@Test
public void testCalculateXlogPFromCML()
throws BioclipseException, FileNotFoundException, IOException, CoreException {
ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
Bundle bun = Platform.getBundle(net.bioclipse.cdk.qsar.test.Activator.PLUGIN_ID);
URL url = FileLocator.find(bun, new Path("src/testFiles/0037.cml"), null);
String str = FileLocator.toFileURL(url).getFile();
ICDKMolecule mol = cdk.loadMolecule(new MockIFile(str));
IDescriptorResult dres1 = qsar.calculate(mol, xlogpID, CDK_REST_SHORTNAME);
IDescriptorResult dres2 = qsar.calculate(mol, xlogpID, "CDK");
assertNotNull(dres1);
assertNull(dres1.getErrorMessage(), dres1.getErrorMessage());
assertEquals(xlogpID, dres1.getDescriptor().getOntologyid());
assertNotNull(dres2);
assertNull(dres2.getErrorMessage(), dres1.getErrorMessage());
assertEquals(xlogpID, dres2.getDescriptor().getOntologyid());
assertEquals(
"CDK and CDK REST gives different labels", dres2.getLabels()[0], dres1.getLabels()[0]);
assertEquals(
"CDK and CDK REST gives different values", dres2.getValues()[0], dres1.getValues()[0]);
}
@Test
public void testCalculateBpolFromSMILES() throws BioclipseException {
IMolecule mol = new SMILESMolecule("C1CNCCC1CC(COC)CCNC");
IDescriptorResult dres1 = qsar.calculate(mol, bpolID, CDK_REST_SHORTNAME);
assertNotNull(dres1);
assertNull(dres1.getErrorMessage());
assertEquals(bpolID, dres1.getDescriptor().getOntologyid());
assertEquals(cdkRestProviderID, dres1.getDescriptor().getProvider());
System.out.println(
"Mol: " + mol.toSMILES() + " ; Desc: " + dres1.getDescriptor().getOntologyid() + ": ");
for (int i = 0; i < dres1.getValues().length; i++) {
System.out.println(" " + dres1.getLabels()[i] + "=" + dres1.getValues()[i]);
}
assertEquals(6, dres1.getValues().length);
assertEquals(6, dres1.getLabels().length);
assertEquals("BCUTw-1l", dres1.getLabels()[0]);
assertEquals(new Float(11.993387), dres1.getValues()[0]);
assertEquals("BCUTw-1h", dres1.getLabels()[1]);
assertEquals(new Float(15.994919), dres1.getValues()[1]);
assertEquals("BCUTc-1l", dres1.getLabels()[2]);
assertEquals(new Float(0.89), dres1.getValues()[2]);
assertEquals("BCUTc-1h", dres1.getLabels()[3]);
assertEquals(new Float(1.1102645), dres1.getValues()[3]);
assertEquals("BCUTp-1l", dres1.getLabels()[4]);
assertEquals(new Float(4.6727624), dres1.getValues()[4]);
assertEquals("BCUTp-1h", dres1.getLabels()[5]);
assertEquals(new Float(9.596294), dres1.getValues()[5]);
}
@Test
public void testGetDescriptorImplNotInOntology() {
System.out.println("=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.");
System.out.println("Impl not in onology:");
System.out.println("=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.");
boolean toFail = false;
for (DescriptorImpl impl : qsar.getFullDescriptorImpls()) {
if (qsar.getDescriptorIDs().contains(impl.getDefinition())) {
// All is well
} else {
System.out.println(
"=.= Descriptor impl: " + impl.getName() + " with def: " + impl.getDefinition());
toFail = true;
}
}
System.out.println("=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.");
assertFalse("Not all CDK impl are present in ontology, see list on stdout", toFail);
}
@Test
public void testGetDescriptorsByID() throws BioclipseException {
// Get decriptor by hardcoded id
DescriptorImpl desc = qsar.getDescriptorImpl(bpolID, cdkRestProviderID);
assertNotNull(desc);
assertNull(desc.getParameters());
assertFalse(desc.isRequires3D());
assertEquals(cdkRestProviderID, desc.getProvider().getId());
assertNotNull(desc.getDescription());
assertNotNull(desc.getDefinition());
}
@Test
public void testGetDescriptors() throws BioclipseException {
// Matches plugin.xml, just test some classes
// Get provider by ID
