// Create the cap of primitive
Polygon CreateCap(bool isLower)
{
Point3D[] centers = Centers;
Vector3D[] horizontalVectors = HorizontalVectors;
Vector3D[] verticalVectors = VerticalVectors;
double halfWidth = 0.5 * Width;
double halfHeight = 0.5 * Height;
// Check the data of primitives
if (!Tube.IsValid(centers, horizontalVectors, verticalVectors, halfWidth, halfHeight))
return null;
// Create the cap
int index = isLower ? 0 : centers.Length - 1;
Point3D center = centers[index];
Vector3D horizontalVector = halfWidth * horizontalVectors[index];
Vector3D verticalVector = halfHeight * verticalVectors[index];
// Calculate positions
Point3D[] positions = new Point3D[Tube.RadialSegementCount];
for (int i = 0; i < Tube.RadialSegementCount; i++)
{
double angle = i * 2 * Math.PI / Tube.RadialSegementCount;
positions[i] = center + Math.Cos(angle) * horizontalVector + Math.Sin(angle) * verticalVector;
}
// Reverse points for upper cap
if (!isLower) Array.Reverse(positions);
Polygon result = new Polygon();
result.Positions = positions;
// Set the same material
result.Material = Material;
return result;
}
void UpdateShadow()
{
if (substance == null) return;
if (style == null) return;
Thread.Sleep(300);
// Black material
DiffuseMaterial material = new DiffuseMaterial(Brushes.Black);
material.Freeze();
// Create molecules
ModelVisual3D container = new ModelVisual3D();
foreach (Data.Molecule molecule in substance.Molecules)
{
foreach (Data.Atom atom in molecule.Atoms)
{
if (style.ColorStyle.ColorScheme[atom.Element].Diffuse.A < 5) continue;
Sphere sphere = new Sphere();
sphere.Material = material;
sphere.Radius = Atom.GetAtomRadius(atom, style.GeometryStyle);
sphere.Center = atom.Position;
container.Children.Add(sphere);
}
double bondRadius = Bond.GetBondRadius(style.GeometryStyle);
foreach (Data.Bond bond in molecule.Bonds)
{
if (style.ColorStyle.UseSingleBondMaterial)
{
if (style.ColorStyle.BondMaterial.Diffuse.A < 5) continue;
}
else if (style.ColorStyle.ColorScheme[bond.Begin.Element].Diffuse.A < 5 ||
style.ColorStyle.ColorScheme[bond.End.Element].Diffuse.A < 5) continue;
Cylinder cylinder = new Cylinder(bond.Begin.Position, bond.End.Position, bondRadius);
cylinder.Material = material;
container.Children.Add(cylinder);
}
#region Build approximation of ribbon
double radius = 0.45;
foreach (Data.Chain chain in molecule.Chains)
{
for (int i = 0; i < chain.Residues.Count; i++)
{
if (chain.Residues[i].GetStructureType() == SecondaryStructureType.Helix)
if (style.GeometryStyle.HelixHeight < 0.05 || style.GeometryStyle.HelixWidth < 0.05) continue;
else radius = Residue.HelixWidth * ((style.GeometryStyle.HelixHeight + style.GeometryStyle.HelixWidth) / 2.0);
if (chain.Residues[i].GetStructureType() == SecondaryStructureType.Sheet)
if (style.GeometryStyle.SheetHeight < 0.05 || style.GeometryStyle.SheetWidth < 0.05) continue;
else radius = Residue.SheetWidth * ((style.GeometryStyle.SheetHeight + style.GeometryStyle.SheetWidth) / 2.0);
if (chain.Residues[i].GetStructureType() == SecondaryStructureType.NotDefined)
if (style.GeometryStyle.TurnHeight < 0.05 || style.GeometryStyle.TurnWidth < 0.05) continue;
else radius = Residue.TurnWidth * ((style.GeometryStyle.TurnHeight + style.GeometryStyle.TurnWidth) / 2.0);
if (chain.Residues[i].GetStructureType() == SecondaryStructureType.Helix && style.ColorStyle.HelixMaterial.Diffuse.A < 5) continue;
if (chain.Residues[i].GetStructureType() == SecondaryStructureType.Sheet && style.ColorStyle.SheetMaterial.Diffuse.A < 5) continue;
if (chain.Residues[i].GetStructureType() == SecondaryStructureType.NotDefined && style.ColorStyle.TurnMaterial.Diffuse.A < 5) continue;
Data.Atom alfaCarbon = chain.Residues[i].AlfaCarbon;
if (alfaCarbon != null)
{
Point3D begin = alfaCarbon.Position;
alfaCarbon = null;
for (int j = i + 1; j < chain.Residues.Count; j++)
{
alfaCarbon = chain.Residues[j].AlfaCarbon;
if (alfaCarbon != null) break;
}
if (alfaCarbon != null)
{
Point3D end = alfaCarbon.Position;
