MoleculeUtilsTest.java

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package denoptim.utils;
 
/*
 *   DENOPTIM
 *   Copyright (C) 2019 Vishwesh Venkatraman <vishwesh.venkatraman@ntnu.no>
 *   and 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/>.
 */
import static denoptim.utils.MoleculeUtils.getPoint3d;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
 
import javax.vecmath.Point2d;
import javax.vecmath.Point3d;
 
import org.junit.jupiter.api.Test;
import org.openscience.cdk.Atom;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
 
public class MoleculeUtilsTest
{
    private IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
    
//------------------------------------------------------------------------------
    
    @Test
    public void testGetPoint3d() throws Exception
    {
        IAtom a = new Atom();
        assertTrue(areCloseEnough(getPoint3d(a).x,0.0));
        assertTrue(areCloseEnough(getPoint3d(a).y,0.0));
        assertTrue(areCloseEnough(getPoint3d(a).z,0.0));
        
        a.setPoint2d(new Point2d(2.6, -4.2));
        assertTrue(areCloseEnough(getPoint3d(a).x,2.6));
        assertTrue(areCloseEnough(getPoint3d(a).y,-4.2));
        assertTrue(areCloseEnough(getPoint3d(a).z,0.0));
        
        a.setPoint3d(new Point3d(2.6, -4.2, 6.4));
        assertTrue(areCloseEnough(getPoint3d(a).x,2.6));
        assertTrue(areCloseEnough(getPoint3d(a).y,-4.2));
        assertTrue(areCloseEnough(getPoint3d(a).z,6.4));
        
        assertFalse(areCloseEnough(1.00001, 1.00002));
    }
    
//------------------------------------------------------------------------------
 
    private boolean areCloseEnough(double a, double b)
    {
        double delta = 0.0000001;
        return Math.abs(a-b) <= delta;
    }
    
//------------------------------------------------------------------------------
 
    @Test
    public void testCalculateCentroid() throws Exception
    {
        IAtomContainer mol = builder.newAtomContainer();
        mol.addAtom(new Atom("H", new Point3d(1.2,-2.9,2.5)));
        mol.addAtom(new Atom("H", new Point3d(2.3,-4.8,4.2)));
        mol.addAtom(new Atom("H", new Point3d(4.5,2.6,-5.4)));
        
        Point3d c = MoleculeUtils.calculateCentroid(mol);
        assertTrue(areCloseEnough(2.6666666,c.x), "Wrong value in X");
        assertTrue(areCloseEnough(-1.7,c.y), "Wrong value in Y");
        assertTrue(areCloseEnough(0.4333333,c.z), "Wrong value in Z");
    }
    
//------------------------------------------------------------------------------
 
}