gaussian03reader.java

化学图形处理软件

                    // 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 IOException("Error reading coordinates");
            }
            token.nextToken();

            // ignore third token
            double x = 0.0;
            double y = 0.0;
            double z = 0.0;
            if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
                x = token.nval;
            } else {
                throw new IOException("Error reading coordinates");
            }
            if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
                y = token.nval;
            } else {
                throw new IOException("Error reading coordinates");
            }
            if (token.nextToken() == StreamTokenizer.TT_NUMBER) {
                z = token.nval;
            } else {
                throw new IOException("Error reading coordinates");
            }
            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));
            container.addAtom(atom);
        }
        IMoleculeSet moleculeSet = model.getBuilder().newMoleculeSet();
        moleculeSet.addMolecule(model.getBuilder().newMolecule(container));
        model.setMoleculeSet(moleculeSet);
    }

    /**
     * Reads partial atomic charges and add the to the given ChemModel.
     */
    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 = 0.0;
                if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
                    charge = (double) 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 ChemModel.
     *
     * @param model the destination ChemModel
     * @throws IOException if an I/O error occurs
     */
//    private void readFrequencies(IChemModel model) throws IOException {
        /* This is yet to be ported. Vibrations don't exist yet in CDK.
        String 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(); // skip "Red. masses"
            line = input.readLine(); // skip "Rfc consts"
            line = input.readLine(); // skip "IR Inten"
            while (!line.startsWith(" Atom AN")) {
                // skip all lines upto and including the " Atom AN" line
                line = input.readLine(); // skip
            }
            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.
     */
//    private void readNMRData(IChemModel model, String labelLine) throws IOException {
        /* FIXME: this is yet to be ported. CDK does not have shielding stuff.
        // 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 < frame.getAtomCount(); ++i) {
            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();
            NMRShielding ns1 = new NMRShielding(label, shielding);
            ((org.openscience.jmol.Atom)frame.getAtomAt(atomIndex)).addProperty(ns1);
            ++atomIndex;
        } */
//    }

    /**
     * Select the theory and basis set from the first archive line.
     */
    /*private String parseLevelOfTheory(String line) {
        
        StringTokenizer st1 = new StringTokenizer(line, "\\");
        
        // 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();
    }*/

}