DescriptorProvider provider = qsar.getProviderByID(cdkRestProviderID);
assertNotNull(provider);
List<String> descImplIDs = qsar.getDescriptorImplsByProvider(cdkRestProviderID);
List<DescriptorImpl> descs = qsar.getFullDescriptorImpls(provider);
// Check list of IDs and list of classes equal size
assertEquals(descImplIDs.size(), descs.size());
List<String> descIDs = new ArrayList<String>();
for (DescriptorImpl impl : descs) {
descIDs.add(impl.getDefinition());
}
assertTrue(descIDs.contains(xlogpID));
assertTrue(descIDs.contains(bpolID));
}
@Test
public void testGetPrefferedImplByDescriptorID() {
IEclipsePreferences prefs = new DefaultScope().getNode(Activator.PLUGIN_ID);
assertNotNull(prefs);
String prefsString = prefs.get(QSARConstants.QSAR_PROVIDERS_ORDER_PREFERENCE, null);
assertNotNull(prefsString);
System.out.println("Got prefs string: " + prefsString);
DescriptorImpl impl = qsar.getPreferredImpl(chiChainID);
assertNotNull(impl);
System.out.println("pref impl: " + impl.getId());
// assertEquals("net.bioclipse.qsar.test.descriptor2", impl.getId());
System.out.println("wee");
}
@Test
public void testCalculateXlogPFromSMILES() throws BioclipseException {
IMolecule mol = new SMILESMolecule("C1CNCCC1CC(COC)CCNC");
IDescriptorResult dres1 = qsar.calculate(mol, xlogpID, CDK_REST_SHORTNAME);
assertNotNull(dres1);
assertNull(dres1.getErrorMessage());
assertEquals(xlogpID, dres1.getDescriptor().getOntologyid());
System.out.println(
"Mol: " + mol.toSMILES() + " ; Desc: " + dres1.getDescriptor().getOntologyid() + ": ");
for (int i = 0; i < dres1.getValues().length; i++) {
System.out.println(" " + dres1.getLabels()[i] + "=" + dres1.getValues()[i]);
}
assertEquals("XLogP", dres1.getLabels()[0]);
assertEquals(new Float(0.184), dres1.getValues()[0]);
}
@Test
public void testCalculateBpolFromSmiles() throws BioclipseException {
IMolecule mol = new SMILESMolecule("C1CNCCC1CC(COC)CCNC");
// DescriptorImpl desc=qsar.getDescriptorImpl(bpolID, cdkRestProviderID);
IDescriptorResult dres = qsar.calculate(mol, bpolID, CDK_REST_SHORTNAME);
assertNull(dres.getErrorMessage());
assertEquals(bpolID, dres.getDescriptor().getOntologyid());
System.out.println(
"Mol: " + mol.toSMILES() + " ; Desc: " + dres.getDescriptor().getOntologyid() + ": ");
for (int i = 0; i < dres.getValues().length; i++) {
System.out.println(" " + dres.getLabels()[i] + "=" + dres.getValues()[i]);
}
assertEquals("bpol", dres.getLabels()[0]);
assertEquals(new Float(31.659382), dres.getValues()[0]);
}
@Test
public void testCalculateMolDescMap() throws BioclipseException {
IMolecule mol1 = new SMILESMolecule("C1CCCCC1CC(CC)CC");
IMolecule mol2 = new SMILESMolecule("C1CCCCC1CC(CC)CCCCCO");
Descriptor desc1 = qsar.getDescriptorByID(bpolID);
Descriptor desc2 = qsar.getDescriptorByID(xlogpID);
DescriptorImpl impl1 = qsar.getPreferredImpl(bpolID);
DescriptorImpl impl2 = qsar.getPreferredImpl(xlogpID);
DescriptorType dtype1 = qsar.createDescriptorType(null, null, desc1, impl1, null);
DescriptorType dtype2 = qsar.createDescriptorType(null, null, desc2, impl2, null);
Map<IMolecule, List<DescriptorType>> moldescmap =
new HashMap<IMolecule, List<DescriptorType>>();
List<DescriptorType> list1 = new ArrayList<DescriptorType>();
list1.add(dtype1);
list1.add(dtype2);
moldescmap.put(mol1, list1);
List<DescriptorType> list2 = new ArrayList<DescriptorType>();
list2.add(dtype2);
moldescmap.put(mol2, list2);
Map<? extends IMolecule, List<IDescriptorResult>> res =
qsar.doCalculation(moldescmap, new NullProgressMonitor());
assertNotNull("QSAR calculation returned NULL", res);
assertNotNull(res);
List<IDescriptorResult> res1 = res.get(mol1);
List<IDescriptorResult> res2 = res.get(mol2);
assertEquals(2, res1.size());
