LWAtom.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.json;
 
import javax.vecmath.Point3d;
 
import org.openscience.cdk.Atom;
import org.openscience.cdk.PseudoAtom;
import org.openscience.cdk.interfaces.IAtom;
 
import denoptim.utils.MoleculeUtils;
 
public class LWAtom
{
    protected String elSymbol = "";
    
    protected Point3d p3d = null;
    
//------------------------------------------------------------------------------
    
    public LWAtom(String elSymbol, Point3d p3d)
    {
        this.elSymbol = elSymbol;
        this.p3d = p3d;
    }
    
//------------------------------------------------------------------------------
    
    public IAtom toIAtom()
    {
        IAtom atm = null;
        if (MoleculeUtils.isElement(elSymbol))
        {
            atm = new Atom(elSymbol);
        } else {
            atm = new PseudoAtom(elSymbol);
        }
        atm.setPoint3d(new Point3d(p3d));
        return atm;
    }
    
//------------------------------------------------------------------------------
    
}