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/* $Revision: 8201 $ $Author: egonw $ $Date: 2007-04-16 10:40:19 +0200 (Mon, 16 Apr 2007) $
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* Copyright (C) 2002-2003 Bradley A. Smith <yeldar@home.com>
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* Copyright (C) 2003-2007 Egon Willighagen <egonw@users.sf.net>
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* Copyright (C) 2003-2007 Christoph Steinbeck <steinbeck@users.sf.net>
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* Contact: cdk-devel@lists.sourceforge.net
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* License as published by the Free Software Foundation; either
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* version 2.1 of the License, or (at your option) any later version.
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* This library is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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* Lesser General Public License for more details.
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* You should have received a copy of the GNU Lesser General Public
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* License along with this library; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
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package org.openscience.cdk.io;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.Reader;
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import java.io.StreamTokenizer;
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import java.io.StringReader;
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import java.util.List;
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import java.util.StringTokenizer;
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import javax.vecmath.Point3d;
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import org.openscience.cdk.CDKConstants;
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import org.openscience.cdk.config.IsotopeFactory;
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import org.openscience.cdk.exception.CDKException;
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import org.openscience.cdk.interfaces.IAtom;
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import org.openscience.cdk.interfaces.IAtomContainer;
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import org.openscience.cdk.interfaces.IChemFile;
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import org.openscience.cdk.interfaces.IChemModel;
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import org.openscience.cdk.interfaces.IChemObject;
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import org.openscience.cdk.interfaces.IChemSequence;
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import org.openscience.cdk.interfaces.IMolecule;
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import org.openscience.cdk.interfaces.IMoleculeSet;
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import org.openscience.cdk.io.formats.Gaussian98Format;
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import org.openscience.cdk.io.formats.IResourceFormat;
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import org.openscience.cdk.io.setting.BooleanIOSetting;
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import org.openscience.cdk.io.setting.IOSetting;
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import org.openscience.cdk.tools.LoggingTool;
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import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
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* A reader for Gaussian98 output. Gaussian 98 is a quantum chemistry program
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* by Gaussian, Inc. (<a href="http://www.gaussian.com/">http://www.gaussian.com/</a>).
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* <p>Molecular coordinates, energies, and normal coordinates of vibrations are
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* read. Each set of coordinates is added to the ChemFile in the order they are
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* found. Energies and vibrations are associated with the previously read set
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* <p>This reader was developed from a small set of example output files, and
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* therefore, is not guaranteed to properly read all Gaussian98 output. If you
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* have problems, please contact the author of this code, not the developers of
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* @author Bradley A. Smith <yeldar@home.com>
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* @author Egon Willighagen
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* @author Christoph Steinbeck
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public class Gaussian98Reader extends DefaultChemObjectReader {
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private BufferedReader input;
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private LoggingTool logger;
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private int atomCount = 0;
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private String lastRoute = "";
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* Customizable setting
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private BooleanIOSetting readOptimizedStructureOnly;
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* Constructor for the Gaussian98Reader object
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public Gaussian98Reader() {
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this(new StringReader(""));
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public Gaussian98Reader(InputStream input) {
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this(new InputStreamReader(input));
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public IResourceFormat getFormat() {
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return Gaussian98Format.getInstance();
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* Sets the reader attribute of the Gaussian98Reader object
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* @param input The new reader value
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* @throws CDKException Description of the Exception
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public void setReader(Reader input) throws CDKException {
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if (input instanceof BufferedReader) {
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this.input = (BufferedReader) input;
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this.input = new BufferedReader(input);
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public void setReader(InputStream input) throws CDKException {
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setReader(new InputStreamReader(input));
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* Create an Gaussian98 output reader.
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* @param input source of Gaussian98 data
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public Gaussian98Reader(Reader input) {
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logger = new LoggingTool(this);
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if (input instanceof BufferedReader) {
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this.input = (BufferedReader) input;
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this.input = new BufferedReader(input);
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public boolean accepts(Class classObject) {
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Class[] interfaces = classObject.getInterfaces();
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for (int i = 0; i < interfaces.length; i++) {
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if (IChemFile.class.equals(interfaces[i])) return true;
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public IChemObject read(IChemObject object) throws CDKException {
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if (object instanceof IChemFile) {
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IChemFile file = (IChemFile) object;
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file = readChemFile(file);
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} catch (IOException exception) {
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throw new CDKException(
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"Error while reading file: " + exception.toString(),
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throw new CDKException("Reading of a " + object.getClass().getName() +
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" is not supported.");
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public void close() throws IOException {
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* Read the Gaussian98 output.
