@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]); }
@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]); }