gaussian03reader.java

化学图形处理软件

/* $Revision: 7001 $ $Author: kaihartmann $ $Date: 2006-09-20 21:12:37 +0200 (Wed, 20 Sep 2006) $
 *
 * Copyright (C) 2002-2003  Bradley A. Smith <[e-mail]>
 *
 * Contact: [e-mail]
 *
 * This library 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.
 *
 *  This library 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 library; 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 org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.io.formats.Gaussian03Format;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.tools.LoggingTool;

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

/**
 * A reader for Gaussian03 output.
 * Gaussian 03 is a quantum chemistry program
 * by Gaussian, Inc. (<a href="http://www.gaussian.com/">http://www.gaussian.com/</a>).
 * 
 * <p>Molecular coordinates, energies, and normal coordinates of
 * vibrations are read. Each set of coordinates is added to the
 * ChemFile in the order they are found. Energies and vibrations
 * are associated with the previously read set of coordinates.
 * 
 * <p>This reader was developed from a small set of
 * example output files, and therefore, is not guaranteed to
 * properly read all Gaussian03 output. If you have problems,
 * please contact the author of this code, not the developers
 * of Gaussian03.
 * 
 * <p>This code was adaptated by Jonathan from Gaussian98Reader written by
 * Bradley, and ported to CDK by Egon.
 *
 * @author Jonathan C. Rienstra-Kiracofe <[e-mail]>
 * @author Bradley A. Smith <[e-mail]>
 * @author Egon Willighagen
 * @cdk.module io
 */
public class Gaussian03Reader extends DefaultChemObjectReader {

    private BufferedReader input;
    private LoggingTool logger;

    public Gaussian03Reader(Reader reader) {
        input = new BufferedReader(reader);
        logger = new LoggingTool(this);
    }

    public Gaussian03Reader(InputStream input) {
        this(new InputStreamReader(input));
    }

    public Gaussian03Reader() {
        this(new StringReader(""));
    }

    public IResourceFormat getFormat() {
        return Gaussian03Format.getInstance();
    }

    public void setReader(Reader reader) throws CDKException {
        this.input = new BufferedReader(input);
    }

    public void setReader(InputStream input) throws CDKException {
        setReader(new InputStreamReader(input));
    }

    public boolean accepts(Class classObject) {
        Class[] interfaces = classObject.getInterfaces();
        for (int i = 0; i < interfaces.length; i++) {
            if (IChemFile.class.equals(interfaces[i])) return true;
            if (IChemSequence.class.equals(interfaces[i])) return true;
        }
        return false;
    }

    public IChemObject read(IChemObject object) throws CDKException {
        if (object instanceof IChemSequence) {
            return readChemSequence((IChemSequence) object);
        } else if (object instanceof IChemFile) {
            return readChemFile((IChemFile) object);
        } else {
            throw new CDKException("Object " + object.getClass().getName() + " is not supported");
        }
    }

    public void close() throws IOException {
        input.close();
    }

    private IChemFile readChemFile(IChemFile chemFile) throws CDKException {
        IChemSequence sequence = readChemSequence(chemFile.getBuilder().newChemSequence());
        chemFile.addChemSequence(sequence);
        return chemFile;
    }

    private IChemSequence readChemSequence(IChemSequence sequence) throws CDKException {
        IChemModel model = null;

        try {
            String line = input.readLine();
            //String levelOfTheory = null;

            // Find first set of coordinates
            while (input.ready() && (line != null)) {
                if (line.indexOf("Standard orientation:") >= 0) {

                    // Found a set of coordinates
                    model = sequence.getBuilder().newChemModel();
                    try {
                        readCoordinates(model);
                    } catch (IOException exception) {
                        throw new CDKException("Error while reading coordinates: " + exception.toString(), exception);
                    }
                    break;
                }
                line = input.readLine();
            }
            if (model != null) {
                // Read all other data
                line = input.readLine();
                while (input.ready() && (line != null)) {
                    if (line.indexOf("Standard orientation:") >= 0) {
                        // Found a set of coordinates
                        // Add current frame to file and create a new one.
                        sequence.addChemModel(model);
                        fireFrameRead();
                        model = sequence.getBuilder().newChemModel();
                        readCoordinates(model);
                    } else if (line.indexOf("SCF Done:") >= 0) {
                        // Found an energy
                        model.setProperty("org.openscience.cdk.io.Gaussian03Reaer:SCF Done", line.trim());
                    } else if (line.indexOf("Harmonic frequencies") >= 0) {
                        // Found a set of vibrations
//                        try {
//                            readFrequencies(model);
//                        } catch (IOException exception) {
//                            throw new CDKException("Error while reading frequencies: " + exception.toString(), exception);
//                        }
                    } else if (line.indexOf("Mulliken atomic charges") >= 0) {
                        readPartialCharges(model);
                    } else if (line.indexOf("Magnetic shielding") >= 0) {
                        // Found NMR data
//                        try {
//                            readNMRData(model, line);
//                        } catch (IOException exception) {
//                            throw new CDKException("Error while reading NMR data: " + exception.toString(), exception);
//                        }
                    } else if (line.indexOf("GINC") >= 0) {
                        // Found calculation level of theory
                        //levelOfTheory = parseLevelOfTheory(line);
                        // FIXME: is doing anything with it?
                    }
                    line = input.readLine();
                }

                // Add current frame to file
                sequence.addChemModel(model);
                fireFrameRead();
            }
        } catch (IOException exception) {
            throw new CDKException("Error while reading general structure: " + exception.toString(), exception);
        }
        return sequence;
    }

    /**
     * Reads a set of coordinates into ChemModel.
     *
     * @param model the destination ChemModel
     * @throws IOException if an I/O error occurs
     */
    private void readCoordinates(IChemModel model) throws CDKException, IOException {
        IAtomContainer container = model.getBuilder().newAtomContainer();
        String line = input.readLine();
        line = input.readLine();
        line = input.readLine();
        line = input.readLine();
        while (input.ready()) {
            line = input.readLine();
            if ((line == null) || (line.indexOf("-----") >= 0)) {
                break;
            }
            int atomicNumber = 0;
            StringReader sr = new StringReader(line);
            StreamTokenizer token = new StreamTokenizer(sr);
            token.nextToken();

            // ignore first token
            if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
                atomicNumber = (int) token.nval;
                if (atomicNumber == 0) {

                    // Skip dummy atoms. Dummy atoms must be skipped