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CDKDescriptorCalculator.java
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CDKDescriptorCalculator.java
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/*******************************************************************************
* Copyright (c) 2009 Ola Spjuth.
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*
* Contributors:
* Ola Spjuth - initial API and implementation
******************************************************************************/
package net.bioclipse.cdk.qsar.impl;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.OperationCanceledException;
import org.eclipse.emf.common.util.EList;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.NoSuchAtomException;
import org.openscience.cdk.graph.SpanningTree;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.qsar.DescriptorEngine;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IDescriptor;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.BooleanResult;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.qsar.result.IntegerArrayResult;
import org.openscience.cdk.qsar.result.IntegerResult;
import org.openscience.cdk.tools.CDKHydrogenAdder;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
import net.bioclipse.cdk.business.Activator;
import net.bioclipse.cdk.business.ICDKManager;
import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.domain.IMolecule;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.qsar.DescriptorType;
import net.bioclipse.qsar.ParameterType;
import net.bioclipse.qsar.business.IQsarManager;
import net.bioclipse.qsar.descriptor.DescriptorResult;
import net.bioclipse.qsar.descriptor.IDescriptorCalculator;
import net.bioclipse.qsar.descriptor.IDescriptorResult;
public class CDKDescriptorCalculator implements IDescriptorCalculator {
private static final Logger logger = Logger.getLogger(CDKDescriptorCalculator.class);
ICDKManager cdk;
private DescriptorEngine engine = null;
private Map<String, IMolecularDescriptor> descriptorInstances;
IQsarManager qsar;
public CDKDescriptorCalculator() {
cdk=Activator.getDefault().getJavaCDKManager();
qsar=net.bioclipse.qsar.init.Activator.getDefault().getJavaQsarManager();
}
public Map<String, IMolecularDescriptor> getDescriptorMap() {
if (descriptorInstances == null){
getEngine();
descriptorInstances = new HashMap<String, IMolecularDescriptor>();
List<IDescriptor> lst = engine.getDescriptorInstances();
for (IDescriptor descriptor : lst) {
IMolecularDescriptor mdesc=(IMolecularDescriptor)descriptor;
descriptorInstances.put(mdesc.getSpecification().getSpecificationReference(), mdesc);
}
}
return descriptorInstances;
}
private void getEngine() {
if (engine == null) {
List<String> descriptors = new ArrayList<String>();
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor");
//Why is this not added?
// descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor");
descriptors.add("org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor");
engine = new DescriptorEngine(descriptors);
engine.getDescriptorInstances();
}
}
public Map<? extends IMolecule, List<IDescriptorResult>> calculateDescriptor(
List<? extends IMolecule> molecules,
List<DescriptorType> descriptorTypes,
IProgressMonitor monitor) throws OperationCanceledException {
Map<IMolecule, List<IDescriptorResult>> allResults=
new HashMap<IMolecule, List<IDescriptorResult>>();
for (IMolecule mol : molecules){
try {
ICDKMolecule cdkmol=cdk.asCDKMolecule(mol);
List<IDescriptorResult> retlist = doCalculate(cdkmol, descriptorTypes, monitor);
allResults.put(mol, retlist);
} catch (BioclipseException e) {
logger.error("Unable to create CDKMolecule from Imolecule. " +
"Skipping descriptor calculation for this mol.");
LogUtils.debugTrace(logger, e);
}
}
return allResults;
}
/**
* Calculate descriptors for a single molecule
* @param monitor
* @param mol Input molecule
* @param descriptorInstances2 List<String> of descriptor IDs
* @return IDescriptorResult with results of the calculation
* @throws BioclipseException
*/
private List<IDescriptorResult> doCalculate(ICDKMolecule cdkmol,
List<DescriptorType> descriptorTypes,
IProgressMonitor monitor) throws OperationCanceledException{
//Get atomcontainer from IMolecule
IAtomContainer container=cdkmol.getAtomContainer();
//Make sure e have a Molecule, otherwise create it
if (!(container instanceof IMolecule)) container =
container.getBuilder().newInstance(
org.openscience.cdk.interfaces.IMolecule.class, container);
//Store results here
List<IDescriptorResult> results = new ArrayList<IDescriptorResult>();
//Preprocess atomcontainer. Return null if all is well, else String with error
//========================
String atomcontainerError=doCDKPreprocessing(container);
//Loop over all descriptors
//=========================
for (DescriptorType descType : descriptorTypes){
if (monitor.isCanceled()) {
throw new OperationCanceledException();
}
// logger.debug("CDK calculating descriptor: " + descType.getOntologyid() + " for mol: " + cdkmol.getName());
monitor.subTask("Molecule: " + cdkmol.getName()
+ "\nCDK Descriptor: " + descType.getOntologyid());
monitor.worked(1);
//This is where we store the result
DescriptorResult res=new DescriptorResult();
res.setDescriptor( descType );
//Get descriptor by id
IMolecularDescriptor cdkDescriptor = getDescriptorMap().get(descType.getOntologyid());
//If we had errors in atomcontainer, add error here
if (atomcontainerError!=null){
res.setErrorMessage(atomcontainerError);
logger.debug("Error message set to: " + res.getErrorMessage());
}else if (cdkDescriptor==null){
res.setErrorMessage("Descriptor not supported in cdk: " + descType.getOntologyid());
logger.debug("Error message set to: " + res.getErrorMessage());
}
//We have a valid descriptorID and a good atomcontainer, do calculation
else{
//Do we have parameters available for this descriptorID in Map?
