Mol2Graph.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2019 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.programs.mol2graph;
 
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Level;
 
import org.openscience.cdk.interfaces.IAtomContainer;
 
import denoptim.exception.DENOPTIMException;
import denoptim.ga.EAUtils;
import denoptim.graph.DGraph;
import denoptim.io.DenoptimIO;
import denoptim.programs.RunTimeParameters.ParametersType;
import denoptim.programs.fragmenter.FragmenterParameters;
import denoptim.task.ProgramTask;
 
 
public class Mol2Graph extends ProgramTask
{
 
//------------------------------------------------------------------------------
    
    public Mol2Graph(File configFile, File workDir)
    {
        super(configFile,workDir);
    }
    
//------------------------------------------------------------------------------
 
    @Override
    public void runProgram() throws Throwable
    {
        Mol2GraphParameters m2gParams = new Mol2GraphParameters();
        m2gParams.readParameterFile(configFilePathName.getAbsolutePath());
        m2gParams.checkParameters();
        m2gParams.processParameters();
        m2gParams.startProgramSpecificLogger(loggerIdentifier, false); //to STDOUT
        
        FragmenterParameters frgParams = new FragmenterParameters();
        if (m2gParams.containsParameters(ParametersType.FRG_PARAMS))
        {
            frgParams = (FragmenterParameters) m2gParams.getParameters(
                    ParametersType.FRG_PARAMS);
        }
        if (m2gParams.containsParameters(ParametersType.FS_PARAMS))
        {
            frgParams.setParameters(m2gParams.getParameters(
                    ParametersType.FS_PARAMS));
        }
        
        List<DGraph> graphs = new ArrayList<DGraph>();
        for (int i=0; i<m2gParams.getInputMolsCount(); i++)
        {
            IAtomContainer mol = m2gParams.getInputMol(i);
            DGraph graph = null;
            try {
                graph = EAUtils.makeGraphFromFragmentationOfMol(mol, frgParams);
            } catch (DENOPTIMException de)
            {
                m2gParams.getLogger().log(Level.SEVERE, "Unable to convert "
                        + "molecule " + i + " to DENOPTIM graph. " 
                        + de.getMessage());
                return;
            }
            
            graphs.add(graph);
        }
        
        if (graphs.size()>1)
        {
            DenoptimIO.writeGraphsToFile(new File(m2gParams.getOutFile()), 
                m2gParams.getOutFormat(), graphs, m2gParams.getLogger(),
                m2gParams.getRandomizer());
        } else {
            DenoptimIO.writeGraphToFile(new File(m2gParams.getOutFile()), 
                    m2gParams.getOutFormat(), graphs.get(0), m2gParams.getLogger(),
                    m2gParams.getRandomizer());
        }
    }
    
//-----------------------------------------------------------------------------
    
}