/// <summary>
/// Generates a slightly larger transparent sphere to highlight the atom.
/// Creates a slightly larger sphere using GenerateSphere out of the backend.
/// Applies a transparent solid color brush and an emissive material to the mesh.
/// Adds the model to the modelGroup
/// </summary>
/// <param name="atom">Atom that is being highlighted</param>
private void MakeAtomHighlight(Atom atom)
{
// .8 angstrom is slightly larger than any of the atoms
MeshGeometry3D mesh = m_backend.GenerateSphere(new Point3D(atom.X, atom.Y, atom.Z), .8, 9, 9);
GeometryModel3D geomod = new GeometryModel3D();
geomod.Geometry = mesh;
SolidColorBrush solidBrush = new SolidColorBrush(Colors.Yellow);
solidBrush.Opacity = .5;
geomod.Material = new EmissiveMaterial(solidBrush);
m_myModel3DGroup.Children.Add(geomod);
}
/// <summary>
/// Creates the 3d atom model. Calls GenerateSphere out of the backend to make the mesh.
/// Applies a solid color brush and diffuse material to the mesh to texture the model.
/// Adds the model to the modelGroup
/// </summary>
/// <param name="atom">The atom that is being represented</param>
/// <param name="radius">Radius of the sphere to generate</param>
/// <param name="color">Color of the sphere to generate</param>
private void MakeAtom(Atom atom, double radius, Color color)
{
MeshGeometry3D mesh = m_backend.GenerateSphere(new Point3D(atom.X, atom.Y, atom.Z), radius, 9, 9);
GeometryModel3D geomod = new GeometryModel3D();
geomod.Geometry = mesh;
SolidColorBrush solidBrush = new SolidColorBrush(color);
geomod.Material = new DiffuseMaterial(solidBrush);
m_myModel3DGroup.Children.Add(geomod);
}
/// <summary>
/// For an alpha carbon on protein 1, it will find the nearest alpha carbon in protein 2.
/// It then creates a ResNumPair object to be added to the m_CAPair list for RMSD calculations.
/// </summary>
/// <param name="a_CAIndex">Index in the list of proteins for the alpha carbon on protein 1</param>
/// <returns>Distance between the two alpha carbons</returns>
private double Nearest(int a_CAIndex)
{
double NearDist = double.PositiveInfinity;
Atom pairedAtom = new Atom();
if (a_CAIndex < Protein1.Count)
{
double templateX = Protein1.Atoms[a_CAIndex].X;
double templateY = Protein1.Atoms[a_CAIndex].Y;
double templateZ = Protein1.Atoms[a_CAIndex].Z;
foreach (Atom atom in Protein2.Atoms)
{
if (atom.CA)
{
//distance in 3d space
double tempDist = Math.Sqrt(Math.Pow(atom.X - templateX, 2) + Math.Pow(atom.Y - templateY, 2) + Math.Pow(atom.Z - templateZ, 2));
if (tempDist < NearDist)
{
NearDist = tempDist;
pairedAtom = atom;
}
}
}
}
else
{
throw (new Exception("Distance calculation error: Template CAIndex out of range."));
}
m_CAPair.Add(new ResNumPair(Protein1.Atoms[a_CAIndex].Residue_Num, pairedAtom.Residue_Num, Protein1.Atoms[a_CAIndex].Chain, pairedAtom.Chain,NearDist));
return NearDist;
}