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Gaussian98Reader.java
/* $Revision$ $Author$ $Date$
 *
 *  Copyright (C) 2002-2003  Bradley A. Smith <yeldar@home.com>
 *  Copyright (C) 2003-2007  Egon Willighagen <egonw@users.sf.net>
 *  Copyright (C) 2003-2007  Christoph Steinbeck <steinbeck@users.sf.net>
 *
 *  Contact: cdk-devel@lists.sourceforge.net
 *
 *  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.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
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 <yeldar@home.com>
 * @author Egon Willighagen
 * @author Christoph Steinbeck
 * @cdk.module io
 * @cdk.githash
 */
@TestClass("org.openscience.cdk.io.Gaussian98ReaderTest")
00078 public class Gaussian98Reader extends DefaultChemObjectReader {

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

    /**
     * Customizable setting
     */
00088     private BooleanIOSetting readOptimizedStructureOnly;


    /**
     * Constructor for the Gaussian98Reader object
     */
00094     public Gaussian98Reader() {
        this(new StringReader(""));
    }

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

    @TestMethod("testGetFormat")
00103     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
     */
    @TestMethod("testSetReader_Reader")
00114     public void setReader(Reader input) throws CDKException {
        if (input instanceof BufferedReader) {
            this.input = (BufferedReader) input;
        } else {
            this.input = new BufferedReader(input);
        }
    }

    @TestMethod("testSetReader_InputStream")
00123     public void setReader(InputStream input) throws CDKException {
        setReader(new InputStreamReader(input));
    }


    /**
     * Create an Gaussian98 output reader.
     *
     * @param input source of Gaussian98 data
     */
00133     public Gaussian98Reader(Reader input) {
        logger = new LoggingTool(this);
        if (input instanceof BufferedReader) {
            this.input = (BufferedReader) input;
        } else {
            this.input = new BufferedReader(input);
        }
        initIOSettings();
    }

    @TestMethod("testAccepts")
    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;
        }
        Class superClass = classObject.getSuperclass();
        if (superClass != null) return this.accepts(superClass);
        return false;
    }

00154     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.");
        }
    }

    @TestMethod("testClose")
00175     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
     */
00188     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
     */
00276     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
            if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
                atomicNumber = (int) token.nval;
                if (atomicNumber == 0) {

                    // Skip dummy atoms. Dummy atoms must be skipped
                    // if frequencies are to be read because Gaussian
                    // does not report dummy atoms in frequencies, and
                    // the number of atoms is used for reading frequencies.
                    continue;
                }
            } else {
                throw new CDKException("Error while reading coordinates: expected integer.");
            }
            token.nextToken();

            // ignore third token
            double x;
            double y;
            double z;
            if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
                x = token.nval;
            } else {
                throw new IOException("Error reading x coordinate");
            }
            if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
                y = token.nval;
            } else {
                throw new IOException("Error reading y coordinate");
            }
            if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
                z = token.nval;
            } else {
                throw new IOException("Error reading z coordinate");
            }
            String symbol = "Du";
            try {
                symbol = IsotopeFactory.getInstance(model.getBuilder()).getElementSymbol(atomicNumber);
            } catch (Exception exception) {
                throw new CDKException("Could not determine element symbol!", exception);
            }
            IAtom atom = model.getBuilder().newAtom(symbol);
            atom.setPoint3d(new Point3d(x, y, z));
            molecule.addAtom(atom);
        }
        /*
           *  this is the place where we store the atomcount to
           *  be used as a counter in the nmr reading
           */
        atomCount = molecule.getAtomCount();
        moleculeSet.addMolecule(molecule);
        model.setMoleculeSet(moleculeSet);
    }


    /**
     * Reads partial atomic charges and add the to the given ChemModel.
     *
     * @param model Description of the Parameter
     * @throws CDKException Description of the Exception
     * @throws IOException  Description of the Exception
     */
00355     private void readPartialCharges(IChemModel model) throws CDKException, IOException {
        logger.info("Reading partial atomic charges");
        IMoleculeSet moleculeSet = model.getMoleculeSet();
        IMolecule molecule = moleculeSet.getMolecule(0);
        String line = input.readLine();
        // skip first line after "Total atomic charges"
        while (input.ready()) {
            line = input.readLine();
            logger.debug("Read charge block line: " + line);
            if ((line == null) || (line.indexOf("Sum of Mulliken charges") >= 0)) {
                logger.debug("End of charge block found");
                break;
            }
            StringReader sr = new StringReader(line);
            StreamTokenizer tokenizer = new StreamTokenizer(sr);
            if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
                int atomCounter = (int) tokenizer.nval;

                tokenizer.nextToken();
                // ignore the symbol

                double charge;
                if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
                    charge = tokenizer.nval;
                    logger.debug("Found charge for atom " + atomCounter +
                            ": " + charge);
                } else {
                    throw new CDKException("Error while reading charge: expected double.");
                }
                IAtom atom = molecule.getAtom(atomCounter - 1);
                atom.setCharge(charge);
            }
        }
    }

