public IChemModel ParseSubstance(XElement parser)
{
IChemModel model = builder.NewChemModel();
// assume the current element is PC-Compound
if (!parser.Name.Equals(Name_EL_PCSUBSTANCE))
{
return(null);
}
foreach (var elm in parser.Descendants(Name_EL_PCCOMPOUNDS))
{
var set = ParseCompoundsBlock(elm);
model.MoleculeSet = set;
}
foreach (var elm in parser.Descendants(Name_EL_PCSUBSTANCE_SID))
{
string sid = GetSID(elm);
model.SetProperty(CDKPropertyName.Title, sid);
}
return(model);
}
/// <summary>
/// Read the Gaussian98 output.
/// </summary>
/// <param name="chemFile"></param>
/// <returns>a ChemFile with the coordinates, energies, and vibrations.</returns>
private IChemFile ReadChemFile(IChemFile chemFile)
{
IChemSequence sequence = chemFile.Builder.NewChemSequence();
IChemModel model = null;
string line = input.ReadLine();
string levelOfTheory;
string description;
int modelCounter = 0;
// Find first set of coordinates by skipping all before "Standard orientation"
while (line != null)
{
if (line.Contains("Standard orientation:"))
{
// 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 (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.Contains("Standard orientation:"))
{
// Found a set of coordinates
// Add current frame to file and create a new one.
if (!readOptimizedStructureOnly.IsSet)
{
sequence.Add(model);
}
else
{
Trace.TraceInformation("Skipping frame, because I was told to do");
}
FrameRead();
model = chemFile.Builder.NewChemModel();
modelCounter++;
ReadCoordinates(model);
}
else if (line.Contains("SCF Done:"))
{
// Found an energy
model.SetProperty(CDKPropertyName.Remark, line.Trim());
}
else if (line.Contains("Harmonic frequencies"))
{
// Found a set of vibrations
// ReadFrequencies(frame);
}
else if (line.Contains("Total atomic charges"))
{
ReadPartialCharges(model);
}
else if (line.Contains("Magnetic shielding"))
{
// Found NMR data
ReadNMRData(model, line);
}
else if (line.Contains("GINC"))
{
// Found calculation level of theory
levelOfTheory = ParseLevelOfTheory(line);
Debug.WriteLine($"Level of Theory for this model: {levelOfTheory}");
description = lastRoute + ", model no. " + modelCounter;
model.SetProperty(CDKPropertyName.Description, description);
}
else
{
}
line = input.ReadLine();
}
// Add last frame to file
sequence.Add(model);
FrameRead();
}
chemFile.Add(sequence);
return(chemFile);
}
private IChemSequence ReadChemSequence(IChemSequence sequence)
{
IChemModel model = null;
try
{
string line = input.ReadLine();
// Find first set of coordinates
while (line != null)
{
if (line.Contains("Standard orientation:"))
{
// Found a set of coordinates
model = sequence.Builder.NewChemModel();
try
{
ReadCoordinates(model);
}
catch (IOException exception)
{
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 (line != null)
{
if (line.Contains("Standard orientation:"))
{
// Found a set of coordinates
// Add current frame to file and create a new one.
sequence.Add(model);
FrameRead();
model = sequence.Builder.NewChemModel();
ReadCoordinates(model);
}
else if (line.Contains("SCF Done:"))
{
// Found an energy
model.SetProperty("NCDK.IO.Gaussian03Reaer:SCF Done", line.Trim());
}
else if (line.Contains("Harmonic frequencies"))
{
// Found a set of vibrations
}
else if (line.Contains("Mulliken atomic charges"))
{
ReadPartialCharges(model);
}
else if (line.Contains("Magnetic shielding"))
{
// Found NMR data
}
else if (line.Contains("GINC"))
{
// Found calculation level of theory
// FIXME: is doing anything with it?
}
line = input.ReadLine();
}
// Add current frame to file
sequence.Add(model);
FrameRead();
}
}
catch (IOException exception)
{
throw new CDKException("Error while reading general structure: " + exception.ToString(), exception);
}
return(sequence);
}