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* @return a ChemFile with the coordinates, energies, and
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* @throws IOException if an I/O error occurs
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* @throws CDKException Description of the Exception
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private IChemFile readChemFile(IChemFile chemFile) throws CDKException, IOException {
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IChemSequence sequence = chemFile.getBuilder().newChemSequence();
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IChemModel model = null;
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String line = input.readLine();
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String levelOfTheory;
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int modelCounter = 0;
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// Find first set of coordinates by skipping all before "Standard orientation"
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while (input.ready() && (line != null)) {
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if (line.indexOf("Standard orientation:") >= 0) {
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// Found a set of coordinates
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model = chemFile.getBuilder().newChemModel();
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readCoordinates(model);
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line = input.readLine();
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// Read all other data
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line = input.readLine().trim();
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while (input.ready() && (line != null)) {
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if (line.indexOf("#") == 0) {
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// Found the route section
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// Memorizing this for the description of the chemmodel
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} else if (line.indexOf("Standard orientation:") >= 0) {
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// Found a set of coordinates
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// Add current frame to file and create a new one.
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if (!readOptimizedStructureOnly.isSet()) {
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sequence.addChemModel(model);
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logger.info("Skipping frame, because I was told to do");
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model = chemFile.getBuilder().newChemModel();
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readCoordinates(model);
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} else if (line.indexOf("SCF Done:") >= 0) {
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model.setProperty(CDKConstants.REMARK, line.trim());
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} else if (line.indexOf("Harmonic frequencies") >= 0) {
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// Found a set of vibrations
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// readFrequencies(frame);
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} else if (line.indexOf("Total atomic charges") >= 0) {
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readPartialCharges(model);
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} else if (line.indexOf("Magnetic shielding") >= 0) {
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readNMRData(model, line);
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} else if (line.indexOf("GINC") >= 0) {
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// Found calculation level of theory
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levelOfTheory = parseLevelOfTheory(line);
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logger.debug("Level of Theory for this model: " + levelOfTheory);
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description = lastRoute + ", model no. " + modelCounter;
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model.setProperty(CDKConstants.DESCRIPTION, description);
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//logger.debug("Skipping line: " + line);
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line = input.readLine();
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// Add last frame to file
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sequence.addChemModel(model);
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chemFile.addChemSequence(sequence);
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* Reads a set of coordinates into ChemFrame.
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* @param model Description of the Parameter
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* @throws IOException if an I/O error occurs
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* @throws CDKException Description of the Exception
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private void readCoordinates(IChemModel model) throws CDKException, IOException {
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IMoleculeSet moleculeSet = model.getBuilder().newMoleculeSet();
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IMolecule molecule = model.getBuilder().newMolecule();
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String line = input.readLine();
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line = input.readLine();
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line = input.readLine();
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line = input.readLine();
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while (input.ready()) {
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line = input.readLine();
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if ((line == null) || (line.indexOf("-----") >= 0)) {
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StringReader sr = new StringReader(line);
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StreamTokenizer token = new StreamTokenizer(sr);
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// ignore first token
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if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
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atomicNumber = (int) token.nval;
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if (atomicNumber == 0) {
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// Skip dummy atoms. Dummy atoms must be skipped
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// if frequencies are to be read because Gaussian
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// does not report dummy atoms in frequencies, and
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// the number of atoms is used for reading frequencies.
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throw new CDKException("Error while reading coordinates: expected integer.");
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// ignore third token
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if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
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throw new IOException("Error reading x coordinate");
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if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
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throw new IOException("Error reading y coordinate");
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if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
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throw new IOException("Error reading z coordinate");
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String symbol = "Du";
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symbol = IsotopeFactory.getInstance(model.getBuilder()).getElementSymbol(atomicNumber);
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} catch (Exception exception) {
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throw new CDKException("Could not determine element symbol!", exception);
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IAtom atom = model.getBuilder().newAtom(symbol);
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atom.setPoint3d(new Point3d(x, y, z));
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molecule.addAtom(atom);
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* this is the place where we store the atomcount to
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* be used as a counter in the nmr reading
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atomCount = molecule.getAtomCount();
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moleculeSet.addMolecule(molecule);
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model.setMoleculeSet(moleculeSet);
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* Reads partial atomic charges and add the to the given ChemModel.
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* @param model Description of the Parameter
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* @throws CDKException Description of the Exception
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* @throws IOException Description of the Exception
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private void readPartialCharges(IChemModel model) throws CDKException, IOException {
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logger.info("Reading partial atomic charges");
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IMoleculeSet moleculeSet = model.getMoleculeSet();
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IMolecule molecule = moleculeSet.getMolecule(0);
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String line = input.readLine();
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// skip first line after "Total atomic charges"
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while (input.ready()) {
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line = input.readLine();
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logger.debug("Read charge block line: " + line);
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if ((line == null) || (line.indexOf("Sum of Mulliken charges") >= 0)) {
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logger.debug("End of charge block found");
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StringReader sr = new StringReader(line);
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StreamTokenizer tokenizer = new StreamTokenizer(sr);
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if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
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int atomCounter = (int) tokenizer.nval;
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tokenizer.nextToken();
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if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
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charge = tokenizer.nval;
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logger.debug("Found charge for atom " + atomCounter +
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throw new CDKException("Error while reading charge: expected double.");
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IAtom atom = molecule.getAtom(atomCounter - 1);
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atom.setCharge(charge);
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* Reads a set of vibrations into ChemFrame.
