/// <summary>
/// Private method that actually parses the input to read a <see cref="IChemFile"/> object.
/// </summary>
/// <param name="file">the file to read from</param>
/// <returns>A ChemFile containing the data parsed from input.</returns>
private IChemFile ReadChemFile(IChemFile file)
{
IChemSequence chemSequence = file.Builder.NewChemSequence();
int number_of_atoms;
try
{
string line = input.ReadLine();
while (line.StartsWithChar('#'))
{
line = input.ReadLine();
}
// while (input.Ready() && line != null) {
// Debug.WriteLine("lauf");
// parse frame by frame
string token = Strings.Tokenize(line, '\t', ' ', ',', ';')[0];
number_of_atoms = int.Parse(token, NumberFormatInfo.InvariantInfo);
string info = input.ReadLine();
IChemModel chemModel = file.Builder.NewChemModel();
var setOfMolecules = file.Builder.NewAtomContainerSet();
IAtomContainer m = file.Builder.NewAtomContainer();
m.Title = info;
string[] types = new string[number_of_atoms];
double[] d = new double[number_of_atoms];
int[] d_atom = new int[number_of_atoms]; // Distances
double[] a = new double[number_of_atoms];
int[] a_atom = new int[number_of_atoms]; // Angles
double[] da = new double[number_of_atoms];
int[] da_atom = new int[number_of_atoms]; // Diederangles
//Vector3[] pos = new Vector3[number_of_atoms]; // calculated positions
int i = 0;
while (i < number_of_atoms)
{
line = input.ReadLine();
// Debug.WriteLine("line:\""+line+"\"");
if (line == null)
{
break;
}
if (line.StartsWithChar('#'))
{
// skip comment in file
}
else
{
d[i] = 0d;
d_atom[i] = -1;
a[i] = 0d;
a_atom[i] = -1;
da[i] = 0d;
da_atom[i] = -1;
var tokens = Strings.Tokenize(line, '\t', ' ', ',', ';');
int fields = int.Parse(tokens[0], NumberFormatInfo.InvariantInfo);
if (fields < Math.Min(i * 2 + 1, 7))
{
// this is an error but cannot throw exception
}
else if (i == 0)
{
types[i] = tokens[1];
i++;
}
else if (i == 1)
{
types[i] = tokens[1];
d_atom[i] = int.Parse(tokens[2], NumberFormatInfo.InvariantInfo) - 1;
d[i] = double.Parse(tokens[3], NumberFormatInfo.InvariantInfo);
i++;
}
else if (i == 2)
{
types[i] = tokens[1];
d_atom[i] = int.Parse(tokens[2], NumberFormatInfo.InvariantInfo) - 1;
d[i] = double.Parse(tokens[3], NumberFormatInfo.InvariantInfo);
a_atom[i] = int.Parse(tokens[4], NumberFormatInfo.InvariantInfo) - 1;
a[i] = double.Parse(tokens[5], NumberFormatInfo.InvariantInfo);
i++;
}
else
{
types[i] = tokens[1];
d_atom[i] = int.Parse(tokens[2], NumberFormatInfo.InvariantInfo) - 1;
d[i] = double.Parse(tokens[3], NumberFormatInfo.InvariantInfo);
a_atom[i] = int.Parse(tokens[4], NumberFormatInfo.InvariantInfo) - 1;
a[i] = double.Parse(tokens[5], NumberFormatInfo.InvariantInfo);
da_atom[i] = int.Parse(tokens[6], NumberFormatInfo.InvariantInfo) - 1;
da[i] = double.Parse(tokens[7], NumberFormatInfo.InvariantInfo);
i++;
}
}
}
// calculate cartesian coordinates
var cartCoords = ZMatrixTools.ZMatrixToCartesian(d, d_atom, a, a_atom, da, da_atom);
for (i = 0; i < number_of_atoms; i++)
{
m.Atoms.Add(file.Builder.NewAtom(types[i], cartCoords[i]));
}
// Debug.WriteLine("molecule:"+m);
setOfMolecules.Add(m);
chemModel.MoleculeSet = setOfMolecules;
chemSequence.Add(chemModel);
line = input.ReadLine();
file.Add(chemSequence);
}
catch (IOException)
{
// should make some noise now
file = null;
}
return(file);
}
/// <summary> Private method that actually parses the input to read a ChemFile
/// object.
