/// <summary> Reads a set of vibrations into ChemFrame.
///
/// </summary>
/// <param name="model"> Description of the Parameter
/// </param>
/// <exception cref="IOException"> if an I/O error occurs
/// </exception>
// 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();
* }
*/
// }
/// <summary> Reads NMR nuclear shieldings.
///
/// </summary>
/// <param name="model"> Description of the Parameter
/// </param>
/// <param name="labelLine">Description of the Parameter
/// </param>
/// <throws> CDKException Description of the Exception </throws>
private void readNMRData(IChemModel model, System.String labelLine)
{
IAtomContainer ac = ChemModelManipulator.getAllInOneContainer(model);
// Determine label for properties
System.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
{
System.String line = input.ReadLine().Trim();
while (line.IndexOf("Isotropic") < 0)
{
if (line == null)
{
return;
}
line = input.ReadLine().Trim();
}
SupportClass.Tokenizer st1 = new SupportClass.Tokenizer(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 = System.Double.Parse(st1.NextToken());
//logger.info("Type of shielding: " + label);
ac.getAtomAt(atomIndex).setProperty(CDKConstants.ISOTROPIC_SHIELDING, (System.Object)shielding);
++atomIndex;
}
catch (System.Exception exc)
{
//logger.debug("failed to read line from gaussian98 file where I expected one.");
}
}
}
private static void ProcessChemModel(IChemModel chemModel, ISettings settings, FileUsage usage,
MoleculeLoadingResults results, MoleculeProcessingProgress progress,
float sectionSz)
{
//if (ChemModelManipulator.getAllInOneContainer(chemModel).getBondCount() == 0)
//{
// return;
//}
// check for coordinates
if ((GeometryTools.has2DCoordinatesNew(ChemModelManipulator.getAllInOneContainer(chemModel)) != 0))//
{
results.Num2DCoords++;
}
// usage == FileUsage.TwoD)
//{
// throw new UserLevelException("File has no 2D coords", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), null);
//}
if ((GeometryTools.has2DCoordinatesNew(ChemModelManipulator.getAllInOneContainer(chemModel)) != 0))// &&
{
results.Num3DCoords++;
}
// usage == FileUsage.ThreeD)
//{
// throw new UserLevelException("File has no 3D coords", UserLevelException.ExceptionType.FileLoading,
// typeof(MoleculeLoader), null);
//}
ElementPTFactory elements = ElementPTFactory.Instance;
// calc item sz
int numItems = 0;
if (chemModel.SetOfMolecules != null)
{
results.NumMolecules += chemModel.SetOfMolecules.MoleculeCount;
for (int mol = 0; mol < chemModel.SetOfMolecules.MoleculeCount; mol++)
{
numItems += chemModel.SetOfMolecules.Molecules[mol].Atoms.Length;
//numItems += chemModel.SetOfMolecules.Molecules[mol].Bonds.Length;
}
}
float itemSz = sectionSz / (float)numItems;
if (chemModel.SetOfMolecules != null)
{
results.NumMolecules += chemModel.SetOfMolecules.MoleculeCount;
for (int mol = 0; mol < chemModel.SetOfMolecules.MoleculeCount; mol++)
{
IMolecule molecule = chemModel.SetOfMolecules.Molecules[mol];
results.NumAtoms += molecule.Atoms.Length;
results.NumBonds += molecule.Bonds.Length;
foreach (IAtom atom in molecule.Atoms)
{
PeriodicTableElement pe = elements.getElement(atom.Symbol);
if (pe != null)
{
atom.AtomicNumber = pe.AtomicNumber;
atom.Properties["PeriodicTableElement"] = pe;
atom.Properties["Period"] = int.Parse(pe.Period);
}
else
{
progress.Log(string.Format("Failed to find periodic element: {0}", atom.Symbol), LogItem.ItemLevel.Failure);
}
progress.UpdateProgress(itemSz);
}
progress.Log(string.Format("Processed {0} atoms", molecule.Atoms.Length), LogItem.ItemLevel.Info);
}
}
progress.Log("Processed Model", LogItem.ItemLevel.Success);
}