gaussian98reader.java

化学图形处理软件

            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
     */
    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.
     */
    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
     */
    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
     */
    public IOSetting[] getIOSettings() {
        IOSetting[] settings = new IOSetting[1];
        settings[0] = readOptimizedStructureOnly;
		return settings;
	}

}