@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 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 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]);
}