gaussian98reader.java

化学图形处理软件

/* $Revision: 8201 $ $Author: egonw $ $Date: 2007-04-16 10:40:19 +0200 (Mon, 16 Apr 2007) $
 *
 *  Copyright (C) 2002-2003  Bradley A. Smith <[e-mail]>
 *  Copyright (C) 2003-2007  Egon Willighagen <[e-mail]>
 *  Copyright (C) 2003-2007  Christoph Steinbeck <[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 java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StreamTokenizer;
import java.io.StringReader;
import java.util.List;
import java.util.StringTokenizer;

import javax.vecmath.Point3d;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
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.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.io.formats.Gaussian98Format;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.setting.BooleanIOSetting;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;

/**
 * A reader for Gaussian98 output. Gaussian 98 is a quantum chemistry program
 * by Gaussian, Inc. (<a href="http://www.gaussian.com/">http://www.gaussian.com/</a>).
 * <p/>
 * <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/>
 * <p>This reader was developed from a small set of example output files, and
 * therefore, is not guaranteed to properly read all Gaussian98 output. If you
 * have problems, please contact the author of this code, not the developers of
 * Gaussian98.
 *
 * @author Bradley A. Smith <[e-mail]>
 * @author Egon Willighagen
 * @author Christoph Steinbeck
 * @cdk.module io
 */
public class Gaussian98Reader extends DefaultChemObjectReader {

    private BufferedReader input;
    private LoggingTool logger;
    private int atomCount = 0;
    private String lastRoute = "";

    /**
     * Customizable setting
     */
    private BooleanIOSetting readOptimizedStructureOnly;


    /**
     * Constructor for the Gaussian98Reader object
     */
    public Gaussian98Reader() {
        this(new StringReader(""));
    }

    public Gaussian98Reader(InputStream input) {
        this(new InputStreamReader(input));
    }

    public IResourceFormat getFormat() {
        return Gaussian98Format.getInstance();
    }

    /**
     * Sets the reader attribute of the Gaussian98Reader object
     *
     * @param input The new reader value
     * @throws CDKException Description of the Exception
     */
    public void setReader(Reader input) throws CDKException {
        if (input instanceof BufferedReader) {
            this.input = (BufferedReader) input;
        } else {
            this.input = new BufferedReader(input);
        }
    }

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


    /**
     * Create an Gaussian98 output reader.
     *
     * @param input source of Gaussian98 data
     */
    public Gaussian98Reader(Reader input) {
        logger = new LoggingTool(this);
        if (input instanceof BufferedReader) {
            this.input = (BufferedReader) input;
        } else {
            this.input = new BufferedReader(input);
        }
        initIOSettings();
    }

    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;
        }
        return false;
    }

    public IChemObject read(IChemObject object) throws CDKException {
        customizeJob();

        if (object instanceof IChemFile) {
            IChemFile file = (IChemFile) object;
            try {
                file = readChemFile(file);
            } catch (IOException exception) {
                throw new CDKException(
                        "Error while reading file: " + exception.toString(),
                        exception
                );
            }
            return file;
        } else {
            throw new CDKException("Reading of a " + object.getClass().getName() +
                    " is not supported.");
        }
    }

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


    /**
     * Read the Gaussian98 output.
     *
     * @return a ChemFile with the coordinates, energies, and
     *         vibrations.
     * @throws IOException  if an I/O error occurs
     * @throws CDKException Description of the Exception
     */
    private IChemFile readChemFile(IChemFile chemFile) throws CDKException, IOException {
        IChemSequence sequence = chemFile.getBuilder().newChemSequence();
        IChemModel model = null;
        String line = input.readLine();
        String levelOfTheory;
        String description;
        int modelCounter = 0;

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

                // Found a set of coordinates
                model = chemFile.getBuilder().newChemModel();
                readCoordinates(model);
                break;
            }
            line = input.readLine();
        }
        if (model != null) {

            // Read all other data
            line = input.readLine().trim();
            while (input.ready() && (line != null)) {
                if (line.indexOf("#") == 0) {
                    // Found the route section
                    // Memorizing this for the description of the chemmodel
                    lastRoute = line;
                    modelCounter = 0;

                } else if (line.indexOf("Standard orientation:") >= 0) {

                    // Found a set of coordinates
                    // Add current frame to file and create a new one.
                    if (!readOptimizedStructureOnly.isSet()) {
                        sequence.addChemModel(model);
                    } else {
                        logger.info("Skipping frame, because I was told to do");
                    }
                    fireFrameRead();
                    model = chemFile.getBuilder().newChemModel();
                    modelCounter++;
                    readCoordinates(model);
                } else if (line.indexOf("SCF Done:") >= 0) {

                    // Found an energy
                    model.setProperty(CDKConstants.REMARK, line.trim());
                } else if (line.indexOf("Harmonic frequencies") >= 0) {

                    // Found a set of vibrations
                    // readFrequencies(frame);
                } else if (line.indexOf("Total atomic charges") >= 0) {
                    readPartialCharges(model);
                } else if (line.indexOf("Magnetic shielding") >= 0) {

                    // Found NMR data
                    readNMRData(model, line);

                } else if (line.indexOf("GINC") >= 0) {

                    // Found calculation level of theory
                    levelOfTheory = parseLevelOfTheory(line);
                    logger.debug("Level of Theory for this model: " + levelOfTheory);
                    description = lastRoute + ", model no. " + modelCounter;
                    model.setProperty(CDKConstants.DESCRIPTION, description);
                } else {
                    //logger.debug("Skipping line: " + line);
                }
                line = input.readLine();
            }

            // Add last frame to file
            sequence.addChemModel(model);
            fireFrameRead();
        }
        chemFile.addChemSequence(sequence);

        return chemFile;
    }


    /**
     * Reads a set of coordinates into ChemFrame.
     *
     * @param model Description of the Parameter
     * @throws IOException  if an I/O error occurs
     * @throws CDKException Description of the Exception
     */
    private void readCoordinates(IChemModel model) throws CDKException, IOException {
        IMoleculeSet moleculeSet = model.getBuilder().newMoleculeSet();
        IMolecule molecule = model.getBuilder().newMolecule();
        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;
            StringReader sr = new StringReader(line);
            StreamTokenizer token = new StreamTokenizer(sr);
            token.nextToken();

            // ignore first token