FitnessProvider.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2022 Marco Foscato <marco.foscato@uib.no>
 *
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU Affero General Public License as published
 *   by the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU Affero General Public License for more details.
 *
 *   You should have received a copy of the GNU Affero General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
package denoptim.fitness;
 
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
 
import org.openscience.cdk.IImplementationSpecification;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.isomorphism.Mappings;
import org.openscience.cdk.qsar.DescriptorEngine;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomPairDescriptor;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.IBondDescriptor;
import org.openscience.cdk.qsar.IDescriptor;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.qsar.result.IntegerArrayResult;
import org.openscience.cdk.qsar.result.IntegerResult;
 
import denoptim.constants.DENOPTIMConstants;
import denoptim.exception.DENOPTIMException;
import denoptim.utils.DummyAtomHandler;
import denoptim.utils.ManySMARTSQuery;
import denoptim.utils.MathUtils;
import jakarta.el.ELContext;
import jakarta.el.ELException;
import jakarta.el.ELResolver;
import jakarta.el.ExpressionFactory;
import jakarta.el.FunctionMapper;
import jakarta.el.ValueExpression;
import jakarta.el.VariableMapper;
 
public class FitnessProvider 
{
    protected DescriptorEngine engine;
    
    private List<DescriptorForFitness> descriptors;
    
    private String expression;
    
    private Logger logger = null;
    
    
//------------------------------------------------------------------------------
 
    public FitnessProvider(List<DescriptorForFitness> descriptors, 
            String expression, Logger logger)
    {
        this.logger = logger;
        this.expression = expression;
    
        // We cannot use the list<DescriptorsForFitness> parameter directly
        // because they are not thread-safe.
        // otherwise we hit concurrent modification exception because multiple
        // threads will run the exact same instance of the implementation
        this.descriptors = new ArrayList<DescriptorForFitness>();
 
        // Make new instances of DescriptorForFitness
        ArrayList<String> classnames = new ArrayList<String>();
        for (int i=0; i<descriptors.size(); i++)
        {
            DescriptorForFitness dff = descriptors.get(i);
            classnames.add(dff.getClassName());
            this.descriptors.add(dff.cloneAllButImpl());
        }
        // Instantiate new instances of the descriptors implementations
        engine = new DescriptorEngine(classnames, null);
        List<IDescriptor> newInstances = engine.getDescriptorInstances();
        
        for (int i=0; i<this.descriptors.size(); i++)
        {
            this.descriptors.get(i).implementation = newInstances.get(i);
            try
            {
                this.descriptors.get(i).implementation.setParameters(
                        descriptors.get(i).implementation.getParameters());
            } catch (CDKException e)
            {
                // This should never happen
                e.printStackTrace();
            }
        }
        
        engine.setDescriptorInstances(newInstances);
        engine.setDescriptorSpecifications(engine.initializeSpecifications(
                newInstances));
    }
    
//------------------------------------------------------------------------------
 
    public double getFitness(IAtomContainer iac) throws Exception 
    {
        if (engine == null)
        {
            throw new DENOPTIMException("Internal fitness provider has not been"
                    + " configured.");
        }
        
        // Preparation of the chemical representation
        
        // TODO add possibility to submit external molecular modeling task
        // this could be done by a Modeller class
        
        // Cleanup: remove dummy atoms
        DummyAtomHandler dah = new DummyAtomHandler(
                DENOPTIMConstants.DUMMYATMSYMBOL, logger);
        iac = dah.removeDummyInHapto(iac);
        iac = dah.removeDummy(iac);
        
        // Calculate all descriptors. 
        // The results are put in the properties of
        // the IAtomContainer (as DescriptorValue identified by 
        // DescriptorSpecification keys) and we later translate these into
        // plain human readable strings.
        engine.process(iac);
        
        logger.log(Level.FINE, "Descriptor instances: " 
                + engine.getDescriptorInstances().size());
        
        // Collect numerical values needed to calculate the fitness
 
        // Just to simplify retrieval of the values
        HashMap<String, Double> valuesMap = new HashMap<String,Double>();
        // first we initialize them to null
        for (DescriptorForFitness d : this.descriptors)
        {
            for (Variable v : d.getVariables())
            {
                valuesMap.put(v.getName(), null);
            }
        }
        for (int i=0; i<engine.getDescriptorInstances().size(); i++)
        {
            DescriptorForFitness descriptor = descriptors.get(i);
            IDescriptor desc = engine.getDescriptorInstances().get(i);
            
            String descName = descriptor.shortName;
            logger.log(Level.FINE, "Working on descriptor '" 
                    + descName + "'");
            
            IImplementationSpecification descSpec = 
                    engine.getDescriptorSpecifications().get(i);
            
