TanimotoMolSimilarityTest.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.descriptors;
 
import static org.junit.jupiter.api.Assertions.assertTrue;
 
import java.lang.reflect.Constructor;
 
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.fingerprint.IBitFingerprint;
import org.openscience.cdk.fingerprint.PubchemFingerprinter;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.smiles.SmilesParser;
 
public class TanimotoMolSimilarityTest
{
    private TanimotoMolSimilarity descriptor;
    
    @BeforeEach
    public void setUp() throws Exception
    {
        Constructor<TanimotoMolSimilarity> defaultConstructor = 
                TanimotoMolSimilarity.class.getConstructor();
        this.descriptor = defaultConstructor.newInstance();
        this.descriptor.initialise(DefaultChemObjectBuilder.getInstance());
    }
    
//------------------------------------------------------------------------------
        
    @Test
    public void testTanimotoMolSimilarity() throws Exception
    {
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IAtomContainer ref = sp.parseSmiles("CNC(=O)c1cc(OC)ccc1");
        PubchemFingerprinter fpMaker = new PubchemFingerprinter(
                DefaultChemObjectBuilder.getInstance());
        IBitFingerprint fpRef = fpMaker.getBitFingerprint(ref);
        
        Object[] params = {"PubchemFingerprinter", fpRef};
        descriptor.setParameters(params);
        
        IAtomContainer mol1 = sp.parseSmiles("COc1ccccc1");
        double value = ((DoubleResult) descriptor.calculate(mol1).getValue())
                .doubleValue();
        assertTrue(closeEnough(0.6065, value), "Tanimoto similarity with mol1: "
                + value);
 
        IAtomContainer mol2 = sp.parseSmiles("P");
        value = ((DoubleResult) descriptor.calculate(mol2).getValue())
                .doubleValue();
        assertTrue(closeEnough(0.0, value), "Tanimoto similarity with mol2: "
                + value);
 
        IAtomContainer mol3 = sp.parseSmiles("COc1cc(C(=O)NC)ccc1");
        value = ((DoubleResult) descriptor.calculate(mol3).getValue())
                .doubleValue();
        assertTrue(closeEnough(1.0, value), "Tanimoto similarity with mol3: "
                + value);
    }
    
//------------------------------------------------------------------------------
    
    private boolean closeEnough(double expected, double actual)
    {
        double threshold = 0.0001;
        double delta = Math.abs(expected-actual);
        return delta < threshold;
    }
 
//------------------------------------------------------------------------------
 
}