/// <summary>
/// Builds the 3D model for the cartoon view a the given residue.
/// </summary>
/// <param name="residue">A residue.</param>
/// <param name="initialColor">The residue's current color.</param>
internal Cartoon(Residue residue, Color initialColor)
{
this.residue = residue;
this.materialGroup = new MaterialGroup();
this.diffuseMaterial = new DiffuseMaterial(new SolidColorBrush(initialColor));
this.materialGroup.Children.Add(diffuseMaterial);
SpecularMaterial specularMaterial = new SpecularMaterial();
specularMaterial.Brush = new SolidColorBrush(Color.FromArgb(192, 255, 255, 255));
specularMaterial.SpecularPower = 50;
this.materialGroup.Children.Add(specularMaterial);
this.model = new Model3DGroup();
this.residue.Ribbon.GetResidueSpline(this.residue, out this.ribbonPoints,
out this.torsionVectors, out this.normalVectors);
if (this.residue.IsHelix)
{
this.AddTube(Cartoon.helixWidth, Cartoon.helixHeight);
if (this.residue.IsStructureStart)
this.AddTubeCap(Cartoon.helixWidth, Cartoon.helixHeight);
if (this.residue.IsStructureEnd)
this.AddTubeCap(Cartoon.helixWidth, Cartoon.helixHeight);
}
else if (this.residue.IsSheet)
{
this.AddSheet();
if (this.residue.IsStructureStart || this.residue.IsStructureEnd)
this.AddSheetCap();
}
else
{
this.AddTube(Cartoon.turnWidth, Cartoon.turnWidth);
if (this.residue.IsStructureStart)
this.AddTubeCap(Cartoon.turnWidth, Cartoon.turnWidth);
if (this.residue.IsStructureEnd)
this.AddTubeCap(Cartoon.turnWidth, Cartoon.turnWidth);
}
}
/// <summary>
/// Gets all of the values that represent the spline for a particular residue.
/// </summary>
/// <param name="residue">A residue in the corresponding secondary structure.</param>
/// <param name="residueRibbonPoints">A list control points for the spline.</param>
/// <param name="residueTorsionVectors">A list of the torsion vectors for the
/// spline.</param>
/// <param name="residueNormalVectors">A list of the normal vectors for the spline.</param>
internal void GetResidueSpline(Residue residue, out List<Point3D> residueRibbonPoints,
out List<Vector3D> residueTorsionVectors, out List<Vector3D> residueNormalVectors)
{
residueRibbonPoints = new List<Point3D>();
residueTorsionVectors = new List<Vector3D>();
residueNormalVectors = new List<Vector3D>();
int startIndex = this.residues.IndexOf(residue) * Ribbon.linearSegmentCount;
for (int i = startIndex; i <= startIndex + Ribbon.linearSegmentCount; i++)
{
residueRibbonPoints.Add(this.ribbonPoints[i]);
residueTorsionVectors.Add(this.torsionVectors[i]);
residueNormalVectors.Add(this.normalVectors[i]);
}
}
/// <summary>
/// Called by the constructor to create <see cref="Residue"/> objects and group their
/// constituent atoms.
/// </summary>
private void CreateResidues()
{
this.residues = new List<Residue>();
Residue residue = null;
foreach (Atom atom in this.atoms)
{
if (residue == null || atom.ResidueSequenceNumber != residue.ResidueSequenceNumber ||
atom.ChainIdentifier != residue.ChainIdentifier)
{
residue = new Residue(this, atom);
this.residues.Add(residue);
}
else
{
residue.Atoms.Add(atom);
}
atom.Residue = residue;
}
}
/// <summary>
/// Static method for parsing atom entries in a pdb file and instantiating the correct
/// <see cref="Atom" /> subclass.
/// </summary>
/// <param name="molecule">The molecule this atom belongs to.</param>
/// <param name="pdbLine">An atom entry from a pdb file.</param>
/// <returns>An instance of an <see cref="Atom" /> subclass.</returns>
internal static Atom CreateAtom(Molecule molecule, string pdbLine)
{
Atom atom;
string atomName = pdbLine.Substring(12, 4).Trim();
string residueName = pdbLine.Substring(17, 3).Trim();
if (Residue.IsAminoName(residueName))
{
if (atomName == "CA")
{
atom = new CAlpha();
}
else
{
atom = new ChainAtom();
}
}
else
{
if (residueName == "HOH")
{
atom = new Water();
}
else
{
atom = new HetAtom();
}
}
atom.molecule = molecule;
atom.bonds = new Dictionary <Atom, double>();
atom.atomName = pdbLine.Substring(12, 4).Trim();
atom.residueName = pdbLine.Substring(17, 3).Trim();
atom.residueSequenceNumber = Convert.ToInt32(pdbLine.Substring(22, 4));
atom.chainIdentifier = pdbLine.Substring(21, 1);
if (atom.residueName == "HOH")
{
atom.chainIdentifier = "";
}
else if (atom.chainIdentifier == " ")
{
atom.chainIdentifier = "1";
}
double x = Double.Parse(pdbLine.Substring(30, 8));
double y = Double.Parse(pdbLine.Substring(38, 8));
double z = Double.Parse(pdbLine.Substring(46, 8));
atom.position = new Point3D(x, y, z);
atom.temperatureFactor = Double.Parse(pdbLine.Substring(60, 6));
if (atom.atomName.StartsWith("C"))
{
atom.atomColor = Colors.LightGray;
}
else if (atom.atomName.StartsWith("N"))
{
atom.atomColor = Colors.Blue;
}
else if (atom.atomName.StartsWith("O"))
{
atom.atomColor = Colors.Red;
}
else if (atom.atomName.StartsWith("H"))
{
atom.atomColor = Colors.Purple;
}
else if (atom.atomName.StartsWith("S"))
{
atom.atomColor = Colors.Yellow;
}
else
{
atom.atomColor = Colors.Green;
}
atom.structureColor = atom.atomColor;
atom.colorScheme = ColorScheme.Structure;
atom.diffuseMaterial = new DiffuseMaterial(new SolidColorBrush(atom.atomColor));
atom.model = new Model3DGroup();
atom.translationTransform = new TranslateTransform3D(
atom.position.X, atom.position.Y, atom.position.Z);
atom.CreateSelectionSphere();
return(atom);
}