///
/// </summary>
/// <returns> A ChemFile containing the data parsed from input.
/// </returns>
private IChemFile readChemFile(IChemFile file)
{
IChemSequence chemSequence = file.Builder.newChemSequence();
int number_of_atoms = 0;
SupportClass.Tokenizer tokenizer;
try
{
System.String line = input.ReadLine();
while (line.StartsWith("#"))
{
line = input.ReadLine();
}
/*while (input.ready() && line != null)
* {*/
// System.out.println("lauf");
// parse frame by frame
tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
System.String token = tokenizer.NextToken();
number_of_atoms = System.Int32.Parse(token);
System.String info = input.ReadLine();
IChemModel chemModel = file.Builder.newChemModel();
ISetOfMolecules setOfMolecules = file.Builder.newSetOfMolecules();
IMolecule m = file.Builder.newMolecule();
m.setProperty(CDKConstants.TITLE, info);
System.String[] types = new System.String[number_of_atoms];
double[] d = new double[number_of_atoms]; int[] d_atom = new int[number_of_atoms]; // Distances
double[] a = new double[number_of_atoms]; int[] a_atom = new int[number_of_atoms]; // Angles
double[] da = new double[number_of_atoms]; int[] da_atom = new int[number_of_atoms]; // Diederangles
//Point3d[] pos = new Point3d[number_of_atoms]; // calculated positions
int i = 0;
while (i < number_of_atoms)
{
line = input.ReadLine();
// System.out.println("line:\""+line+"\"");
if (line == null)
{
break;
}
if (line.StartsWith("#"))
{
// skip comment in file
}
else
{
d[i] = 0d; d_atom[i] = -1;
a[i] = 0d; a_atom[i] = -1;
da[i] = 0d; da_atom[i] = -1;
tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
int fields = tokenizer.Count;
if (fields < System.Math.Min(i * 2 + 1, 7))
{
// this is an error but cannot throw exception
}
else if (i == 0)
{
types[i] = tokenizer.NextToken();
i++;
}
else if (i == 1)
{
types[i] = tokenizer.NextToken();
d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
d[i] = (System.Double.Parse(tokenizer.NextToken()));
i++;
}
else if (i == 2)
{
types[i] = tokenizer.NextToken();
d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
d[i] = (System.Double.Parse(tokenizer.NextToken()));
a_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
a[i] = (System.Double.Parse(tokenizer.NextToken()));
i++;
}
else
{
types[i] = tokenizer.NextToken();
d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
d[i] = (System.Double.Parse(tokenizer.NextToken()));
a_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
a[i] = (System.Double.Parse(tokenizer.NextToken()));
da_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
da[i] = (System.Double.Parse(tokenizer.NextToken()));
i++;
}
}
}
// calculate cartesian coordinates
Point3d[] cartCoords = ZMatrixTools.zmatrixToCartesian(d, d_atom, a, a_atom, da, da_atom);
for (i = 0; i < number_of_atoms; i++)
{
m.addAtom(file.Builder.newAtom(types[i], cartCoords[i]));
}
// System.out.println("molecule:\n"+m);
setOfMolecules.addMolecule(m);
chemModel.SetOfMolecules = setOfMolecules;
chemSequence.addChemModel(chemModel);
line = input.ReadLine();
file.addChemSequence(chemSequence);
}
catch (System.IO.IOException e)
{
// should make some noise now
file = null;
}
return(file);
}
