/// <summary>
/// Calculates bond radius for the given style
/// </summary>
/// <param name="geometryStyle"></param>
public static double GetBondRadius(GeometryStyle geometryStyle)
{
// Here hydrogen has taken as the smallest one
switch (geometryStyle.AtomSizeStyle)
{
case AtomSizeStyle.VanderWaals:
return 1.2 * geometryStyle.AtomSize * geometryStyle.BondSize;
case AtomSizeStyle.Uniform:
return 0.35 * geometryStyle.AtomSize * geometryStyle.BondSize;
case AtomSizeStyle.Empirical:
return 0.35 * geometryStyle.AtomSize * geometryStyle.BondSize;
case AtomSizeStyle.Covalent:
return 0.38 * geometryStyle.AtomSize * geometryStyle.BondSize;
case AtomSizeStyle.Calculated:
return 0.53 * geometryStyle.AtomSize * geometryStyle.BondSize;
}
return 0.35;
}
static GeometryStyle()
{
if (Storage.DirectoryExists(GeometryStylesStorageDirectoryName))
{
string[] files = Storage.GetFileNames(GeometryStylesStorageDirectoryName + "\\*");
for (int i = 0; i < files.Length; i++)
{
geometryStyles.Add(Path.GetFileNameWithoutExtension(files[i]));
}
}
else
{
Storage.CreateDirectory(GeometryStylesStorageDirectoryName);
#region Add default geometry styles
GeometryStyle style = new GeometryStyle();
style.atomSize.Value = 1;
style.atomSizeStyle.Value = AtomSizeStyle.VanderWaals;
style.bondSize.Value = 0;
style.sheetHeight.Value = 0;
style.turnWidth.Value = 0;
style.helixWidth.Value = 0;
style.SaveAs("Space filled");
style = new GeometryStyle();
style.atomSize.Value = 0.80;
style.atomSizeStyle.Value = AtomSizeStyle.Calculated;
style.bondSize.Value = 0.50;
style.sheetHeight.Value = 0;
style.turnWidth.Value = 0;
style.helixWidth.Value = 0;
style.SaveAs("Ball-and-Stick (Calculated)");
style = new GeometryStyle();
style.atomSize.Value = 0.80;
style.atomSizeStyle.Value = AtomSizeStyle.Empirical;
style.bondSize.Value = 0.50;
style.sheetHeight.Value = 0;
style.turnWidth.Value = 0;
style.helixWidth.Value = 0;
style.SaveAs("Ball-and-Stick (Empirical)");
style = new GeometryStyle();
style.atomSize.Value = 0.5;
style.atomSizeStyle.Value = AtomSizeStyle.Uniform;
style.bondSize.Value = 1;
style.sheetHeight.Value = 0;
style.turnWidth.Value = 0;
style.helixWidth.Value = 0;
style.SaveAs("Wireframe");
style = new GeometryStyle();
style.atomSize.Value = 0;
style.atomSizeStyle.Value = AtomSizeStyle.VanderWaals;
style.bondSize.Value = 1;
style.sheetHeight.Value = 1;
style.turnWidth.Value = 1;
style.helixWidth.Value = 1;
style.SaveAs("Cartoon");
#endregion
}
}
/// <summary>
/// Calculates radius of a visual atom
/// </summary>
/// <param name="atom">Data of the atom</param>
/// <param name="geometryStyle">Geometry Style</param>
/// <returns>Radius</returns>
public static double GetAtomRadius(Data.Atom atom, GeometryStyle geometryStyle)
{
switch (geometryStyle.AtomSizeStyle)
{
case AtomSizeStyle.VanderWaals:
return atom.Element.VanderWaalsRadius * geometryStyle.AtomSize;
case AtomSizeStyle.Uniform:
return 0.35 * geometryStyle.AtomSize;
case AtomSizeStyle.Empirical:
return atom.Element.EmpiricalRadius * geometryStyle.AtomSize;
case AtomSizeStyle.Covalent:
return atom.Element.CovalentRadius * geometryStyle.AtomSize;
case AtomSizeStyle.Calculated:
return atom.Element.CalculatedRadius * geometryStyle.AtomSize;
}
return 1.0;
}
