IAtomContainerSerializer.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 java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.List;
 
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
 
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonSerializationContext;
import com.google.gson.JsonSerializer;
 
import denoptim.utils.MoleculeUtils;
 
 
public class IAtomContainerSerializer implements JsonSerializer<IAtomContainer>
{
    protected static final String ATOMSKEY = "atoms";
 
    protected static final String BONDSKEY = "bonds";
 
    @Override
    public JsonElement serialize(IAtomContainer iac, Type typeOfSrc,
            JsonSerializationContext context)
    {
        JsonObject jsonObject = new JsonObject();
        List<LWAtom> atoms = new ArrayList<LWAtom>();
        for (IAtom atm : iac.atoms())
        {
            atoms.add(new LWAtom(MoleculeUtils.getSymbolOrLabel(atm),
                    MoleculeUtils.getPoint3d(atm)));
        }
        List<LWBond> bonds = new ArrayList<LWBond>();
        for (IBond bnd : iac.bonds())
        {
            bonds.add(new LWBond(iac.indexOf(bnd.getAtom(0)), 
                    iac.indexOf(bnd.getAtom(1)), bnd.getOrder()));
        }
        
        jsonObject.add(ATOMSKEY, context.serialize(atoms));
        jsonObject.add(BONDSKEY, context.serialize(bonds));
        
        return jsonObject;
    }
}