TestCDKQsar.java

package net.bioclipse.cdk.qsar.test;

import static org.junit.Assert.*;

import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;

import net.bioclipse.cdk.business.ICDKManager;
import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.MockIFile;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.domain.IMolecule;
import net.bioclipse.core.domain.SMILESMolecule;
import net.bioclipse.qsar.DescriptorType;
import net.bioclipse.qsar.QSARConstants;
import net.bioclipse.qsar.business.IQsarManager;
import net.bioclipse.qsar.business.QsarManager;
import net.bioclipse.qsar.descriptor.IDescriptorResult;
import net.bioclipse.qsar.descriptor.model.Descriptor;
import net.bioclipse.qsar.descriptor.model.DescriptorImpl;
import net.bioclipse.qsar.descriptor.model.DescriptorParameter;
import net.bioclipse.qsar.descriptor.model.DescriptorProvider;
import net.bioclipse.qsar.init.Activator;

import org.eclipse.core.runtime.CoreException;
import org.eclipse.core.runtime.FileLocator;
import org.eclipse.core.runtime.Path;
import org.eclipse.core.runtime.Platform;
import org.eclipse.core.runtime.preferences.DefaultScope;
import org.eclipse.core.runtime.preferences.IEclipsePreferences;
import org.junit.Test;
import org.osgi.framework.Bundle;

public class TestCDKQsar {

	IQsarManager qsar;
	private String cdkProviderID="net.bioclipse.cdk.descriptorprovider";
	private String cdkProviderName="Chemistry Development Kit";
	
	String bpolID="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#bpol";
 	String xlogpID="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#xlogP";
	String chiChainID="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#chiChain";
 	String bcutID="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#BCUT";
	String atomCountlID="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#atomCount";
	String rotBondsCntID="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#rotatableBondsCount";
	
	public TestCDKQsar() {
		
		//Unnecessary to use OSGI.
		qsar=new QsarManager();
	}
	
	


	@Test
	public void testGetProviders(){

		//Get provider by ID
		DescriptorProvider provider=qsar.getProviderByID(cdkProviderID);
		assertNotNull(provider);
		
		assertEquals(cdkProviderID, provider.getId());
		assertEquals("Chemistry Development Kit", provider.getVendor());
		assertEquals("Chemistry Development Kit", provider.getName());
		assertEquals("http://cdk.sourceforge.net", provider.getNamesapce());
		assertEquals("CDK", provider.getShortName());
		assertEquals("1.1.0.v20080808", provider.getVersion());

		//Get provider classes
		List<DescriptorProvider> lstFull = qsar.getFullProviders();
		assertNotNull(lstFull);
		assertTrue(lstFull.contains(provider));

	}

	@Test
	public void testGetDescriptors(){

		//Matches plugin.xml, just test some classes

		//Get provider by ID
		DescriptorProvider provider=qsar.getProviderByID(cdkProviderID);
		assertNotNull(provider);

		List<String> descImplIDs=qsar.getDescriptorImplsByProvider(cdkProviderID);
		
		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 testGetDescriptorsByID(){

		//Get decriptor by hardcoded id
		DescriptorImpl desc=qsar.getDescriptorImpl(bpolID, cdkProviderID);
		assertNotNull(desc);
		assertNull(desc.getParameters());
		assertFalse(desc.isRequires3D());
		assertEquals(cdkProviderID, desc.getProvider().getId());
		assertNotNull(desc.getDescription());
		assertNotNull(desc.getDefinition());
	}

	@Test
	public void testGetDescriptorsByIDWithParameters(){

		//Get decriptor by hardcoded id with parameters
		DescriptorImpl desc=qsar.getDescriptorImpl(xlogpID, cdkProviderID);
		assertNotNull(desc);
		assertNotNull(desc.getParameters());
		assertNotNull(desc.getDescription());
		assertNotNull(desc.getDefinition());

		List<String> paramKeys=new ArrayList<String>();
		List<String> paramVals=new ArrayList<String>();
		List<String> paramDesc=new ArrayList<String>();
		for (DescriptorParameter param: desc.getParameters()){
			System.out.println("Param: " + param.getKey() + " = " + param.getDefaultvalue() + " ; " + param.getDescription());
			paramKeys.add(param.getKey());
			paramVals.add(param.getDefaultvalue());
			paramDesc.add(param.getDescription());
		}
		
		assertEquals("salicylFlag", paramKeys.get(0));
		assertEquals("true", paramVals.get(0));

		assertNotNull(paramDesc.get(0));

