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SDFWriter.java

/* $Revision$ $Author$ $Date$
 * 
 * Copyright (C) 1997-2007  The Chemistry Development Kit (CDK) project
 * 
 * Contact: cdk-devel@lists.sourceforge.net
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * 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 Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.openscience.cdk.io;

import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.StringWriter;
import java.io.Writer;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.SDFFormat;
import org.openscience.cdk.io.setting.BooleanIOSetting;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.smiles.InvPair;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

/**
 * Writes MDL SD files ({@cdk.cite DAL92}). A MDL SD file contains one or more molecules,
 * complemented by properties.
 *
 * @cdk.module  io
 * @cdk.githash
 * @cdk.keyword file format, MDL SD file
 */
@TestClass("org.openscience.cdk.io.SDFWriterTest")
00064 public class SDFWriter extends DefaultChemObjectWriter {

    private final static LoggingTool logger = new LoggingTool(SDFWriter.class);

    private BufferedWriter writer;
    private BooleanIOSetting writerProperties;
    
    /**
     * Constructs a new SDFWriter that writes to the given {@link Writer}.
     *
     * @param   out  The {@link Writer} to write to
     */
00076     public SDFWriter(Writer out) {
        if (out instanceof BufferedWriter) {
            writer = (BufferedWriter)out;
        } else {
            writer = new BufferedWriter(out);
        }
        initIOSettings();
    }

    /**
     * Constructs a new MDLWriter that can write to a given
     * {@link OutputStream}.
     *
     * @param   output  The {@link OutputStream} to write to
     */
00091     public SDFWriter(OutputStream output) {
        this(new OutputStreamWriter(output));
    }
    
    public SDFWriter() {
        this(new StringWriter());
    }

    @TestMethod("testGetFormat")
00100     public IResourceFormat getFormat() {
        return SDFFormat.getInstance();
    }
    
00104     public void setWriter(Writer out) throws CDKException {
      if (out instanceof BufferedWriter) {
            writer = (BufferedWriter)out;
        } else {
            writer = new BufferedWriter(out);
        }
    }

00112     public void setWriter(OutputStream output) throws CDKException {
      setWriter(new OutputStreamWriter(output));
    }
    
    /**
     * Flushes the output and closes this object.
     */
    @TestMethod("testClose")
00120     public void close() throws IOException {
        writer.close();
    }

      @TestMethod("testAccepts")
    public boolean accepts(Class classObject) {
            Class[] interfaces = classObject.getInterfaces();
            for (int i=0; i<interfaces.length; i++) {
                  if (IAtomContainer.class.equals(interfaces[i])) return true;
                  if (IChemFile.class.equals(interfaces[i])) return true;
                  if (IChemModel.class.equals(interfaces[i])) return true;
                  if (IAtomContainerSet.class.equals(interfaces[i])) return true;
            }
          Class superClass = classObject.getSuperclass();
          if (superClass != null) return this.accepts(superClass);
            return false;
      }

    /**
     * Writes a IChemObject to the MDL SD file formated output. It can only
     * output IChemObjects of type {@link IChemFile}, {@link IAtomContainerSet}
     * and {@link IMoleculeSet}.
     *
     * @param object an acceptable {@link IChemObject} 
     *
     * @see #accepts(Class)
     */
00147       public void write(IChemObject object) throws CDKException {
            try {
                  if (object instanceof IAtomContainerSet) {
                        writeMoleculeSet((IAtomContainerSet)object);
                        return;
                  } else if (object instanceof IChemFile) {
                        writeChemFile((IChemFile)object);
                        return;
                  } else if (object instanceof IChemModel) {
                        IChemFile file = object.getBuilder().newChemFile();
                        IChemSequence sequence = object.getBuilder().newChemSequence();
                        sequence.addChemModel((IChemModel)object);
                        file.addChemSequence(sequence);
                        writeChemFile((IChemFile)file);
                        return;
                  } else if (object instanceof IAtomContainer) {
                        writeMolecule((IAtomContainer)object);
                        return;
                  }
            } catch (Exception ex) {
                  logger.error(ex.getMessage());
                  logger.debug(ex);
                  throw new CDKException(
                      "Exception while writing MDL file: " + ex.getMessage(), ex
                  );
            }
            throw new CDKException("Only supported is writing of ChemFile, MoleculeSet, AtomContainer and Molecule objects.");
      }
      
      /**
       * Writes an {@link IAtomContainerSet}.
       *
       * @param   som  the {@link IAtomContainerSet} to serialize
       */
00181       private void writeMoleculeSet(IAtomContainerSet som) throws Exception {
            for (IAtomContainer mol : som.atomContainers()) {
                writeMolecule(mol);
            }
      }
      
      private void writeChemFile(IChemFile file) throws Exception {
            for (IAtomContainer container :
                 ChemFileManipulator.getAllAtomContainers(file)) {
                  writeMolecule(container);
            }
      }

    private void writeMolecule(IAtomContainer container) throws CDKException {
        try {
            // write the MDL molfile bits
            StringWriter stringWriter = new StringWriter();
            MDLWriter mdlWriter = new MDLWriter(stringWriter);
            mdlWriter.write(container);
            mdlWriter.close();
            writer.write(stringWriter.toString());

            // write the properties
            Map<Object,Object> sdFields = container.getProperties();
            if(sdFields != null){
                for (Object propKey : sdFields.keySet()) {
                    if (!isCDKInternalProperty(propKey)) {
                        writer.write("> <" + propKey + ">");
                        writer.newLine();
                        writer.write("" + sdFields.get(propKey));
                        writer.newLine();
                        writer.newLine();
                    }
                }
            }
            writer.write("$$$$\n");
        } catch (IOException exception) {
            throw new CDKException(
                "Error while writing a SD file entry: " +
                exception.getMessage(), exception
            );
        }
    }

    /**
     * A list of properties used by CDK algorithms which must never be
     * serialized into the SD file format.
     */
00229     private static List<String> cdkInternalProperties = new ArrayList<String>();

    static {
        cdkInternalProperties.add(InvPair.CANONICAL_LABEL);
        cdkInternalProperties.add(InvPair.INVARIANCE_PAIR);
        // I think there are a few more, but cannot find them right now
    }

    private boolean isCDKInternalProperty(Object propKey) {
        return cdkInternalProperties.contains(propKey);
    }

    private void initIOSettings() {
        writerProperties = new BooleanIOSetting("writeProperties",
          IOSetting.LOW,
          "Should molecular properties be written?", 
          "true"
        );
    }

    public void customizeJob() {
        fireIOSettingQuestion(writerProperties);
    }

00253     public IOSetting[] getIOSettings() {
        IOSetting[] settings = new IOSetting[1];
        settings[0] = writerProperties;
        return settings;
    }
}



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