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 testSybylAtomTypePerceptionFromSMILES()
throws FileNotFoundException, IOException, BioclipseException, CoreException,
InvocationTargetException {
ICDKMolecule mol = cdk.fromSMILES("C1CCCCC1CCOC");
debug.perceiveSybylAtomTypes(mol);
for (int i = 0; i < mol.getAtomContainer().getAtomCount(); i++) {
IAtom a = mol.getAtomContainer().getAtom(i);
System.out.println("Atom: " + a.getSymbol() + i + ", type=" + a.getAtomTypeName());
}
}
public DBMolecule(String name, ICDKMolecule cdkMolecule) throws BioclipseException {
super();
this.name = name;
try {
fingerPrint =
cdkMolecule.getFingerprint(
net.bioclipse.core.domain.IMolecule.Property.USE_CACHED_OR_CALCULATED);
} catch (BioclipseException e) {
logger.error("Could not create fingerprint for molecule", e);
}
persistedFingerPrint = makePersistedFingerPrint(fingerPrint);
setAtomContainer(cdkMolecule.getAtomContainer());
smiles = "";
annotations = new ArrayList<Annotation>();
}
@Test
public void testSybylAtomTypePerception()
throws FileNotFoundException, IOException, BioclipseException, CoreException,
InvocationTargetException {
String path = getClass().getResource("/testFiles/atp.mol").getPath();
ICDKMolecule mol = cdk.loadMolecule(new MockIFile(path));
System.out.println("mol: " + mol.toString());
debug.perceiveSybylAtomTypes(mol);
for (int i = 0; i < mol.getAtomContainer().getAtomCount(); i++) {
IAtom a = mol.getAtomContainer().getAtom(i);
System.out.println("Atom: " + a.getSymbol() + i + ", type=" + a.getAtomTypeName());
}
}
@Test
public void testSybylAtomTypePerceptionBenzene()
throws CDKException, FileNotFoundException, IOException, BioclipseException, CoreException,
InvocationTargetException {
IAtomContainer ac = MoleculeFactory.makeBenzene();
ICDKMolecule mol = new CDKMolecule(ac);
debug.perceiveSybylAtomTypes(mol);
System.out.println("** BENZENE **");
System.out.println(AtomContainerDiff.diff(ac, mol.getAtomContainer()));
for (int i = 0; i < mol.getAtomContainer().getAtomCount(); i++) {
IAtom a = mol.getAtomContainer().getAtom(i);
System.out.println("Atom: " + a.getSymbol() + i + ", type=" + a.getAtomTypeName());
}
assertEquals("C.ar", mol.getAtomContainer().getAtom(0).getAtomTypeName());
assertEquals("C.ar", mol.getAtomContainer().getAtom(1).getAtomTypeName());
assertEquals("C.ar", mol.getAtomContainer().getAtom(2).getAtomTypeName());
assertEquals("C.ar", mol.getAtomContainer().getAtom(3).getAtomTypeName());
assertEquals("C.ar", mol.getAtomContainer().getAtom(4).getAtomTypeName());
assertEquals("C.ar", mol.getAtomContainer().getAtom(5).getAtomTypeName());
}
public void runTest(
String testID,
IMolecule mol,
IReturner<List<? extends ITestResult>> returner,
IProgressMonitor monitor)
throws BioclipseException {
ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
IDSTest test = getTest(testID);
List<? extends ITestResult> ret = null;
try {
// Preprocess the molecule
ICDKMolecule cdkmol = cdk.asCDKMolecule(mol);
// Clone the mol
IAtomContainer clonedAC = null;
try {
clonedAC = (IAtomContainer) cdkmol.getAtomContainer().clone();
} catch (CloneNotSupportedException e) {
logger.error("Could not clone mol: " + cdkmol);
return;
}
ICDKMolecule clonedMol = new CDKMolecule(clonedAC);
ret = test.runWarningTest(clonedMol, monitor);
} catch (Exception e) {
// in case of error...
LogUtils.debugTrace(logger, e);
ITestResult er = new SimpleResult("Error: " + e.getMessage(), ITestResult.ERROR);
er.setDetailedMessage(e.getMessage());
List<ITestResult> trlist = new ArrayList<ITestResult>();
trlist.add(er);
monitor.done();
returner.completeReturn(trlist);
return;
}
monitor.done();
returner.completeReturn(ret);
}
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();
}
public String debug(ICDKMolecule mol) {
return mol.getAtomContainer().toString();
}
public String diff(ICDKMolecule mol, ICDKMolecule mol2) {
return AtomContainerDiff.diff(
mol.getAtomContainer(), mol2.getAtomContainer()
);
}