	}
	
	
	@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 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);
		assertTrue(prefsString.contains(cdkProviderName));
		
		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 testCalculateBpolFromSmiles() throws BioclipseException{

		IMolecule mol=new SMILESMolecule("C1CNCCC1CC(COC)CCNC");
		
		IDescriptorResult dres = qsar.calculate(mol, bpolID);

		//We know only one result as we only asked for one descriptor
		assertNotNull(dres);
		assertNull(dres.getErrorMessage());
		assertEquals(bpolID, dres.getDescriptorId());

		System.out.println("Mol: " + mol.getSMILES() + 
				" ; Desc: " + dres.getDescriptorId() +": ");
		for (int i=0; i<dres.getValues().length;i++){
			System.out.println("    " + dres.getLabels()[i] 
			                                     + "=" + dres.getValues()[i] ); 
		}
		
		assertEquals("bpol", dres.getLabels()[0]);
		assertEquals(31.659382, dres.getValues()[0]);
		
		
	}

	@Test
	public void testCalculateXlogPFromSMILES() throws BioclipseException{

		IMolecule mol=new SMILESMolecule("C1CNCCC1CC(COC)CCNC");
		
		IDescriptorResult dres1=qsar.calculate(mol, xlogpID);
		assertNotNull(dres1);
		assertNull(dres1.getErrorMessage());
		assertEquals(xlogpID, dres1.getDescriptorId());

		System.out.println("Mol: " + mol.getSMILES() + 
				" ; Desc: " + dres1.getDescriptorId() +": ");
		for (int i=0; i<dres1.getValues().length;i++){
			System.out.println("    " + dres1.getLabels()[i] 
			                                     + "=" + dres1.getValues()[i] ); 
		}
		
		assertEquals("XLogP", dres1.getLabels()[0]);
		assertEquals(0.184, dres1.getValues()[0]);
		
		
	}
	
	@Test
	public void testCalculateXlogPFromCML() throws BioclipseException, FileNotFoundException, IOException, CoreException{

		ICDKManager cdk=net.bioclipse.cdk.business.Activator.getDefault().getCDKManager();
		
		Bundle bun=Platform.getBundle(net.bioclipse.cdk.qsar.test.Activator.PLUGIN_ID);
		System.out.println("wee bun: " + bun);

		URL url=FileLocator.find(bun, new Path("src/testFiles/0037.cml"), null);
		System.out.println("wee url: " + url);
		
		String str=FileLocator.toFileURL(url).getFile();
		System.out.println("wee File: " + str);
		
        ICDKMolecule mol = cdk.loadMolecule( new MockIFile(str), null );
		
		IDescriptorResult dres1=qsar.calculate(mol, xlogpID);
		assertNotNull(dres1);
		assertNull(dres1.getErrorMessage(),dres1.getErrorMessage());
		assertEquals(xlogpID, dres1.getDescriptorId());

		System.out.println("Mol: " + mol.getSMILES() + 
				" ; Desc: " + dres1.getDescriptorId() +": ");
		for (int i=0; i<dres1.getValues().length;i++){
			System.out.println("    " + dres1.getLabels()[i] 
			                                     + "=" + dres1.getValues()[i] ); 
		}
		
		assertEquals("XLogP", dres1.getLabels()[0]);
		assertEquals(0.184, dres1.getValues()[0]);
		
		
	}


	@Test
	public void testCalculateBCUTFromSMILES() throws BioclipseException{

		IMolecule mol=new SMILESMolecule("C1CNCCC1CC(COC)CCNC");
		
		IDescriptorResult dres1=qsar.calculate(mol, bcutID);
		assertNotNull(dres1);
		assertNull(dres1.getErrorMessage());
		assertEquals(bcutID, dres1.getDescriptorId());

