/* Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project
 *
 * 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 javax.vecmath.Point3d;

import org.openscience.cdk.PhysicalConstants;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
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.io.formats.GamessFormat;
import org.openscience.cdk.io.formats.IResourceFormat;

/**
 * A reader for GAMESS log file.
 *
 * <p><b>Expected behaviour</b>:
 * <br>The "GamessReader" object is able to read GAMESS output log file format.
 *
 * <p><b>Limitations</b>: <br>This reader was developed from a small set of
 * example log files, and therefore, is not guaranteed to properly read all
 * GAMESS output. If you have problems, please contact the author of this code,
 * not the developers of GAMESS.
 *
 * <!-- <p><b>State information</b>: <br> [] -->
 * <!-- <p><b>Dependencies</b>: <br> [all OS/Software/Hardware dependencies] -->
 *
 * <p><b>Implementation</b>
 * <br>Available feature(s):
 * <ul>
 * 	<li><b>Molecular coordinates</b>: Each set of coordinates is added to the ChemFile in the order they are found.</li>
 * </ul>
 * Unavailable feature(s):
 * <ul>
 * <!--	<li><b>GAMESS version number</b>: The version number can be retrieved.</li> -->
 * <!--	<li><b>Point group symmetry information</b>: The point group is associated with the set of molecules.</li> -->
 * <!--	<li><b>MOPAC charges</b>: The point group is associated with the set of molecules.</li> -->
 * 	<li><b>Energies</b>: They are associated with the previously read set of coordinates.</li>
 * 	<li><b>Normal coordinates of vibrations</b>: They are associated with the previously read set of coordinates.</li>
 * </ul>
 *
 * <!-- <p><b>Security:</b> -->
 *
 * <p><b>References</b>:
 * <br><a href="http://www.msg.ameslab.gov/GAMESS/GAMESS.html">GAMESS</a> is a
 * quantum chemistry program by Gordon research group atIowa State University.
 *
 * @cdk.module  extra
 * @cdk.githash
 * @cdk.keyword Gamess
 * @cdk.keyword file format
 * @cdk.keyword output
 * @cdk.keyword log file
 * @cdk.iooptions
 *
 * @author Bradley A. Smith
 *
 * <!-- @see #GamessWriter(Reader) -->
 */
//TODO Update class comments with appropriate information.
//TODO Update "see" tag with reference to GamessWriter when it will be implemented.
//TODO Update "author" tag with appropriate information.
public class GamessReader extends DefaultChemObjectReader {

    /**
     * Boolean constant used to specify that the coordinates are given in Bohr units.
     */
    public static final boolean BOHR_UNIT        = true;

    /**
     * Double constant that contains the conversion factor from Bohr unit to
     * &Aring;ngstrom unit.
     */
    //TODO Check the accuracy of this comment.
    public static final double  BOHR_TO_ANGSTROM = 0.529177249;

    /**
     * Boolean constant used to specify that the coordinates are given in &Aring;ngstrom units.
     */
    public static final boolean ANGSTROM_UNIT    = false;

    /**
     * The "BufferedReader" object used to read data from the "file system" file.
     *
     * @see	org.openscience.cdk.io.GamessReader#GamessReader(Reader)
     */
    //TODO Improve field comment.
    //TODO Answer the question : When is it opened and when is it closed?
    private BufferedReader      input;

    /**
     * Constructs a new "GamessReader" object given a "Reader" object as input.
     *
     * <p>The "Reader" object may be an instantiable object from the "Reader"
     * hierarchy.
     * <br>For more detail about the "Reader" objects that are really accepted
     * by this "GamessReader" see <code>accepts(IChemObject)</code> method
     * documentation.
     *
     * @param	inputReader		The "Reader" object given as input parameter.
     *
     * @see #accepts(Class)
     * @see	java.io.Reader
     *
     */
    public GamessReader(Reader inputReader) {
        this.input = new BufferedReader(inputReader);
    }

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

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

    /*
     * (non-Javadoc) (Javadoc is automaticly inherited from the link below)
     * @see
     * org.openscience.cdk.io.ChemObjectIO#accepts(org.openscience.cdk.ChemObject
     * )
     */
    //TODO Update comment with appropriate information to comply Constructor's documentation.

