/// <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);
}
