Logo Search packages:      
Sourcecode: cdk version File versions  Download package

MDLRXNWriter.java

/* $RCSfile$
 * $Author$ 
 * $Date$
 * $Revision$
 * 
 * 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.text.NumberFormat;
import java.util.Iterator;
import java.util.Locale;
import java.util.Map;
import java.util.Set;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.MDLFormat;
import org.openscience.cdk.tools.LoggingTool;



/**
 * Writes a reaction to a MDL rxn or SDF file. Attention: Stoichiometric
 * coefficients have to be natural numbers.
 *
 * <pre>
 * MDLRXNWriter writer = new MDLRXNWriter(new FileWriter(new File("output.mol")));
 * writer.write((Molecule)molecule);
 * writer.close();
 * </pre>
 *
 * See {@cdk.cite DAL92}.
 *
 * @cdk.module io
 * @cdk.githash
 *
 * @cdk.keyword file format, MDL RXN file
 */
@TestClass("org.openscience.cdk.io.MDLRXNReaderTest")
00076 public class MDLRXNWriter extends DefaultChemObjectWriter {

    private BufferedWriter writer;
    private LoggingTool logger;
    private int reactionNumber;
    public Map rdFields=null;

    
    /**
     * Contructs a new MDLWriter that can write an array of 
     * Molecules to a Writer.
     *
     * @param   out  The Writer to write to
     */
00090     public MDLRXNWriter(Writer out){
      logger = new LoggingTool(this);
      try {
            if (out instanceof BufferedWriter) {
                writer = (BufferedWriter)out;
            } else {
                writer = new BufferedWriter(out);
            }
        } catch (Exception exc) {
        }
        this.reactionNumber = 1;
    }

    /**
     * Contructs a new MDLWriter that can write an array of
     * Molecules to a given OutputStream.
     *
     * @param   output  The OutputStream to write to
     */
00109     public MDLRXNWriter(OutputStream output){
        this(new OutputStreamWriter(output));
    }
    
    public MDLRXNWriter(){
        this(new StringWriter());
    }

    @TestMethod("testGetFormat")
00118     public IResourceFormat getFormat() {
        return MDLFormat.getInstance();
    }
    
00122     public void setWriter(Writer out) throws CDKException {
      if (out instanceof BufferedWriter) {
            writer = (BufferedWriter)out;
        } else {
            writer = new BufferedWriter(out);
        }
    }

00130     public void setWriter(OutputStream output) throws CDKException {
      setWriter(new OutputStreamWriter(output));
    }
    
    /**
     * Here you can set a map which will be used to build rd fields in the file.
     * The entries will be translated to rd fields like this:<br>
     * &gt; &lt;key&gt;<br>
     * &gt; value<br>
     * empty line<br>
     *
     * @param  map The map to be used, map of String-String pairs
     */
00143     public void setRdFields(Map map){
      rdFields = map;
    }
    
    /**
     * Flushes the output and closes this object.
     */
    @TestMethod("testClose")
00151     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 (IReaction.class.equals(interfaces[i])) return true;
                  if (IReactionSet.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 RXN file formated output. 
     * It can only output ChemObjects of type Reaction
     *
     * @param object class must be of type Molecule or MoleculeSet.
     *
     * @see org.openscience.cdk.ChemFile
     */
00175       public void write(IChemObject object) throws CDKException
      {
            if (object instanceof IReactionSet) {
                  writeReactionSet((IReactionSet)object);
                  return;
            }else if (object instanceof IReaction){
                  
                writeReaction((IReaction)object);
            }else{
                throw new CDKException("Only supported is writing ReactionSet, Reaction objects.");
            }
      }
      /**
       *  Writes an array of Reaction to an OutputStream in MDL rdf format.
       *
       * @param   som  Array of Reactions that is written to an OutputStream
       */
00192       private void writeReactionSet(IReactionSet reactions) throws CDKException{
            
            for(Iterator<IReaction> it = reactions.reactions().iterator();it.hasNext();){
                  writeReaction(it.next());
            }
      }
      
