/// <summary>
/// Called by the constructor to set secondary structure related properties on the residues
/// and atoms that compose each structure.
/// </summary>
private void SetStructureInfo()
{
foreach (Atom atom in this.atoms)
{
if (atom is ChainAtom)
{
atom.StructureColor = Colors.LightGray;
}
}
foreach (Residue residue in this.residues)
{
foreach (Structure structure in this.structures)
{
if (residue.ChainIdentifier == structure.ChainIdentifier &&
residue.ResidueSequenceNumber >= structure.StartResidueSequenceNumber &&
residue.ResidueSequenceNumber <= structure.EndResidueSequenceNumber)
{
if (structure is Sheet)
{
residue.IsSheet = true;
}
else if (structure is Helix)
{
residue.IsHelix = true;
}
residue.StructureColor = structure.Color;
foreach (Atom atom in residue.Atoms)
{
atom.StructureColor = structure.Color;
}
break;
}
}
}
Residue previousResidue = null;
foreach (Residue residue in this.residues)
{
CAlpha cAlpha = null;
ChainAtom carbonylOxygen = null;
foreach (Atom atom in residue.Atoms)
{
if (atom is CAlpha)
{
cAlpha = (CAlpha)atom;
}
}
if (cAlpha != null)
{
foreach (Atom atom in residue.Atoms)
{
if (atom is ChainAtom && atom.AtomName == "O")
{
carbonylOxygen = (ChainAtom)atom;
}
}
}
if (cAlpha == null || carbonylOxygen == null)
{
if (previousResidue != null)
{
previousResidue.IsStructureEnd = true;
previousResidue = null;
}
continue;
}
else
{
residue.CAlphaPosition = cAlpha.Position;
residue.CarbonylOxygenPosition = carbonylOxygen.Position;
}
if (previousResidue != null && previousResidue.Chain != residue.Chain)
{
previousResidue.IsStructureEnd = true;
previousResidue = null;
}
if (previousResidue != null)
{
previousResidue.NextResidue = residue;
residue.PreviousResidue = previousResidue;
if (previousResidue.Chain != residue.Chain ||
previousResidue.IsSheet != residue.IsSheet ||
previousResidue.IsHelix != residue.IsHelix)
{
previousResidue.IsStructureEnd = true;
residue.IsStructureStart = true;
}
}
else
{
residue.IsStructureStart = true;
}
previousResidue = residue;
}
if (previousResidue != null)
{
previousResidue.IsStructureEnd = true;
}
}
/// <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;
}
/// <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);
}