/// <summary> Reads a set of coordinates into ChemModel.
///
/// </summary>
/// <param name="model">the destination ChemModel
/// </param>
/// <throws> IOException if an I/O error occurs </throws>
private void readCoordinates(IChemModel model)
{
IAtomContainer container = model.Builder.newAtomContainer();
System.String line = input.ReadLine();
line = input.ReadLine();
line = input.ReadLine();
line = input.ReadLine();
while (input.Peek() != -1)
{
line = input.ReadLine();
if ((line == null) || (line.IndexOf("-----") >= 0))
{
break;
}
int atomicNumber = 0;
System.IO.StringReader sr = new System.IO.StringReader(line);
SupportClass.StreamTokenizerSupport token = new SupportClass.StreamTokenizerSupport(sr);
token.NextToken();
// ignore first token
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
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 System.IO.IOException("Error reading coordinates");
}
token.NextToken();
// ignore third token
double x = 0.0;
double y = 0.0;
double z = 0.0;
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
x = token.nval;
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
y = token.nval;
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
z = token.nval;
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
System.String symbol = "Du";
try
{
symbol = IsotopeFactory.getInstance(model.Builder).getElementSymbol(atomicNumber);
}
catch (System.Exception exception)
{
throw new CDKException("Could not determine element symbol!", exception);
}
IAtom atom = model.Builder.newAtom(symbol);
atom.setPoint3d(new Point3d(x, y, z));
container.addAtom(atom);
}
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
moleculeSet.addMolecule(model.Builder.newMolecule(container));
model.SetOfMolecules = moleculeSet;
}
/// <summary> Reads partial atomic charges and add the to the given ChemModel.</summary>
private void readPartialCharges(IChemModel model)
{
//logger.info("Reading partial atomic charges");
ISetOfMolecules moleculeSet = model.SetOfMolecules;
IMolecule molecule = moleculeSet.getMolecule(0);
System.String line = input.ReadLine(); // skip first line after "Total atomic charges"
while (input.Peek() != -1)
{
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;
}
System.IO.StringReader sr = new System.IO.StringReader(line);
SupportClass.StreamTokenizerSupport tokenizer = new SupportClass.StreamTokenizerSupport(sr);
if (tokenizer.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
int atomCounter = (int)tokenizer.nval;
tokenizer.NextToken(); // ignore the symbol
double charge = 0.0;
if (tokenizer.NextToken() == SupportClass.StreamTokenizerSupport.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.getAtomAt(atomCounter - 1);
atom.setCharge(charge);
}
}
}
/// <summary> Reads a set of coordinates from the "file system" file through the use of
/// the "input" field, scales coordinate to angstr???m unit, builds each atom with
/// the right associated coordinates, builds a new molecule with these atoms
/// and returns the complete molecule.
///
/// <p><b>Implementation</b>:
/// <br>Dummy atoms are ignored.
///
/// </summary>
/// <param name="coordinatesUnits The">unit in which coordinates are given.
///
/// </param>
/// <throws IOException may> be thrown by the "input" object. </throws IOException may>
/// <summary>
/// </summary>
/// <seealso cref="org.openscience.cdk.io.GamessReader.input">
/// </seealso>
//TODO Update method comments with appropriate information.
private IMolecule readCoordinates(IMolecule molecule, bool coordinatesUnits)
{
/*
* Coordinates must all be given in angstr???ms.
*/
double unitScaling = GamessReader.scalesCoordinatesUnits(coordinatesUnits);
System.String retrievedLineFromFile;
while (this.input.Peek() != -1 == true)
{
retrievedLineFromFile = this.input.ReadLine();
/*
* A coordinate set is followed by an empty line, so when this line
* is reached, there are no more coordinates to add to the current set.
*/
if ((retrievedLineFromFile == null) || (retrievedLineFromFile.Trim().Length == 0))
{
break;
}
int atomicNumber;
System.String atomicSymbol;
//StringReader sr = new StringReader(retrievedLineFromFile);
SupportClass.StreamTokenizerSupport token = new SupportClass.StreamTokenizerSupport(new System.IO.StringReader(retrievedLineFromFile));
/*
* The first token is ignored. It contains the atomic symbol and may
* be concatenated with a number.
*/
token.NextToken();
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
atomicNumber = (int)token.nval;
atomicSymbol = this.identifyAtomicSymbol(atomicNumber);
/*
* Dummy atoms are assumed to be given with an atomic number set
* to zero. We will do not add them to the molecule.
*/
if (atomicNumber == 0)
{
continue;
}
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
/*
* Atom's coordinates are stored in an array.
*/
double[] coordinates = new double[3];
for (int i = 0; i < coordinates.Length; i++)
{
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
coordinates[i] = token.nval * unitScaling;
}
else
{
throw new System.IO.IOException("Error reading coordinates");
}
}
IAtom atom = molecule.Builder.newAtom(atomicSymbol, new Point3d(coordinates[0], coordinates[1], coordinates[2]));
molecule.addAtom(atom);
}
return molecule;
}