public Bond(Node node1, Node node2, int order)
{
this.node1 = node1;
this.node2 = node2;
this.bondOrder = order;
this.whichSide = false;
}
private static void ParseAtomBlock(StreamReader reader, ref Molecule mol)
{
//It goes xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee for each atom
//From the counts line we know how many atoms to expect
for (int i = 1; i <= mol.NumberOfAtoms; i++)
{
string line = reader.ReadLine();
//First the coords
Node atomToAdd = new Node();
double x, y, z;
bool result = double.TryParse(line.Substring(0, 10), out x);
if (!result)
Console.WriteLine("Could not parse x coords");
result = double.TryParse(line.Substring(10, 10), out y);
if (!result)
Console.WriteLine("Could not parse y coords");
result = double.TryParse(line.Substring(20,10), out z);
if (!result)
Console.WriteLine("Could not parse z coords");
if (z == 0) z = 0.0000;
Vector3 coords = new Vector3(x, y, z);
atomToAdd.Position = coords;
//Next we split the string into parts and the 3rd entry is the atomic symbol
string[] delim = { " " };
string[] parts = line.Split(delim, StringSplitOptions.RemoveEmptyEntries);
atomToAdd.Symbol = parts[3];
//The fourth is mass difference ?!?!? NOT added
int massDifference;
result = int.TryParse(parts[4], out massDifference);
if (!result)
Console.WriteLine("Could not parse mass difference");
else
atomToAdd.MassDiff = massDifference;
//The fifth is charge
int charge;
result = int.TryParse(parts[5], out charge);
if (!result)
Console.WriteLine("Could not parse atomic charge");
else
{
atomToAdd.Charge = charge;
Console.WriteLine("ATOM " + atomToAdd.Symbol + " CHARGE " + charge);
}
//The sixth is atom stereo parity which is ignored
//The seventh is hydrogen count
int hCount;
result = int.TryParse(parts[7], out hCount);
if (!result)
Console.WriteLine("Could not parse hydrogen count");
else
{
if (hCount > 0)
Console.WriteLine("hcount above 0");
Console.WriteLine("ATOM " + atomToAdd.Symbol + " HS " + hCount);
atomToAdd.RequiredHydrogens = hCount;
}
//Stereo care box is skipped
//The ninth is valence 0 = no marking default, includes number of bonds on this atom including implied
//hydrogens
int valence;
result = int.TryParse(parts[9], out valence);
if (!result)
Console.WriteLine("Could not parse valence");
else
atomToAdd.Valence = valence;
atomToAdd.ID = i;
//finally we add the atom to the list
mol.Atoms.Add(i, atomToAdd);
}
}
public Bond(Node node1, Node node2)
{
this.node1 = node1;
this.node2 = node2;
}
bool whichSide; //which side a double bond is on
#endregion Fields
#region Constructors
public Bond()
{
node1 = new Node();
node2 = new Node();
}