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*@param model Description of the Parameter
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*@exception IOException if an I/O error occurs
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// private void readFrequencies(IChemModel model) throws IOException
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* FIXME: this is yet to be ported
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* line = input.readLine();
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* line = input.readLine();
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* line = input.readLine();
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* line = input.readLine();
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* line = input.readLine();
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* while ((line != null) && line.startsWith(" Frequencies --")) {
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* Vector currentVibs = new Vector();
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* StringReader vibValRead = new StringReader(line.substring(15));
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* StreamTokenizer token = new StreamTokenizer(vibValRead);
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* while (token.nextToken() != StreamTokenizer.TT_EOF) {
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* Vibration vib = new Vibration(Double.toString(token.nval));
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* currentVibs.addElement(vib);
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* line = input.readLine();
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* line = input.readLine();
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* line = input.readLine();
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* line = input.readLine();
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* line = input.readLine();
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* line = input.readLine();
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* for (int i = 0; i < frame.getAtomCount(); ++i) {
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* line = input.readLine();
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* StringReader vectorRead = new StringReader(line);
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* token = new StreamTokenizer(vectorRead);
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* / ignore first token
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* / ignore second token
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* for (int j = 0; j < currentVibs.size(); ++j) {
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* double[] v = new double[3];
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* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
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* throw new IOException("Error reading frequency");
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* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
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* throw new IOException("Error reading frequency");
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* if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
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* throw new IOException("Error reading frequency");
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* ((Vibration) currentVibs.elementAt(j)).addAtomVector(v);
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* for (int i = 0; i < currentVibs.size(); ++i) {
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* frame.addVibration((Vibration) currentVibs.elementAt(i));
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* line = input.readLine();
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* line = input.readLine();
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* line = input.readLine();
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* Reads NMR nuclear shieldings.
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private void readNMRData(IChemModel model, String labelLine) throws CDKException {
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List containers = ChemModelManipulator.getAllAtomContainers(model);
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if (containers.size() == 0) {
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// nothing to store the results into
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} // otherwise insert in the first AC
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IAtomContainer ac = (IAtomContainer)containers.get(0);
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// Determine label for properties
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if (labelLine.indexOf("Diamagnetic") >= 0) {
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label = "Diamagnetic Magnetic shielding (Isotropic)";
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} else if (labelLine.indexOf("Paramagnetic") >= 0) {
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label = "Paramagnetic Magnetic shielding (Isotropic)";
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label = "Magnetic shielding (Isotropic)";
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for (int i = 0; i < atomCount; ++i) {
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String line = input.readLine().trim();
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while (line.indexOf("Isotropic") < 0) {
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line = input.readLine().trim();
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StringTokenizer st1 = new StringTokenizer(line);
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// Find Isotropic label
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while (st1.hasMoreTokens()) {
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if (st1.nextToken().equals("Isotropic")) {
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// Find Isotropic value
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while (st1.hasMoreTokens()) {
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if (st1.nextToken().equals("=")) break;
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double shielding = Double.valueOf(st1.nextToken()).doubleValue();
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logger.info("Type of shielding: " + label);
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ac.getAtom(atomIndex).setProperty(CDKConstants.ISOTROPIC_SHIELDING, new Double(shielding));
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} catch (Exception exc) {
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logger.debug("failed to read line from gaussian98 file where I expected one.");
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* Select the theory and basis set from the first archive line.
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* @param line Description of the Parameter
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* @return Description of the Return Value
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private String parseLevelOfTheory(String line) {
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StringBuffer summary = new StringBuffer();
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summary.append(line);
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line = input.readLine().trim();
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summary.append(line);
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} while (!(line.indexOf("@") >= 0));
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catch (Exception exc) {
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logger.debug("syntax problem while parsing summary of g98 section: ");
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logger.debug("parseLoT(): " + summary.toString());
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StringTokenizer st1 = new StringTokenizer(summary.toString(), "\\");
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// Must contain at least 6 tokens
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if (st1.countTokens() < 6) {
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// Skip first four tokens
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for (int i = 0; i < 4; ++i) {
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return st1.nextToken() + "/" + st1.nextToken();
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private void initIOSettings() {
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readOptimizedStructureOnly = new BooleanIOSetting("ReadOptimizedStructureOnly", IOSetting.LOW,
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"Should I only read the optimized structure from a geometry optimization?",
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private void customizeJob() {
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fireIOSettingQuestion(readOptimizedStructureOnly);
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* Gets the iOSettings attribute of the Gaussian98Reader object
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*@return The iOSettings value
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public IOSetting[] getIOSettings() {
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IOSetting[] settings = new IOSetting[1];
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settings[0] = readOptimizedStructureOnly;
added
removed
src/org/openscience/cdk/io/Gaussian98Reader.java