assertEquals(1, res2.size());
IDescriptorResult dres1 = res1.get(0);
IDescriptorResult dres11 = res1.get(1);
IDescriptorResult dres2 = res2.get(0);
assertNull(dres1.getErrorMessage());
assertNull(dres11.getErrorMessage());
assertNull(dres2.getErrorMessage());
System.out.println(
"Mol: " + mol1.toSMILES() + " ; Desc: " + dres1.getDescriptor().getOntologyid() + ": ");
for (int i = 0; i < dres1.getValues().length; i++) {
System.out.println(" " + dres1.getLabels()[i] + "=" + dres1.getValues()[i]);
}
System.out.println(
"Mol: " + mol1.toSMILES() + " ; Desc: " + dres11.getDescriptor().getOntologyid() + ": ");
for (int i = 0; i < dres11.getValues().length; i++) {
System.out.println(" " + dres11.getLabels()[i] + "=" + dres11.getValues()[i]);
}
System.out.println(
"Mol: " + mol2.toSMILES() + " ; Desc: " + dres2.getDescriptor().getOntologyid() + ": ");
for (int i = 0; i < dres2.getValues().length; i++) {
System.out.println(" " + dres2.getLabels()[i] + "=" + dres2.getValues()[i]);
}
assertEquals("bpol", dres1.getLabels()[0]);
assertEquals(new Float(26.236967), dres1.getValues()[0]);
assertEquals("XLogP", dres11.getLabels()[0]);
assertEquals(new Float(6.706), dres11.getValues()[0]);
assertEquals("XLogP", dres2.getLabels()[0]);
assertEquals(new Float(6.648), dres2.getValues()[0]);
}
@Test
public void testCalculateMultipleMolMultipleDescriptor() throws BioclipseException {
IMolecule mol1 = new SMILESMolecule("C1CNCCC1CC(COC)CCNC");
IMolecule mol2 = new SMILESMolecule("C1CCCCC1CC(CC)CCCCCOCCCN");
List<IMolecule> mols = new ArrayList<IMolecule>();
List<String> descs = new ArrayList<String>();
mols.add(mol1);
mols.add(mol2);
descs.add(bpolID);
descs.add(xlogpID);
DescriptorCalculationResult calres = qsar.calculate(mols, descs, CDK_REST_SHORTNAME);
Map<IMolecule, List<IDescriptorResult>> res = calres.getResultMap();
assertNotNull(res);
List<IDescriptorResult> res1 = res.get(mol1);
List<IDescriptorResult> res2 = res.get(mol2);
assertEquals(2, res1.size());
assertEquals(2, res2.size());
IDescriptorResult dres1 = res1.get(0);
IDescriptorResult dres11 = res1.get(1);
IDescriptorResult dres2 = res2.get(0);
IDescriptorResult dres22 = res2.get(1);
assertNull(dres1.getErrorMessage());
assertNull(dres11.getErrorMessage());
assertNull(dres2.getErrorMessage());
assertNull(dres22.getErrorMessage());
System.out.println(
"Mol: " + mol1.toSMILES() + " ; Desc: " + dres1.getDescriptor().getOntologyid() + ": ");
for (int i = 0; i < dres1.getValues().length; i++) {
System.out.println(" " + dres1.getLabels()[i] + "=" + dres1.getValues()[i]);
}
System.out.println(
"Mol: " + mol1.toSMILES() + " ; Desc: " + dres11.getDescriptor().getOntologyid() + ": ");
for (int i = 0; i < dres11.getValues().length; i++) {
System.out.println(" " + dres11.getLabels()[i] + "=" + dres11.getValues()[i]);
}
System.out.println(
"Mol: " + mol2.toSMILES() + " ; Desc: " + dres2.getDescriptor().getOntologyid() + ": ");
for (int i = 0; i < dres2.getValues().length; i++) {
System.out.println(" " + dres2.getLabels()[i] + "=" + dres2.getValues()[i]);
}
System.out.println(
"Mol: " + mol2.toSMILES() + " ; Desc: " + dres22.getDescriptor().getOntologyid() + ": ");
for (int i = 0; i < dres22.getValues().length; i++) {
System.out.println(" " + dres22.getLabels()[i] + "=" + dres22.getValues()[i]);
}
assertEquals("bpol", dres1.getLabels()[0]);
assertEquals(new Float(31.659382), dres1.getValues()[0]);
assertEquals("XLogP", dres11.getLabels()[0]);
assertEquals(new Float(0.184), dres11.getValues()[0]);
assertEquals("bpol", dres2.getLabels()[0]);
assertEquals(new Float(41.70466), dres2.getValues()[0]);
assertEquals("XLogP", dres22.getLabels()[0]);
assertEquals(new Float(6.749), dres22.getValues()[0]);
}