		System.out.println("Mol: " + mol.getSMILES() + 
				" ; Desc: " + dres1.getDescriptorId() +": ");
		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(11.993387, dres1.getValues()[0]);

		assertEquals("BCUTw-1h", dres1.getLabels()[1]);
		assertEquals(15.994919, dres1.getValues()[1]);
		assertEquals("BCUTc-1l", dres1.getLabels()[2]);
		assertEquals(0.89, dres1.getValues()[2]);
		assertEquals("BCUTc-1h", dres1.getLabels()[3]);
		assertEquals(1.1102645, dres1.getValues()[3]);
		assertEquals("BCUTp-1l", dres1.getLabels()[4]);
		assertEquals(4.6727624, dres1.getValues()[4]);
		assertEquals("BCUTp-1h", dres1.getLabels()[5]);
		assertEquals(9.596294, dres1.getValues()[5]);
		
	}

	@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);
		
		Map<? extends IMolecule, List<IDescriptorResult>> res = qsar.calculateNoParams(mols, descs);
		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.getSMILES() + 
				" ; Desc: " + dres1.getDescriptorId() +": ");
		for (int i=0; i<dres1.getValues().length;i++){
			System.out.println("    " + dres1.getLabels()[i] 
			                                     + "=" + dres1.getValues()[i] ); 
		}
		
		System.out.println("Mol: " + mol1.getSMILES() + 
				" ; Desc: " + dres11.getDescriptorId() +": ");
		for (int i=0; i<dres11.getValues().length;i++){
			System.out.println("    " + dres11.getLabels()[i] 
			                                     + "=" + dres11.getValues()[i] ); 
		}

		System.out.println("Mol: " + mol2.getSMILES() + 
				" ; Desc: " + dres2.getDescriptorId() +": ");
		for (int i=0; i<dres2.getValues().length;i++){
			System.out.println("    " + dres2.getLabels()[i] 
			                                     + "=" + dres2.getValues()[i] ); 
		}
		
		System.out.println("Mol: " + mol2.getSMILES() + 
				" ; Desc: " + dres22.getDescriptorId() +": ");
		for (int i=0; i<dres22.getValues().length;i++){
			System.out.println("    " + dres22.getLabels()[i] 
			                                     + "=" + dres22.getValues()[i] ); 
		}

		assertEquals("bpol", dres1.getLabels()[0]);
		assertEquals(31.659382, dres1.getValues()[0]);
		assertEquals("XLogP", dres11.getLabels()[0]);
		assertEquals(0.184, dres11.getValues()[0]);

		assertEquals("bpol", dres2.getLabels()[0]);
		assertEquals(41.70466, dres2.getValues()[0]);
		assertEquals("XLogP", dres22.getLabels()[0]);
		assertEquals(6.749, dres22.getValues()[0]);
		
	}

	
	
	@Test
	public void testCalculateAtomCountWithDefaultParams() throws BioclipseException{

		//Calculate C and N from this SMILES mol
		IMolecule mol=new SMILESMolecule("C1CNCCC1CC(COC)CCNC");

		IDescriptorResult dres1=qsar.calculate(mol, atomCountlID);
		assertNotNull(dres1);
		assertNull(dres1.getErrorMessage());
		assertEquals(atomCountlID, dres1.getDescriptorId());
		
		assertEquals(1, dres1.getValues().length);
		
		System.out.println("Mol with default param C: " + mol.getSMILES() + 
				" ; Desc: " + dres1.getDescriptorId() +": " + dres1.getValues()[0] );

		
	}

	@Test
	public void testCalculateAtomCountWithStringParams() throws BioclipseException{

		//Calculate C and N from this SMILES mol
		IMolecule mol=new SMILESMolecule("C1CNCCC1CC(COC)CCNCCN");


		DescriptorImpl impl=qsar.getDescriptorImpl(atomCountlID, cdkProviderID);
		assertEquals(1, impl.getParameters().size());

		//Work on a new instance
		DescriptorParameter newParam=impl.getParameters().get(0).clone();
		newParam.setValue("N");

		DescriptorParameter newParam2=impl.getParameters().get(0).clone();
		newParam2.setValue("C");

		
		List<DescriptorParameter> params=new ArrayList<DescriptorParameter>();
		params.add(newParam);

