/// <summary>
/// Called by the contructor after creating the <see cref="Atom"/> objects to identify
/// covalently bonded atoms. Uses a simple distance heuristic of six angstroms.
/// </summary>
private void CreateBonds()
{
for (int i = 0; i < this.atoms.Count - 1; i++)
{
Atom atom1 = this.atoms[i];
if (atom1 is Water)
{
continue;
}
double x1 = atom1.Position.X;
double y1 = atom1.Position.Y;
double z1 = atom1.Position.Z;
for (int j = i + 1; j < this.atoms.Count; j++)
{
Atom atom2 = this.atoms[j];
if (atom2 is Water)
{
continue;
}
double distanceSquared = Math.Pow(x1 - atom2.Position.X, 2);
if (distanceSquared > 3.6)
{
continue;
}
distanceSquared += Math.Pow(y1 - atom2.Position.Y, 2);
if (distanceSquared > 3.6)
{
continue;
}
distanceSquared += Math.Pow(z1 - atom2.Position.Z, 2);
if (distanceSquared > 3.6)
{
continue;
}
double distance = Math.Sqrt(distanceSquared);
atom1.Bonds.Add(atom2, distance);
atom2.Bonds.Add(atom1, distance);
}
}
Atom.SetBFactorColors(this.atoms);
}
/// <summary>
/// Parses a PDB stream and build the constituent objects.
/// </summary>
/// <param name="pdbStream">The PDB stream.</param>
internal Molecule(Stream pdbStream)
{
this.CreateAtomsAndStructures(pdbStream);
this.CreateBackbone();
this.CreateBonds();
this.CreateResidues();
this.CreateChains();
this.CreateMoleculeTransform();
Atom.SetBFactorColors(this.atoms);
this.SetStructureInfo();
this.CreateRibbons();
foreach (Atom atom in this.atoms)
{
atom.Initialize();
}
this.ShowCartoon = true;
this.CreateModel();
}