            // Identify specific atom and bonds
            Map<String, String> smarts = new HashMap<String, String>();
            for (Variable variable : descriptor.getVariables())
            {
                logger.log(Level.FINE, "-Processing varName = '" 
                        + variable.getName() + "'");
                if (variable.smarts != null)
                {
                    if (variable.smarts.size()!=1)
                    {
                        throw new DENOPTIMException("Handling of multiple "
                                + "SMARTS identifiers is not implemented yet. "
                                + "Please, let the DENOPTIM developers know "
                                + "about your interest in this "
                                + "functionality.");
                    }
                    smarts.put(variable.getName(), variable.smarts.get(0));
                }
            }
            
            Map<String, Mappings> allMatches = new HashMap<String, Mappings>();
            if (smarts.size() != 0)
            {
                ManySMARTSQuery msq = new ManySMARTSQuery(iac, smarts);
                if (msq.hasProblems())
                {
                    String msg = "WARNING! Problems while searching for "
                            + "specific atoms/bonds using SMARTS: " 
                            + msq.getMessage();
                    throw new DENOPTIMException(msg,msq.getProblem());
                }
                allMatches = msq.getAllMatches();
            }
            
            logger.log(Level.FINE, "Collecting value of variables "
                    + "derived from descriptor #" + i + ": " + descName);
            
            //Molecular/Atomic/bond descriptors are stored accordingly
            DescriptorValue value = null;
            if (desc instanceof IMolecularDescriptor)
            {
                for (Variable variable : descriptor.getVariables())
                {
                    String varName = variable.getName();
                    value = (DescriptorValue) iac.getProperty(descSpec);
                    double val = processValue(descName, descriptor, desc, 
                            descSpec, value, varName, iac);
                    valuesMap.put(varName, val);
                    iac.setProperty(varName,val);
                }
            } else if (desc instanceof IAtomicDescriptor) {
                for (Variable variable : descriptor.getVariables())
                {
                    String varName = variable.getName();
                    Mappings hits = allMatches.get(varName);
                    if (hits==null)
                    {
                        String msg = "No hits for SMARTS of " + varName + ": "
                                + "setting variable value to 0.0";
                        logger.log(Level.WARNING ,msg);
                        valuesMap.put(varName, 0.0);
                        continue;
                    }
                    logger.log(Level.FINE, "-AtomIDs contributing to " 
                            + varName + ":" + hits);
                    if (hits.count() > 1)
                    {
                        String msg = "Multiple hits with SMARTS identifier for "
                                + varName + ". Taking average of all values.";
                        logger.log(Level.WARNING ,msg);
                    }
                    int valCounter = -1;
                    List<Double> vals = new ArrayList<Double>();
                    for (int[] singleMatch : hits)
                    {
                        if (singleMatch.length != 1)
                        {
                            String msg = "Multiple entries in a single hit "
                                    + "with SMARTS identifier for "
                                    + varName + ". Taking average of values.";
                            logger.log(Level.WARNING ,msg);
                        }
                        for (Integer atmId : singleMatch)
                        {
                            IAtom atm = iac.getAtom(atmId);
                            value = (DescriptorValue) atm.getProperty(descSpec);
                            double val = processValue(descName, descriptor, 
                                     desc, descSpec, value, varName, iac);
                            vals.add(val);
                            valCounter++;
                            iac.setProperty(varName+"_"+valCounter,val);
                        }
                    }
                    logger.log(Level.FINE, "-Values contributing to " 
                            + varName + ": " + vals);
                    double overallValue = MathUtils.mean(vals);
                    valuesMap.put(varName, overallValue);
                    iac.setProperty(varName,overallValue);
                }
            } else if (desc instanceof IBondDescriptor) {
                for (Variable variable : descriptor.getVariables())
                {
                    String varName = variable.getName();
                    Mappings hits = allMatches.get(varName);
                    if (hits==null)
                    {
                        String msg = "No hits for SMARTS of " + varName + ": "
                                + "setting variable value to 0.0";
                        logger.log(Level.WARNING, msg);
                        valuesMap.put(varName, 0.0);
                        continue;
                    }
                    logger.log(Level.FINE, "-AtomIDs contributing to " 
                            + varName + ":" + hits);
                    if (hits.count() > 1)
                    {
                        String msg = "Multiple hits with SMARTS identifier for "
                                + varName + ". Taking average of all values.";
                        logger.log(Level.WARNING, msg);
                    }
                    int valCounter = -1;
                    List<Double> vals = new ArrayList<Double>();
                    for (int[] singleMatch : hits)
                    {
                        if (singleMatch.length != 2)
                        {
                            String msg = "Number of entries is != 2 for a "
                                    + "single hit with SMARTS identifier for "
                                    + varName + ". I do not know how to deal "
                                    + "with this.";
                            throw new DENOPTIMException(msg);
                        }
                        IBond bnd = iac.getBond(iac.getAtom(singleMatch[0]),
                                iac.getAtom(singleMatch[1]));
                        value = (DescriptorValue) bnd.getProperty(descSpec);
                        double val = processValue(descName, descriptor, 
                                     desc, descSpec, value, varName, iac);
                        vals.add(val);
                        valCounter++;
                        iac.setProperty(varName+"_"+valCounter,val);
                    }
                    logger.log(Level.FINE, "-Values contributing to " 
                            + varName + ": "+vals);
                    double overallValue = MathUtils.mean(vals);
                    valuesMap.put(varName, overallValue);
                    iac.setProperty(varName,overallValue);
                }
            } else if (desc instanceof IAtomPairDescriptor) {
                throw new Exception("AtomPair-kind of descriptors are not yet "
                        + " usable. Upgrade the code. ");
                //TODO: implement this part...
            } else {
                throw new Exception("Type of descriptor "+ descName + " is "
                        + "unknown. Cannot understand if it should be threated "
                        + "as molecular, atomic, or bond descriptor.");
            }
        }
        logger.log(Level.FINE, "VARIABLES: "+valuesMap);
 