if (descType.getParameter()!=null && descType.getParameter().size()>0){
// logger.debug("We have: " + descType.getParameter().size()
// + " params available.");
//OK, get it and set it to descriptor
EList<ParameterType> bcParams = descType.getParameter();
//Check that the CDK descriptor accepts parameters
if (cdkDescriptor.getParameterNames()==null && cdkDescriptor
.getParameterNames().length<=0){
logger.warn("Trying to set params for descrImpl: " +
descType.getOntologyid() + " but corresponding " +
"CDKDescriptor does not accept any params.");
}
else{
//These are the ones we should fill
Object[] cdkParams=cdkDescriptor.getParameters();
for (int i=0; i< cdkParams.length; i++){
String cdkName=cdkDescriptor.getParameterNames()[i];
// logger.debug("CDK descr accepts param: " + cdkName);
if (cdkName.equalsIgnoreCase("checkAromaticity")){
// logger.debug("Aromaticity detection set as false, " +
// "as this is already done");
cdkParams[i]=false;
}
else{
for (ParameterType param : bcParams){
if (param.getKey().equals(cdkName)){
//Match, convert from String to data type
Object obj=cdkDescriptor.getParameterType(cdkName);
//Integer
if (obj instanceof Integer) {
try{
Integer ival=Integer.parseInt(param.getValue());
cdkParams[i]=ival;
// logger.debug(" - Set param: " +
// cdkName + " to " + param.getValue());
}catch (NumberFormatException e){
logger.error(" - expected an Integer " +
"param for " + cdkName +
" but found: " +
param.getValue());
}
}
//Boolean
else if (obj instanceof Boolean) {
//Do conversion from String to Boolean
if (param.getValue().equalsIgnoreCase("true")){
cdkParams[i]=true;
// logger.debug(" - Set param: " +
// cdkName + " to " + param.getValue());
}
else if (param.getValue().equalsIgnoreCase("false")){
cdkParams[i]=false;
// logger.debug(" - Set param: " +
// cdkName + " to " + param.getValue());
}
else{
logger.error(" - expected a boolean " +
"param for " + cdkName +
" but found: " +
param.getValue());
}
}
//String
else if (obj instanceof String) {
cdkParams[i]=param.getValue();
// logger.debug(" - Set param: " +
// cdkName + " to " + param.getValue());
}
}
}
}
}
try {
cdkDescriptor.setParameters(cdkParams);
} catch (CDKException e) {
e.printStackTrace();
}
}
}
//Number of return values
Float[] resultVals = new Float[cdkDescriptor.getDescriptorResultType().
length() > 0 ? cdkDescriptor.getDescriptorResultType().
