private static void ParseBondBlock(StreamReader reader, ref Molecule mol)
{
//One bond per line in format
// 111222tttsssxxxrrrccc first atom # second atom # bond type bond stereo
//Generally there will be spaces otherwise this f***s up
string line = string.Empty;
for (int i = 0; i < mol.NumberOfBonds; i++)
{
string[] delim = { " " };
string[] parts = reader.ReadLine().Split(delim, StringSplitOptions.RemoveEmptyEntries);
//The first two pars are atoms 1 and 2
int atom1Key, atom2Key;
bool result = int.TryParse(parts[0], out atom1Key);
if (!result)
Console.WriteLine("Could not get the first atom number");
result = int.TryParse(parts[1], out atom2Key);
if (!result)
Console.WriteLine("Could not get the second atom number");
int bondOrder;
result = int.TryParse(parts[2], out bondOrder);
if (!result)
Console.WriteLine("Could not get the bond order for "+atom1Key+"'s connection to"+atom2Key);
//Now we build the bond
try
{
Bond bondToAdd = new Bond(mol.Atoms[atom1Key], mol.Atoms[atom2Key], bondOrder);
mol.Bonds.Add(bondToAdd);
}
catch (ArgumentOutOfRangeException)
{
Console.WriteLine("The keys found were out of range 1:" + atom1Key + " 2:" + atom2Key + " atom count" +
mol.Atoms.Count);
}
}
}
public object Clone()
{
Bond bondCopy = new Bond((Node)node1.Clone(), (Node)node2.Clone(), this.bondOrder);
return bondCopy;
}
