/// <summary>
/// Creates a new <see cref="Residue" /> object.
/// </summary>
/// <param name="molecule">The molecule this residue belongs to.</param>
/// <param name="atom">An atom in the residue. This is needed to obtain residue properties
/// since there is no corresponding PDB file record.</param>
internal Residue(Molecule molecule, Atom atom)
{
this.molecule = molecule;
this.molecule.ShowCartoonChanged += this.MoleculeShowCartoonChanged;
this.residueName = atom.ResidueName;
this.chainIdentifier = atom.ChainIdentifier;
this.residueSequenceNumber = atom.ResidueSequenceNumber;
this.atoms = new List<Atom>();
this.atoms.Add(atom);
this.residueIdentifier = Residue.GetResidueIdentifier(this.residueName);
this.residueColor = Residue.GetResidueColor(this.residueName);
this.structureColor = this.residueIdentifier != "O" ? Colors.LightGray : Colors.Red;
this.colorScheme = ColorScheme.Structure;
this.residueStripItems = new List<ResidueStripItem>();
foreach (char character in this.residueIdentifier)
{
ResidueStripItem residueStripItem = new ResidueStripItem(character.ToString());
residueStripItem.Residue = this;
this.residueStripItems.Add(residueStripItem);
}
this.model = new Model3DGroup();
this.UpdateColorView();
}
/// <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>
/// Called when the entity is changed.
/// </summary>
protected override void OnEntityChanged()
{
if (this.Entity != null)
{
using (Stream pdbStream = this.Entity.GetStream())
{
this.molecule = new Molecule(pdbStream);
this.structureControl.Molecule = this.molecule;
this.residueControl.Molecule = this.molecule;
}
this.actionPreviewTimer.Start();
}
else
{
this.molecule = null;
this.structureControl.Molecule = null;
this.residueControl.Molecule = null;
this.actionPreviewTimer.Stop();
}
}
/// <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);
}