      /**
       * Writes a Reaction to an OutputStream in MDL sdf format.
       *
       * @param   reaction  A Reaction that is written to an OutputStream 
       */
00204       private void writeReaction(IReaction reaction) throws CDKException
      {
            int reactantCount = reaction.getReactantCount();
        int productCount = reaction.getProductCount();
        if (reactantCount <= 0 || productCount <= 0) {
            throw new CDKException("Either no reactants or no products present.");
        }
        
        try {
            // taking care of the $$$$ signs:
            // we do not write such a sign at the end of the first reaction, thus we have to write on BEFORE the second reaction
            if(reactionNumber == 2) {
              writer.write("$$$$");
              writer.newLine();
            }
            
            writer.write("$RXN");
            writer.newLine();
            // reaction name
            String line = (String)reaction.getProperty(CDKConstants.TITLE);
            if(line == null) line = "";
            if(line.length() > 80) line = line.substring(0,80);
            writer.write(line);
            writer.newLine();
            // user/program/date&time/reaction registry no. line
            writer.newLine();
            // comment line
            line = (String)reaction.getProperty(CDKConstants.REMARK);
            if(line == null) line = "";
            if(line.length() > 80) line = line.substring(0,80);
            writer.write(line);
            writer.newLine();
            
            line = "";
            line += formatMDLInt(reactantCount, 3);
            line += formatMDLInt(productCount, 3);
            writer.write(line);
            writer.newLine();
            
            writeMoleculeSet(reaction.getReactants());
            writeMoleculeSet(reaction.getProducts());
            
            //write sdfields, if any
            if(rdFields!=null){
              Set set = rdFields.keySet();
              Iterator iterator = set.iterator();
              while (iterator.hasNext()) {
                Object element = iterator.next();
                writer.write("> <"+(String)element+">");
                writer.newLine();
                writer.write(rdFields.get(element).toString());
                writer.newLine();
                writer.newLine();
              }
            }
            // taking care of the $$$$ signs:
            // we write such a sign at the end of all except the first molecule
            if(reactionNumber != 1) {
              writer.write("$$$$");
              writer.newLine();
            }
            reactionNumber++;
            
        } catch (IOException ex) {
            logger.error(ex.getMessage());
            logger.debug(ex);
            throw new CDKException("Exception while writing MDL file: " + ex.getMessage(), ex);
        }
      }
      
    /**
       * Writes a MoleculeSet to an OutputStream for the reaction.
       *
       * @param   som  The MoleculeSet that is written to an OutputStream 
       */
00279       private void writeMoleculeSet(IMoleculeSet som) throws IOException, CDKException {
        
        for (int i = 0; i < som.getMoleculeCount(); i++) {
            IMolecule mol = som.getMolecule(i);
            for (int j = 0; j < som.getMultiplier(i); j++) {
                StringWriter sw = new StringWriter();
                writer.write("$MOL");
                writer.newLine();
                MDLWriter mdlwriter = null;
                try {
                    mdlwriter = new MDLWriter(sw);
                } catch (Exception ex) {
                    logger.error(ex.getMessage());
                    logger.debug(ex);
                    throw new CDKException("Exception while creating MDLWriter: " + ex.getMessage(), ex);
                }
                mdlwriter.write(mol);
                writer.write(sw.toString());
            }
        }
    }
    
    
      /**
       * Formats an int to fit into the connectiontable and changes it 
     * to a String.
       *
       * @param   i  The int to be formated
       * @param   l  Length of the String
       * @return     The String to be written into the connectiontable
       */
00310     private String formatMDLInt(int i, int l) {
        String s = "", fs = "";
        NumberFormat nf = NumberFormat.getNumberInstance(Locale.ENGLISH);
        nf.setParseIntegerOnly(true);
        nf.setMinimumIntegerDigits(1);
        nf.setMaximumIntegerDigits(l);
        nf.setGroupingUsed(false);
        s = nf.format(i);
        l = l - s.length();
        for (int f = 0; f < l; f++)
            fs += " ";
        fs += s;
        return fs;
    }
      
      

}



Generated by  Doxygen 1.6.0   Back to index