    @Override
    public IResourceFormat getFormat() {
        return GamessFormat.getInstance();
    }

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

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

    @Override
    public boolean accepts(Class<? extends IChemObject> classObject) {
        if (IChemFile.class.equals(classObject)) return true;
        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;
    }

    /*
     * (non-Javadoc) (Javadoc is automaticly inherited from the link below)
     * @see
     * org.openscience.cdk.io.ChemObjectReader#read(org.openscience.cdk.ChemObject
     * )
     */
    @Override
    public <T extends IChemObject> T read(T object) throws CDKException {
        if (object instanceof IChemFile) {
            try {
                return (T) readChemFile((IChemFile) object);
            } catch (IOException e) {
                return null;
            }
        } else {
            throw new CDKException("Only supported is reading of ChemFile objects.");
        }
    }

    /**
     * Reads data from the "file system" file through the use of the "input"
     * field, parses data and feeds the ChemFile object with the extracted data.
     *
     * @return A ChemFile containing the data parsed from input.
     *
     * @throws	IOException	may be thrown buy the <code>this.input.readLine()</code> instruction.
     *
     * @see org.openscience.cdk.io.GamessReader#input
     */
    //TODO Answer the question : Is this method's name appropriate (given the fact that it do not read a ChemFile object, but return it)?
    private IChemFile readChemFile(IChemFile file) throws IOException {
        IChemSequence sequence = file.getBuilder().newInstance(IChemSequence.class); // TODO Answer the question : Is this line needed ?
        IChemModel model = file.getBuilder().newInstance(IChemModel.class); // TODO Answer the question : Is this line needed ?
        IAtomContainerSet moleculeSet = file.getBuilder().newInstance(IAtomContainerSet.class);

        model.setMoleculeSet(moleculeSet); //TODO Answer the question : Should I do this?
        sequence.addChemModel(model); //TODO Answer the question : Should I do this?
        file.addChemSequence(sequence); //TODO Answer the question : Should I do this?

        String currentReadLine = this.input.readLine();
        while (this.input.ready() == true && (currentReadLine != null)) {

            /*
             * There are 2 types of coordinate sets: - bohr coordinates sets (if
             * statement) - angstr???m coordinates sets (else statement)
             */
            if (currentReadLine.indexOf("COORDINATES (BOHR)") >= 0) {

                /*
                 * The following line do no contain data, so it is ignored.
                 */
                this.input.readLine();
                moleculeSet.addAtomContainer(this.readCoordinates(file.getBuilder().newInstance(IAtomContainer.class),
                        GamessReader.BOHR_UNIT));
                //break; //<- stops when the first set of coordinates is found.
            } else if (currentReadLine.indexOf(" COORDINATES OF ALL ATOMS ARE (ANGS)") >= 0) {

                /*
                 * The following 2 lines do no contain data, so it are ignored.
                 */
                this.input.readLine();
                this.input.readLine();

                moleculeSet.addAtomContainer(this.readCoordinates(file.getBuilder().newInstance(IAtomContainer.class),
                        GamessReader.ANGSTROM_UNIT));
                //break; //<- stops when the first set of coordinates is found.
            }
            currentReadLine = this.input.readLine();
        }
        return file;
    }

    /**
     * Reads a set of coordinates from the "file system" file through the use of
     * the "input" field, scales coordinate to angstr???m unit, builds each atom with
     * the right associated coordinates, builds a new molecule with these atoms
     * and returns the complete molecule.
     *
     * <p><b>Implementation</b>:
     * <br>Dummy atoms are ignored.
     *
     * @param	coordinatesUnits	The unit in which coordinates are given.
     *
     * @throws	IOException	may be thrown by the "input" object.
     *
     * @see org.openscience.cdk.io.GamessReader#input
     */
    //TODO Update method comments with appropriate information.
    private IAtomContainer readCoordinates(IAtomContainer molecule, boolean coordinatesUnits) throws IOException {

        /*
         * Coordinates must all be given in angstr???ms.
         */
        double unitScaling = GamessReader.scalesCoordinatesUnits(coordinatesUnits);

        String retrievedLineFromFile;

        while (this.input.ready() == true) {
            retrievedLineFromFile = this.input.readLine();
            /*
             * A coordinate set is followed by an empty line, so when this line
             * is reached, there are no more coordinates to add to the current
             * set.
             */
            if ((retrievedLineFromFile == null) || (retrievedLineFromFile.trim().length() == 0)) {
                break;
            }

            int atomicNumber;
            String atomicSymbol;

