/// <summary> Read the Gaussian98 output.
///
/// </summary>
/// <returns> a ChemFile with the coordinates, energies, and
/// vibrations.
/// </returns>
/// <throws> IOException if an I/O error occurs </throws>
/// <throws> CDKException Description of the Exception </throws>
private IChemFile readChemFile(IChemFile chemFile)
{
IChemSequence sequence = chemFile.Builder.newChemSequence();
IChemModel model = null;
System.String line = input.ReadLine();
System.String levelOfTheory;
System.String description;
int modelCounter = 0;
// Find first set of coordinates by skipping all before "Standard orientation"
while (input.Peek() != -1 && (line != null))
{
if (line.IndexOf("Standard orientation:") >= 0)
{
// Found a set of coordinates
model = chemFile.Builder.newChemModel();
readCoordinates(model);
break;
}
line = input.ReadLine();
}
if (model != null)
{
// Read all other data
line = input.ReadLine().Trim();
while (input.Peek() != -1 && (line != null))
{
if (line.IndexOf("#") == 0)
{
// Found the route section
// Memorizing this for the description of the chemmodel
lastRoute = line;
modelCounter = 0;
}
else if (line.IndexOf("Standard orientation:") >= 0)
{
// Found a set of coordinates
// Add current frame to file and create a new one.
if (!readOptimizedStructureOnly.Set)
{
sequence.addChemModel(model);
}
else
{
//logger.info("Skipping frame, because I was told to do");
}
fireFrameRead();
model = chemFile.Builder.newChemModel();
modelCounter++;
readCoordinates(model);
}
else if (line.IndexOf("SCF Done:") >= 0)
{
// Found an energy
model.setProperty(CDKConstants.REMARK, line.Trim());
}
else if (line.IndexOf("Harmonic frequencies") >= 0)
{
// Found a set of vibrations
// readFrequencies(frame);
}
else if (line.IndexOf("Total atomic charges") >= 0)
{
readPartialCharges(model);
}
else if (line.IndexOf("Magnetic shielding") >= 0)
{
// Found NMR data
readNMRData(model, line);
}
else if (line.IndexOf("GINC") >= 0)
{
// Found calculation level of theory
levelOfTheory = parseLevelOfTheory(line);
//logger.debug("Level of Theory for this model: " + levelOfTheory);
description = lastRoute + ", model no. " + modelCounter;
model.setProperty(CDKConstants.DESCRIPTION, description);
}
else
{
////logger.debug("Skipping line: " + line);
}
line = input.ReadLine();
}
// Add last frame to file
sequence.addChemModel(model);
fireFrameRead();
}
chemFile.addChemSequence(sequence);
return(chemFile);
}
private IChemSequence readChemSequence(IChemSequence sequence)
{
IChemModel model = null;
try
{
System.String line = input.ReadLine();
//String levelOfTheory = null;
// Find first set of coordinates
while (input.Peek() != -1 && (line != null))
{
if (line.IndexOf("Standard orientation:") >= 0)
{
// Found a set of coordinates
model = sequence.Builder.newChemModel();
try
{
readCoordinates(model);
}
catch (System.IO.IOException exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
throw new CDKException("Error while reading coordinates: " + exception.ToString(), exception);
}
break;
}
line = input.ReadLine();
}
if (model != null)
{
// Read all other data
line = input.ReadLine();
while (input.Peek() != -1 && (line != null))
{
if (line.IndexOf("Standard orientation:") >= 0)
{
// Found a set of coordinates
// Add current frame to file and create a new one.
sequence.addChemModel(model);
fireFrameRead();
model = sequence.Builder.newChemModel();
readCoordinates(model);
}
else if (line.IndexOf("SCF Done:") >= 0)
{
// Found an energy
model.setProperty("org.openscience.cdk.io.Gaussian03Reaer:SCF Done", line.Trim());
}
else if (line.IndexOf("Harmonic frequencies") >= 0)
{
// Found a set of vibrations
try
{
readFrequencies(model);
}
catch (System.IO.IOException exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
throw new CDKException("Error while reading frequencies: " + exception.ToString(), exception);
}
}
else if (line.IndexOf("Mulliken atomic charges") >= 0)
{
readPartialCharges(model);
}
else if (line.IndexOf("Magnetic shielding") >= 0)
{
// Found NMR data
try
{
readNMRData(model, line);
}
catch (System.IO.IOException exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
throw new CDKException("Error while reading NMR data: " + exception.ToString(), exception);
}
}
else if (line.IndexOf("GINC") >= 0)
{
// Found calculation level of theory
//levelOfTheory = parseLevelOfTheory(line);
// FIXME: is doing anything with it?
}
line = input.ReadLine();
}
// Add current frame to file
sequence.addChemModel(model);
fireFrameRead();
}
}
catch (System.IO.IOException exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
throw new CDKException("Error while reading general structure: " + exception.ToString(), exception);
}
return(sequence);
}