		List<DescriptorParameter> params2=new ArrayList<DescriptorParameter>();
		params2.add(newParam2);


		Descriptor descriptor=qsar.getDescriptorByID(impl.getDefinition());

		List<DescriptorType> descriptorInstances=new ArrayList<DescriptorType>();
		DescriptorType descType1=qsar.createDescriptorType(null, null, descriptor, impl, params);
		DescriptorType descType2=qsar.createDescriptorType(null, null, descriptor, impl, params2);
		descriptorInstances.add(descType1);
		descriptorInstances.add(descType2);
		
		List<IDescriptorResult> resList = qsar.calculate(mol, descriptorInstances);

		//We know only one result as we only asked for one descriptor
		assertEquals(2, resList.size());

		IDescriptorResult dres1=resList.get(0);
		assertNotNull(dres1);
		assertNull(dres1.getErrorMessage());
		assertEquals(atomCountlID, dres1.getDescriptorId());
		assertEquals(1, dres1.getValues().length);
		
		System.out.println("Mol with param N: " + mol.getSMILES() + 
				" ; Desc: " + dres1.getDescriptorId() +": " + dres1.getValues()[0] );

		IDescriptorResult dres2=resList.get(1);
		assertNotNull(dres2);
		assertNull(dres2.getErrorMessage());
		assertEquals(atomCountlID, dres2.getDescriptorId());
		assertEquals(1, dres2.getValues().length);
		
		System.out.println("Mol with param C: " + mol.getSMILES() + 
				" ; Desc: " + dres2.getDescriptorId() +": " + dres2.getValues()[0] );

		assertEquals(3, dres1.getValues()[0]);

		assertEquals(13, dres2.getValues()[0]);
		

		
	}
	
	@Test
	public void testCalculateAtomCountWithBooleanParams() throws BioclipseException{

		//Calculate C and N from this SMILES mol
		IMolecule mol=new SMILESMolecule("C1CNCCC1CC(COC)CCNCCN");


		DescriptorImpl impl=qsar.getDescriptorImpl(rotBondsCntID, cdkProviderID);
		assertEquals(1, impl.getParameters().size());

		//Work on a new instance
		DescriptorParameter newParam=impl.getParameters().get(0).clone();
		newParam.setValue("true");

		DescriptorParameter newParam2=impl.getParameters().get(0).clone();
		newParam2.setValue("false");

		
		List<DescriptorParameter> params=new ArrayList<DescriptorParameter>();
		params.add(newParam);

		List<DescriptorParameter> params2=new ArrayList<DescriptorParameter>();
		params2.add(newParam2);


		Descriptor descriptor=qsar.getDescriptorByID(impl.getDefinition());

		List<DescriptorType> descriptorInstances=new ArrayList<DescriptorType>();
		DescriptorType descType1=qsar.createDescriptorType(null, null, descriptor, impl, params);
		DescriptorType descType2=qsar.createDescriptorType(null, null, descriptor, impl, params2);
		descriptorInstances.add(descType1);
		descriptorInstances.add(descType2);
		
		List<IDescriptorResult> resList = qsar.calculate(mol, descriptorInstances);

		//We know only one result as we only asked for one descriptor
		assertEquals(2, resList.size());

		IDescriptorResult dres1=resList.get(0);
		assertNotNull(dres1);
		assertNull(dres1.getErrorMessage());
		assertEquals(rotBondsCntID, dres1.getDescriptorId());
		assertEquals(1, dres1.getValues().length);
		
		System.out.println("Mol with param TRUE: " + mol.getSMILES() + 
				" ; Desc: " + dres1.getDescriptorId() +": " + dres1.getValues()[0] );

		IDescriptorResult dres2=resList.get(1);
		assertNotNull(dres2);
		assertNull(dres2.getErrorMessage());
		assertEquals(rotBondsCntID, dres2.getDescriptorId());
		assertEquals(1, dres2.getValues().length);
		
		System.out.println("Mol with param FALSE: " + mol.getSMILES() + 
				" ; Desc: " + dres2.getDescriptorId() +": " + dres2.getValues()[0] );

		assertEquals(40, dres1.getValues()[0]);

		assertEquals(11, dres2.getValues()[0]);
		

		
	}
	
	

}