            //StringReader sr = new StringReader(retrievedLineFromFile);
            StreamTokenizer token = new StreamTokenizer(new StringReader(retrievedLineFromFile));

            /*
             * The first token is ignored. It contains the atomic symbol and may
             * be concatenated with a number.
             */
            token.nextToken();

            if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
                atomicNumber = (int) token.nval;
                atomicSymbol = this.identifyAtomicSymbol(atomicNumber);
                /*
                 * Dummy atoms are assumed to be given with an atomic number set
                 * to zero. We will do not add them to the molecule.
                 */
                if (atomicNumber == 0) {
                    continue;
                }
            } else {
                throw new IOException("Error reading coordinates");
            }

            /*
             * Atom's coordinates are stored in an array.
             */
            double[] coordinates = new double[3];
            for (int i = 0; i < coordinates.length; i++) {
                if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
                    coordinates[i] = token.nval * unitScaling;
                } else {
                    throw new IOException("Error reading coordinates");
                }
            }
            IAtom atom = molecule.getBuilder().newInstance(IAtom.class, atomicSymbol,
                    new Point3d(coordinates[0], coordinates[1], coordinates[2]));
            molecule.addAtom(atom);
        }
        return molecule;
    }

    /**
     * Identifies the atomic symbol of an atom given its default atomic number.
     *
     * <p><b>Implementation</b>:
     * <br>This is not a definitive method. It will probably be replaced with a
     * more appropriate one. Be advised that as it is not a definitive version,
     * it only recognise atoms from Hydrogen (1) to Argon (18).
     *
     * @param	atomicNumber	The atomic number of an atom.
     *
     * @return	The Symbol corresponding to the atom or "null" is the atom was not recognised.
     */
    //TODO Update method comments with appropriate information.
    private String identifyAtomicSymbol(int atomicNumber) {
        String symbol;
        switch (atomicNumber) {
            case 1:
                symbol = "H";
                break;
            case 2:
                symbol = "He";
                break;
            case 3:
                symbol = "Li";
                break;
            case 4:
                symbol = "Be";
                break;
            case 5:
                symbol = "B";
                break;
            case 6:
                symbol = "C";
                break;
            case 7:
                symbol = "N";
                break;
            case 8:
                symbol = "O";
                break;
            case 9:
                symbol = "F";
                break;
            case 10:
                symbol = "Ne";
                break;
            case 11:
                symbol = "Na";
                break;
            case 12:
                symbol = "Mg";
                break;
            case 13:
                symbol = "Al";
                break;
            case 14:
                symbol = "Si";
                break;
            case 15:
                symbol = "P";
                break;
            case 16:
                symbol = "S";
                break;
            case 17:
                symbol = "Cl";
                break;
            case 18:
                symbol = "Ar";
                break;
            default:
                symbol = null;
                break;
        }
        return symbol;
    }

    /**
     * Scales coordinates to &Aring;ngstr&ouml;m unit if they are given in Bohr unit.
     * If coordinates are already given in &Aring;ngstr&ouml;m unit, then no modifications
     * are performed.
     *
     * @param	coordinatesUnits	<code>BOHR_UNIT</code> if coordinates are given in Bohr unit and <code>ANGSTROM_UNIT</code>
     *                              if they are given in &Aring;ngstr&ouml;m unit.
     *
     * @return	The scaling conversion factor: 1 if no scaling is needed and <code>BOHR_TO_ANGSTROM</code> if scaling has to be performed.
     *
     * @see org.openscience.cdk.PhysicalConstants#BOHR_TO_ANGSTROM
     * @see org.openscience.cdk.io.GamessReader#BOHR_UNIT
     * @see org.openscience.cdk.io.GamessReader#ANGSTROM_UNIT
     */
    //TODO Update method comments with appropriate information.
    private static double scalesCoordinatesUnits(boolean coordinatesUnits) {
        if (coordinatesUnits == GamessReader.BOHR_UNIT) {
            return PhysicalConstants.BOHR_TO_ANGSTROM;
        } else { //condition is: (coordinatesUnits == GamessReader.ANGTROM_UNIT)
            return (double) 1;
        }
    }

    /*
     * (non-Javadoc) (Javadoc is automaticly inherited from the link below)
     * @see org.openscience.cdk.io.ChemObjectIO#close()
     */
    //TODO Answer the question : What are all concerned ressources ?
    @Override
    public void close() throws IOException {
        /*
         * Closes the BufferedReader used to read the file content.
         */
        input.close();
    }
}
