throws InvocationTargetException {
ICDKMolecule cdkmol;
try {
cdkmol = cdk.asCDKMolecule(mol);
}
catch (BioclipseException e) {
System.out.println("Error converting cdk10 to cdk");
e.printStackTrace();
throw new InvocationTargetException(e);
}
IAtomContainer ac = cdkmol.getAtomContainer();
CDKAtomTypeMatcher cdkMatcher
= CDKAtomTypeMatcher.getInstance(ac.getBuilder());
AtomTypeMapper mapper
= AtomTypeMapper.getInstance(
"org/openscience/cdk/dict/data/cdk-sybyl-mappings.owl" );
IAtomType[] sybylTypes = new IAtomType[ac.getAtomCount()];
int atomCounter = 0;
int a=0;
for (IAtom atom : ac.atoms()) {
IAtomType type;
try {
type = cdkMatcher.findMatchingAtomType(ac, atom);
}
catch (CDKException e) {
type = null;
}
if (type==null) {
// logger.debug("AT null for atom: " + atom);
type = atom.getBuilder().newAtomType(atom.getSymbol());
type.setAtomTypeName("X");
}
AtomTypeManipulator.configure(atom, type);
a++;
}
try {
CDKHueckelAromaticityDetector.detectAromaticity(ac);
// System.out.println("Arom: "
// + CDKHueckelAromaticityDetector.detectAromaticity(ac) );
}
catch (CDKException e) {
logger.debug("Failed to perceive aromaticity: " + e.getMessage());
}
for (IAtom atom : ac.atoms()) {
String mappedType = mapper.mapAtomType(atom.getAtomTypeName());
if ("C.2".equals(mappedType)
&& atom.getFlag(CDKConstants.ISAROMATIC)) {
mappedType = "C.ar";
}
else if ("N.pl3".equals(mappedType)
&& atom.getFlag(CDKConstants.ISAROMATIC)) {
mappedType = "N.ar";
}
try {
sybylTypes[atomCounter] = factory.getAtomType(mappedType);
}
catch (NoSuchAtomTypeException e) {
// yes, setting null's here is important
sybylTypes[atomCounter] = null;
}
atomCounter++;
}
StringBuffer result = new StringBuffer();
// now that full perception is finished, we can set atom type names:
for (int i = 0; i < sybylTypes.length; i++) {
if (sybylTypes[i] != null) {
ac.getAtom(i).setAtomTypeName(sybylTypes[i].getAtomTypeName());
}
else {
ac.getAtom(i).setAtomTypeName("X");
}
result.append(i).append(':').append(ac.getAtom(i).getAtomTypeName())
/*.append("\n")*/;
}
return result.toString();
}