// returns an equivalent replica of the molecule
public virtual Molecule Clone()
{
Molecule mol = new Molecule();
for (int n = 1; n <= NumAtoms(); n++)
{
Atom a = atoms[n - 1];
int num = mol.AddAtom(a.Element, a.X, a.Y, a.Charge, a.Unpaired);
mol.SetAtomHExplicit(num, AtomHExplicit(n));
}
for (int n = 1; n <= NumBonds(); n++)
{
Bond b = bonds[n - 1];
mol.AddBond(b.From, b.To, b.Order, b.Type);
}
return mol;
}
public static Molecule ReadNative(System.IO.StreamReader in_Renamed)
{
Molecule mol = new Molecule();
//UPGRADE_NOTE: Final was removed from the declaration of 'GENERIC_ERROR '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String GENERIC_ERROR = "Invalid SketchEl file.";
try
{
System.String line = in_Renamed.ReadLine();
if (!line.StartsWith("SketchEl!"))
throw new System.IO.IOException("Not a SketchEl file.");
int p1 = line.IndexOf('('), p2 = line.IndexOf(','), p3 = line.IndexOf(')');
if (p1 == 0 || p2 == 0 || p3 == 0)
throw new System.IO.IOException(GENERIC_ERROR);
int numAtoms = System.Int32.Parse(line.Substring(p1 + 1, (p2) - (p1 + 1)).Trim());
int numBonds = System.Int32.Parse(line.Substring(p2 + 1, (p3) - (p2 + 1)).Trim());
for (int n = 0; n < numAtoms; n++)
{
line = in_Renamed.ReadLine();
// TODO: verify java's split method syntax: "[\\=\\,\\;]"
System.String[] bits = line.Split('=', ',', ';');
if (bits.Length < 5)
throw new System.IO.IOException(GENERIC_ERROR);
int num = mol.AddAtom(bits[0], System.Double.Parse(bits[1].Trim()), System.Double.Parse(bits[2].Trim()), System.Int32.Parse(bits[3].Trim()), System.Int32.Parse(bits[4].Trim()));
if (bits.Length >= 6 && bits[5].Length > 0 && bits[5][0] == 'e')
mol.SetAtomHExplicit(num, System.Int32.Parse(bits[5].Substring(1)));
}
for (int n = 0; n < numBonds; n++)
{
line = in_Renamed.ReadLine();
System.String[] bits = line.Split('-', '=', ','); // "[\\-\\=\\,]");
if (bits.Length < 4)
throw new System.IO.IOException(GENERIC_ERROR);
mol.AddBond(System.Int32.Parse(bits[0].Trim()), System.Int32.Parse(bits[1].Trim()), System.Int32.Parse(bits[2].Trim()), System.Int32.Parse(bits[3].Trim()));
}
line = in_Renamed.ReadLine();
if (String.CompareOrdinal(line, "!End") != 0)
throw new System.IO.IOException(GENERIC_ERROR);
}
catch (System.Exception)
{
throw new System.IO.IOException(GENERIC_ERROR);
}
return mol;
}