/// <summary>
/// Sets up the fixture.
/// <para>This method is called before a test is executed and performs the
/// following actions:
/// <ul>
/// <item>Constructs a new FileReader.</item>
/// <item>Constructs a new TextReader.</item>
/// <item>Constructs a new GamessReader.</item>
/// </ul>
/// </para>
/// </summary>
public GamessReaderTest()
{
var ins = ResourceLoader.GetAsStream(TestFile);
this.inputReader = new StreamReader(ins);
this.gamessReaderUnderTest = new GamessReader(this.inputReader);
}
/// <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.
/// </summary>
/// <remarks>
/// <para><b>Implementation</b>:
/// Dummy atoms are ignored.</para>
/// </remarks>
/// <param name="molecule"></param>
/// <param name="coordinatesUnits">The unit in which coordinates are given.</param>
/// <exception cref="IOException">may be thrown by the "input" object.</exception>
/// <seealso cref="GamessReader.input"/>
//TODO Update method comments with appropriate information.
private IAtomContainer ReadCoordinates(IAtomContainer molecule, bool coordinatesUnits)
{
// Coordinates must all be given in angstr???ms.
double unitScaling = GamessReader.ScalesCoordinatesUnits(coordinatesUnits);
string retrievedLineFromFile;
while (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;
string atomicSymbol;
//StringReader sr = new StringReader(retrievedLineFromFile);
StreamTokenizer token = new StreamTokenizer(new StringReader(retrievedLineFromFile));
// The first token is ignored. It contains the atomic symbol and may
// be concatenated with a number.
token.NextToken();
if (token.NextToken() == StreamTokenizer.TTypeNumber)
{
atomicNumber = (int)token.NumberValue;
atomicSymbol = 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 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() == StreamTokenizer.TTypeNumber)
{
coordinates[i] = token.NumberValue * unitScaling;
}
else
{
throw new IOException("Error reading coordinates");
}
}
IAtom atom = molecule.Builder.NewAtom(atomicSymbol,
new Vector3(coordinates[0], coordinates[1], coordinates[2]));
molecule.Atoms.Add(atom);
}
return(molecule);
}