length() : 1];
String[] resultLabels = null;
// logger.debug("# result values: " + resultVals.length);
//Calculate descriptor
try {
DescriptorValue value = ((IMolecularDescriptor) cdkDescriptor).calculate(container);
resultLabels = value.getNames();
org.openscience.cdk.qsar.result.IDescriptorResult result = value.getValue();
if (result instanceof BooleanResult) {
if (((BooleanResult)result).booleanValue()) {
resultVals[0] = 1f;
// logger.debug("Calculated value: " + resultVals[0]);
} else {
resultVals[0] = 0f;
// logger.debug("Calculated value: " + resultVals[0]);
}
} else if (result instanceof DoubleResult) {
resultVals[0] = (float)((DoubleResult)result).doubleValue();
// logger.debug("Calculated value: " + resultVals[0]);
} else if (result instanceof IntegerResult) {
resultVals[0] = (float)((IntegerResult)result).intValue();
// logger.debug("Calculated value: " + resultVals[0]);
} else if (result instanceof IntegerArrayResult) {
resultVals = new Float[((IntegerArrayResult)result).length()];
for (int i=0; i<resultVals.length; i++) {
resultVals[i] = (float)((IntegerArrayResult)result).get(i);
// logger.debug("Calculated value " + i +": " + resultVals[i]);
}
} else if (result instanceof DoubleArrayResult) {
resultVals = new Float[((DoubleArrayResult)result).length()];
for (int i=0; i<resultVals.length; i++) {
resultVals[i] = (float)((DoubleArrayResult)result).get(i);
// logger.debug("Calculated value " + i +": " + resultVals[i]);
}
} else {
logger.error("Uknown descriptor result type: " + result.getClass().getName());
res.setErrorMessage("Uknown descriptor result type: " + result.getClass().getName());
}
} catch (Throwable e) {
logger.error("Could not generate descriptor for molecule: " +
cdkmol.getName() + ". Reason: " + e.getMessage());
for (int i=0; i<resultVals.length; i++) {
resultVals[i] = Float.NaN;
}
res.setErrorMessage(e.getMessage());
// e.printStackTrace();
}
//Check that we got back correct number of values
if (resultLabels==null || resultVals==null){
logger.error("No resultValues or labels for CDK descriptor: " + descType.getOntologyid() + " for mol: " + cdkmol.getName());
res.setErrorMessage( "No resultValues or labels");
}
else if (resultLabels.length != resultVals.length) {
logger.error("#labels != #vals for " + descType.getOntologyid());
res.setErrorMessage( "#labels != #vals for " + descType.getOntologyid() );
}
res.setLabels(resultLabels);
res.setValues(resultVals);
}
//Add results. Could be empty with just error msg.
results.add(res);
}
return results;
}
/**
* Preprocess molecules to set ISINRING, percieve atom types, and
* detect aromaticity
* @param container the IAtomcontainer to work on
* @return String with error message or null if OK
*/
private String doCDKPreprocessing(IAtomContainer container) {
//Add hydrogens
try {
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(container.getBuilder());
for (IAtom atom : container.atoms()) {
IAtomType matched = matcher.findMatchingAtomType(container, atom);
if (matched != null){
AtomTypeManipulator.configure(atom, matched);
}else{
logger.error("Could not find matching atom type for atom: " + atom);
}
}
CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(container.getBuilder());
hAdder.addImplicitHydrogens(container);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(container);
} catch (Exception e1) {
String emsg="Error addding hydrogens : " + e1.getMessage();
logger.error(emsg);
return emsg;
}
//Mark rings as ISINRING
IRingSet rs;
try {
rs = new SpanningTree(container).getBasicRings();
} catch (NoSuchAtomException e) {
String emsg="Could not detect rings: " + e.getMessage();
logger.error(emsg);
return emsg;
}
for (int i = 0; i < container.getAtomCount(); i++) {
if (rs.contains(container.getAtom(i))) {
container.getAtom(i).setFlag(CDKConstants.ISINRING, true);
}
}
//Percieve atom types and aromaticity
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
CDKHueckelAromaticityDetector.detectAromaticity(container);
} catch (CDKException e) {
String emsg="Could not percieve atom types or aromaticity: " + e.getMessage();
logger.error(emsg);
return emsg;
}
return null;
}
public Map<? extends IMolecule, List<IDescriptorResult>> calculateDescriptor(
Map<IMolecule, List<DescriptorType>> moldesc,
IProgressMonitor monitor ){
Map<IMolecule, List<IDescriptorResult>> allResults=
new HashMap<IMolecule, List<IDescriptorResult>>();
//The workload for this provider is mols x their descs
int workload=0;
for (IMolecule mol : moldesc.keySet()){
workload=workload+moldesc.get( mol ).size();
}
monitor.beginTask( "Calculating descriptors with CDK" , workload );
for (IMolecule mol : moldesc.keySet()){
try {
ICDKMolecule cdkmol=cdk.asCDKMolecule(mol);
List<IDescriptorResult> retlist = doCalculate(cdkmol, moldesc.get( mol ), monitor);
allResults.put(mol, retlist);
} catch (BioclipseException e) {
logger.error("Unable to create CDKMolecule from Imolecule. " +
"Skipping descriptor calculation for this mol.");
LogUtils.debugTrace(logger, e);
}
}
return allResults;
}
}