        // Calculate the fitness from the expression and descriptor values
        ExpressionFactory expFactory = ExpressionFactory.newInstance();
        ELContext ncc = new ELContext() {
            
            VariableMapper vm = new VariableMapper() {
 
                @SuppressWarnings("serial")
                @Override
                public ValueExpression resolveVariable(String varName)
                {
                    ValueExpression ve = new ValueExpression() {
 
                        @Override
                        public Object getValue(ELContext context)
                        {
                            Double value = null;
                            if (!valuesMap.containsKey(varName))
                            {
                                throw new ELException("Variable '" + varName 
                                        + "' cannot be resolved");
                            } else {
                                value = valuesMap.get(varName);
                            }
                            return value;
                        }
 
                        @Override
                        public void setValue(ELContext context, Object value)
                        {}
 
                        @Override
                        public boolean isReadOnly(ELContext context)
                        {
                            return true;
                        }
 
                        @Override
                        public Class<?> getType(ELContext context)
                        {
                            return Double.class;
                        }
 
                        @Override
                        public Class<?> getExpectedType()
                        {
                            return Double.class;
                        }
 
                        @Override
                        public String getExpressionString()
                        {
                            return null;
                        }
 
                        @Override
                        public boolean equals(Object obj)
                        {
                            return false;
                        }
 
                        @Override
                        public int hashCode()
                        {
                            return 0;
                        }
 
                        @Override
                        public boolean isLiteralText()
                        {
                            return false;
                        }
                    };
                    return ve;
                }
 
                @Override
                public ValueExpression setVariable(String variable,
                        ValueExpression expression)
                {
                    return null;
                }};
 
            @Override
            public ELResolver getELResolver()
            {
                return null;
            }
 
            @Override
            public FunctionMapper getFunctionMapper()
            {
                return null;
            }
 
            @Override
            public VariableMapper getVariableMapper()
            {
                return vm;
            }};
        ValueExpression ve = expFactory.createValueExpression(ncc, expression, 
                Double.class);
        double fitness = (double) ve.getValue(ncc);
        iac.setProperty(DENOPTIMConstants.FITNESSTAG,fitness);
        return fitness;
    }
    
//------------------------------------------------------------------------------
 
    private double processValue(String descName, 
            DescriptorForFitness descriptor,
            IDescriptor implementation, 
            IImplementationSpecification descSpec, DescriptorValue value,
            String varName, IAtomContainer iac) throws Exception 
    {
        if (value == null)
        {
            throw new Exception("Null value from calcualation of descriptor"
                    + " " + descName + " (for variable '" + varName + "'");
        }
        IDescriptorResult result = value.getValue();
        if (result == null)
        {
            throw new Exception("Null result from calcualation of "
                    + "descriptor " + descName + "(for variable '" 
                    + varName + "'");
        }
        
        double valueToFitness = Double.NaN;
        
        if (result instanceof DoubleResult) 
        {
            valueToFitness = ((DoubleResult) result).doubleValue();
        } else if (result instanceof IntegerResult) 
        {
            valueToFitness = ((IntegerResult)result).intValue();
        } else if (result instanceof DoubleArrayResult) 
        {
            DoubleArrayResult a = (DoubleArrayResult) result;
            int id = descriptor.resultId;
            if (id >= a.length())
            {
                throw new Exception("Value ID out of range for descriptor "
                        + descName);
            }
            valueToFitness = a.get(id);
            
            //We also keep track of the entire vector
            List<String> list = new ArrayList<String>();
            for (int j=0; j<a.length(); j++) 
            {
                list.add(String.valueOf(a.get(j)));
            }
            iac.setProperty(implementation.getClass().getName() + "#" + varName,
                    list);
        } else if (result instanceof IntegerArrayResult) 
        {
            IntegerArrayResult array = (IntegerArrayResult) result;
            int id = descriptor.resultId;
            if (id >= array.length())
            {
                throw new Exception("Value ID out of range for descriptor "
                        + descName);
            }
            valueToFitness = array.get(id);
 
            //We also keep track of the entire vector
            List<String> list = new ArrayList<String>();
            for (int j=0; j<array.length(); j++) 
            {
                list.add(String.valueOf(array.get(j)));
            }
            iac.setProperty(implementation.getClass().getName()+ "#" + varName,
                    list);
        }
       
        return valueToFitness;
    }
 
//------------------------------------------------------------------------------
    
}