Cylinder cylinder = new Cylinder(begin, end, radius);
container.Children.Add(cylinder);
}
}
}
}
#endregion
}
// Get bounding box
Rect3D boundingBox = VisualTreeHelper.GetDescendantBounds(container);
if (boundingBox.IsEmpty)
{
shadowRefreshStarted = false;
return;
}
#region Render Shadow
const double blurSize = 25;
const int renderTargetWidth = 200;
int renderTargetHeight = (int)(200.0 * (boundingBox.SizeX / boundingBox.SizeY));
RenderTargetBitmap renderTargetBitmap = new RenderTargetBitmap(renderTargetWidth, renderTargetHeight, 96, 96, PixelFormats.Pbgra32);
Viewport3D shadowViewport3D = new Viewport3D();
Border border = new Border();
border.Padding = new Thickness(blurSize);
border.Child = shadowViewport3D;
// Change size of the visualizer
border.Width = renderTargetBitmap.PixelWidth;
border.Height = renderTargetBitmap.PixelHeight;
border.Measure(new Size(renderTargetBitmap.PixelWidth, renderTargetBitmap.PixelHeight));
border.Arrange(new Rect(0, 0, renderTargetBitmap.PixelWidth, renderTargetBitmap.PixelHeight));
shadowViewport3D.Children.Add(container);
// Create camera
OrthographicCamera orthographicCamera = new OrthographicCamera();
#region Accomodate camera to fit content
orthographicCamera.Position = new Point3D(boundingBox.Location.X + boundingBox.SizeX / 2.0,
boundingBox.Location.Y,
boundingBox.Location.Z + boundingBox.SizeZ / 2.0);
orthographicCamera.LookDirection = new Vector3D(0, 1, 0);
orthographicCamera.UpDirection = new Vector3D(-1, 0, 0);
orthographicCamera.Width = boundingBox.SizeZ;
#endregion
orthographicCamera.NearPlaneDistance = 0;
// Set the camera & correct lights
shadowViewport3D.Camera = orthographicCamera;
BlurEffect blurEffect = new BlurEffect();
blurEffect.Radius = blurSize;
border.Effect = blurEffect;
renderTargetBitmap.Render(border);
renderTargetBitmap.Freeze();
#endregion
// Invoke in main thread
Dispatcher.BeginInvoke((Action) delegate
{
#region Create Plane
Vector3D margin = new Vector3D(boundingBox.SizeX * 0.4, 0, boundingBox.SizeZ * 0.4);
Point3D[] points = new Point3D[]
{
boundingBox.Location + new Vector3D(-margin.X, -margin.Y, -margin.Z),
boundingBox.Location +
new Vector3D(margin.X + boundingBox.SizeX, -margin.Y, -margin.Z),
boundingBox.Location +
new Vector3D(margin.X + boundingBox.SizeX, -margin.Y,
margin.Z + boundingBox.SizeZ),
boundingBox.Location +
new Vector3D(-margin.X, -margin.Y, margin.Z + boundingBox.SizeZ)
};
Polygon shadowPlane = new Polygon();
shadowPlane.Positions = points;
shadowPlane.TextureCoordinates = new Point[] { new Point(0, 0), new Point(0, 1), new Point(1, 1), new Point(1, 0) };
#endregion
shadowBrush.ImageSource = renderTargetBitmap;
shadowBrush.Stretch = Stretch.Fill;
shadowTargetOpacity = 0.8;
shadowPlane.Material = new DiffuseMaterial(shadowBrush);
shadowContainer.Children.Clear();
shadowContainer.Children.Add(shadowPlane);
// Update shadow hash
shadowRefreshStarted = false;
}, DispatcherPriority.SystemIdle);
}
// Create the cap of sheet primitive
Polygon CreateCap(bool isLower)
{
Point3D[] centers = Centers;
Vector3D[] horizontalVectors = HorizontalVectors;
Vector3D[] verticalVectors = VerticalVectors;
double halfWidth = 0.5 * Width;
double halfHeight = 0.5 * Height;
// Check the data of premitives
if(!Sheet.IsValid(centers, horizontalVectors, verticalVectors, halfWidth, halfHeight))
return null;
// Create the cap
int index = isLower ? 0 : centers.Length - 1;
Point3D center = centers[index];
Vector3D horizontalVector = halfWidth * horizontalVectors[index];
Vector3D verticalVector = halfHeight * verticalVectors[index];
Point3D[] positions = new Point3D[4];
positions[0] = center - horizontalVector + verticalVector;
positions[1] = center - horizontalVector - verticalVector;
positions[2] = center + horizontalVector - verticalVector;
positions[3] = center + horizontalVector + verticalVector;
// Reverse points for lower cap
if (!isLower) Array.Reverse(positions);
Polygon result = new Polygon();
result.Positions = positions;
// Set the same material
result.Material = Material;
return result;
}