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ZMatrixReader.java

/* $RCSfile$
 * $Author$
 * $Date$
 * $Revision$
 *
 * Copyright (C) 2001-2007  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.
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 */
package org.openscience.cdk.io;

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.geometry.ZMatrixTools;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.ZMatrixFormat;

import javax.vecmath.Point3d;
import java.io.*;
import java.util.StringTokenizer;

/**
 * It reads Z matrices like in Gaussian input files. It seems that it cannot
 * handle Z matrices where values are given via a stringID for which the value
 * is given later.
 *
 * @cdk.module extra
 * @cdk.githash
 *
 * @cdk.keyword file format, Z-matrix
 */
@TestClass("org.openscience.cdk.io.ZMatrixReaderTest")
00055 public class ZMatrixReader extends DefaultChemObjectReader {

  private BufferedReader input;
  
  /**
   * Constructs a ZMatrixReader from a Reader that contains the
   * data to be parsed.
   *
   * @param     input   Reader containing the data to read
   */
00065   public ZMatrixReader(Reader input) {
    this.input = new BufferedReader(input);
  }
  
    public ZMatrixReader(InputStream input) {
        this(new InputStreamReader(input));
    }
    
    public ZMatrixReader() {
        this(new StringReader(""));
    }
  
    @TestMethod("testGetFormat")
00078     public IResourceFormat getFormat() {
        return ZMatrixFormat.getInstance();
    }

    @TestMethod("testSetReader_Reader")
00083     public void setReader(Reader input) throws CDKException {
        if (input instanceof BufferedReader) {
            this.input = (BufferedReader)input;
        } else {
            this.input = new BufferedReader(input);
        }
    }

    @TestMethod("testSetReader_InputStream")
00092     public void setReader(InputStream input) throws CDKException {
        setReader(new InputStreamReader(input));
    }

      @TestMethod("testAccepts")
    public boolean accepts(Class classObject) {
            Class[] interfaces = classObject.getInterfaces();
        for (Class anInterface : interfaces) {
            if (IChemFile.class.equals(anInterface)) return true;
        }
            return false;
      }

  /**
   *  Returns a IChemObject of type object bye reading from
   *  the input. 
   *
   *  The function supports only reading of ChemFile's.
   *
   * @param     object  IChemObject that types the class to return.
   * @throws    CDKException when a IChemObject is requested that cannot be read.
   */
00114   public IChemObject read(IChemObject object) throws CDKException 
  {
    if (object instanceof IChemFile) 
      return readChemFile((IChemFile)object);
    else 
      throw new CDKException("Only ChemFile objects can be read.");
  }

  /**
   *  Private method that actually parses the input to read a ChemFile
   *  object.
   *
   * @param file  the file to read from
   * @return A ChemFile containing the data parsed from input.
   */
00129   private IChemFile readChemFile(IChemFile file) {
    IChemSequence chemSequence = file.getBuilder().newChemSequence();
        
    int number_of_atoms;
    StringTokenizer tokenizer;
        
    try 
    {
      String line = input.readLine();
      while (line.startsWith("#"))
        line = input.readLine();
      /*while (input.ready() && line != null) 
      {*/
//        logger.debug("lauf");
        // parse frame by frame
        tokenizer = new StringTokenizer(line, "\t ,;");
                
        String token = tokenizer.nextToken();
        number_of_atoms = Integer.parseInt(token);
        String info = input.readLine();
                
        IChemModel chemModel = file.getBuilder().newChemModel();
        IMoleculeSet setOfMolecules = file.getBuilder().newMoleculeSet();
                
        IMolecule m = file.getBuilder().newMolecule();
        m.setProperty(CDKConstants.TITLE ,info);

        String[] types = new String[number_of_atoms];
        double[] d = new double[number_of_atoms]; int[] d_atom = new int[number_of_atoms]; // Distances
        double[] a = new double[number_of_atoms]; int[] a_atom = new int[number_of_atoms]; // Angles
        double[] da = new double[number_of_atoms]; int[] da_atom = new int[number_of_atoms]; // Diederangles
        //Point3d[] pos = new Point3d[number_of_atoms]; // calculated positions
                
        int i = 0;
        while(i < number_of_atoms)
        {
          line = input.readLine();
//          logger.debug("line:\""+line+"\"");
          if (line == null) break;
          if (line.startsWith("#")) 
          {
            // skip comment in file
          } else 
          {
            d[i] = 0d; d_atom[i] = -1;
            a[i] = 0d; a_atom[i] = -1;
            da[i] = 0d; da_atom[i] = -1;

            tokenizer = new StringTokenizer(line, "\t ,;");
            int fields = tokenizer.countTokens();
                        
            if (fields < Math.min(i*2+1,7)) 
            {
              // this is an error but cannot throw exception
            }
            else if (i==0)
            {
              types[i] = tokenizer.nextToken();
              i++;
            }
            else if (i==1)
            {
              types[i] = tokenizer.nextToken();
              d_atom[i] = Integer.valueOf(tokenizer.nextToken()) -1;
              d[i] = new Double(tokenizer.nextToken());
              i++;
            }
            else if (i==2)
            {
              types[i] = tokenizer.nextToken();
              d_atom[i] = Integer.valueOf(tokenizer.nextToken()) -1;
              d[i] = new Double(tokenizer.nextToken());
              a_atom[i] = new Integer(tokenizer.nextToken()) -1;
              a[i] = new Double(tokenizer.nextToken());
              i++;
            }
            else
            {
              types[i] = tokenizer.nextToken();
              d_atom[i] = new Integer(tokenizer.nextToken()) -1;
              d[i] = new Double(tokenizer.nextToken());
              a_atom[i] = new Integer(tokenizer.nextToken()) -1;
              a[i] = new Double(tokenizer.nextToken());
              da_atom[i] = new Integer(tokenizer.nextToken()) -1;
              da[i] = new Double(tokenizer.nextToken());
              i++;
            }
          }
        }
        
        // calculate cartesian coordinates
        Point3d[] cartCoords = ZMatrixTools.zmatrixToCartesian(d, d_atom, a, a_atom, da, da_atom);
        
        for (i=0; i<number_of_atoms; i++) {
              m.addAtom(file.getBuilder().newAtom(types[i], cartCoords[i]));
        }

//        logger.debug("molecule:"+m);

        setOfMolecules.addMolecule(m);
        chemModel.setMoleculeSet(setOfMolecules);
        chemSequence.addChemModel(chemModel);
        line = input.readLine();
        file.addChemSequence(chemSequence);
    } catch (IOException e) 
    {
      // should make some noise now
      file = null;
    }
    return file;
  }

    @TestMethod("testClose")
00242     public void close() throws IOException {
        input.close();
    }
}

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