    /**
     *  Reads a set of vibrations into ChemFrame.
     *
     *@param  model            Description of the Parameter
     *@exception IOException  if an I/O error occurs
     */
//    private void readFrequencies(IChemModel model) throws IOException
//    {
    /*
          *  FIXME: this is yet to be ported
          *  String line;
          *  line = input.readLine();
          *  line = input.readLine();
          *  line = input.readLine();
          *  line = input.readLine();
          *  line = input.readLine();
          *  while ((line != null) && line.startsWith(" Frequencies --")) {
          *  Vector currentVibs = new Vector();
          *  StringReader vibValRead = new StringReader(line.substring(15));
          *  StreamTokenizer token = new StreamTokenizer(vibValRead);
          *  while (token.nextToken() != StreamTokenizer.TT_EOF) {
          *  Vibration vib = new Vibration(Double.toString(token.nval));
          *  currentVibs.addElement(vib);
          *  }
          *  line = input.readLine();
          *  line = input.readLine();
          *  line = input.readLine();
          *  line = input.readLine();
          *  line = input.readLine();
          *  line = input.readLine();
          *  for (int i = 0; i < frame.getAtomCount(); ++i) {
          *  line = input.readLine();
          *  StringReader vectorRead = new StringReader(line);
          *  token = new StreamTokenizer(vectorRead);
          *  token.nextToken();
          *  / ignore first token
          *  token.nextToken();
          *  / ignore second token
          *  for (int j = 0; j < currentVibs.size(); ++j) {
          *  double[] v = new double[3];
          *  if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
          *  v[0] = token.nval;
          *  } else {
          *  throw new IOException("Error reading frequency");
          *  }
          *  if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
          *  v[1] = token.nval;
          *  } else {
          *  throw new IOException("Error reading frequency");
          *  }
          *  if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
          *  v[2] = token.nval;
          *  } else {
          *  throw new IOException("Error reading frequency");
          *  }
          *  ((Vibration) currentVibs.elementAt(j)).addAtomVector(v);
          *  }
          *  }
          *  for (int i = 0; i < currentVibs.size(); ++i) {
          *  frame.addVibration((Vibration) currentVibs.elementAt(i));
          *  }
          *  line = input.readLine();
          *  line = input.readLine();
          *  line = input.readLine();
          *  }
          */
//    }


    /**
     * Reads NMR nuclear shieldings.
     */
00462     private void readNMRData(IChemModel model, String labelLine) throws CDKException {
      List containers = ChemModelManipulator.getAllAtomContainers(model);
      if (containers.size() == 0) {
            // nothing to store the results into
            return;
      } // otherwise insert in the first AC
      
        IAtomContainer ac = (IAtomContainer)containers.get(0);
        // Determine label for properties
        String label;
        if (labelLine.indexOf("Diamagnetic") >= 0) {
            label = "Diamagnetic Magnetic shielding (Isotropic)";
        } else if (labelLine.indexOf("Paramagnetic") >= 0) {
            label = "Paramagnetic Magnetic shielding (Isotropic)";
        } else {
            label = "Magnetic shielding (Isotropic)";
        }
        int atomIndex = 0;
        for (int i = 0; i < atomCount; ++i) {
            try {
                String line = input.readLine().trim();
                while (line.indexOf("Isotropic") < 0) {
                    if (line == null) {
                        return;
                    }
                    line = input.readLine().trim();
                }
                StringTokenizer st1 = new StringTokenizer(line);

                // Find Isotropic label
                while (st1.hasMoreTokens()) {
                    if (st1.nextToken().equals("Isotropic")) {
                        break;
                    }
                }

                // Find Isotropic value
                while (st1.hasMoreTokens()) {
                    if (st1.nextToken().equals("=")) break;
                }
                double shielding = Double.valueOf(st1.nextToken()).doubleValue();
                logger.info("Type of shielding: " + label);
                ac.getAtom(atomIndex).setProperty(CDKConstants.ISOTROPIC_SHIELDING, new Double(shielding));
                ++atomIndex;
            } catch (Exception exc) {
                logger.debug("failed to read line from gaussian98 file where I expected one.");
            }
        }
    }


    /**
     * Select the theory and basis set from the first archive line.
     *
     * @param line Description of the Parameter
     * @return Description of the Return Value
     */
00519     private String parseLevelOfTheory(String line) {
        StringBuffer summary = new StringBuffer();
        summary.append(line);
        try {

            do {
                line = input.readLine().trim();
                summary.append(line);
            } while (!(line.indexOf("@") >= 0));
        }
        catch (Exception exc) {
            logger.debug("syntax problem while parsing summary of g98 section: ");
            logger.debug(exc);
        }
        logger.debug("parseLoT(): " + summary.toString());
        StringTokenizer st1 = new StringTokenizer(summary.toString(), "\\");

        // Must contain at least 6 tokens
        if (st1.countTokens() < 6) {
            return null;
        }

        // Skip first four tokens
        for (int i = 0; i < 4; ++i) {
            st1.nextToken();
        }

        return st1.nextToken() + "/" + st1.nextToken();
    }


    private void initIOSettings() {
        readOptimizedStructureOnly = new BooleanIOSetting("ReadOptimizedStructureOnly", IOSetting.LOW,
                "Should I only read the optimized structure from a geometry optimization?",
                "false");
    }

    private void customizeJob() {
        fireIOSettingQuestion(readOptimizedStructureOnly);
    }


    /**
     *  Gets the iOSettings attribute of the Gaussian98Reader object
     *
     *@return The iOSettings value
     */
00566     public IOSetting[] getIOSettings() {
        IOSetting[] settings = new IOSetting[1];
        settings[0] = readOptimizedStructureOnly;
            return settings;
      }

}


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