public void TestVisiting()
{
VisitedAtoms visited = new VisitedAtoms();
IAtom atom = new Atom("C");
Assert.IsFalse(visited.IsVisited(atom));
visited.Visited(atom);
Assert.IsTrue(visited.IsVisited(atom));
}
/// <summary>
/// Creates a ligand attached to a single chiral atom, where the involved
/// atoms are identified by there index in the <see cref="IAtomContainer"/>. For ligand
/// atom, <see cref="Hydrogen"/> can be passed as index, which will indicate the presence of
/// an implicit hydrogen, not explicitly present in the chemical graph of the
/// given <paramref name="container"/>.
/// </summary>
/// <param name="container"><see cref="IAtomContainer"/> for which the returned <see cref="ILigand"/>s are defined</param>
/// <param name="visitedAtoms">a list of atoms already visited in the analysis</param>
/// <param name="chiralAtom">an integer pointing to the <see cref="IAtom"/> index of the chiral atom</param>
/// <param name="ligandAtom">an integer pointing to the <see cref="IAtom"/> index of the <see cref="ILigand"/></param>
/// <returns>the created <see cref="ILigand"/></returns>
public static ILigand DefineLigand(IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom, int ligandAtom)
{
if (ligandAtom == Hydrogen)
{
return(new ImplicitHydrogenLigand(container, visitedAtoms, container.Atoms[chiralAtom]));
}
else
{
return(new Ligand(container, visitedAtoms, container.Atoms[chiralAtom], container.Atoms[ligandAtom]));
}
}
private static IReadOnlyList <ILigand> MakeLigands()
{
molecule = smiles.ParseSmiles("ClC(Br)(I)[H]");
var visitedAtoms = new VisitedAtoms();
var ligand1 = new Ligand(molecule, visitedAtoms, molecule.Atoms[1], molecule.Atoms[4]);
var ligand2 = new Ligand(molecule, visitedAtoms, molecule.Atoms[1], molecule.Atoms[3]);
var ligand3 = new Ligand(molecule, visitedAtoms, molecule.Atoms[1], molecule.Atoms[2]);
var ligand4 = new Ligand(molecule, visitedAtoms, molecule.Atoms[1], molecule.Atoms[0]);
return(new ILigand[] { ligand1, ligand2, ligand3, ligand4 });
}
/// <summary>
/// Creates a ligancy for chirality around a single chiral atom, where the involved
/// atoms are identified by there index in the <see cref="IAtomContainer"/>. For the four ligand
/// atoms, <see cref="Hydrogen"/> can be passed as index, which will indicate the presence of
/// an implicit hydrogen, not explicitly present in the chemical graph of the
/// given <paramref name="container"/>.
/// </summary>
/// <param name="container"><see cref="IAtomContainer"/> for which the returned <see cref="ILigand"/>s are defined</param>
/// <param name="chiralAtom">int pointing to the <see cref="IAtom"/> index of the chiral atom</param>
/// <param name="ligand1">int pointing to the <see cref="IAtom"/> index of the first <see cref="ILigand"/></param>
/// <param name="ligand2">int pointing to the <see cref="IAtom"/> index of the second <see cref="ILigand"/></param>
/// <param name="ligand3">int pointing to the <see cref="IAtom"/> index of the third <see cref="ILigand"/></param>
/// <param name="ligand4">int pointing to the <see cref="IAtom"/> index of the fourth <see cref="ILigand"/></param>
/// <param name="stereo"><see cref="TetrahedralStereo"/> for the chirality</param>
/// <returns>the created <see cref="LigancyFourChirality"/></returns>
public static LigancyFourChirality DefineLigancyFourChirality(IAtomContainer container, int chiralAtom, int ligand1, int ligand2, int ligand3, int ligand4, TetrahedralStereo stereo)
{
var atomIndices = new int[] { ligand1, ligand2, ligand3, ligand4 };
var visitedAtoms = new VisitedAtoms();
var ligands = new ILigand[4];
for (int i = 0; i < 4; i++)
{
ligands[i] = DefineLigand(container, visitedAtoms, chiralAtom, atomIndices[i]);
}
return(new LigancyFourChirality(container.Atoms[chiralAtom], ligands, stereo));
}
public void TestAddedVisitedAtoms()
{
VisitedAtoms visited = new VisitedAtoms();
IAtom atom = new Atom("C");
VisitedAtoms visitedToAdd = new VisitedAtoms();
visited.Visited(atom);
Assert.IsFalse(visitedToAdd.IsVisited(atom));
visitedToAdd.Visited(visited);
Assert.IsTrue(visitedToAdd.IsVisited(atom));
}
/// <summary>
/// Creates a new data model for chirality for the CIP rules based on a chirality definition
/// in the CDK data model with <see cref="ITetrahedralChirality"/>.
/// </summary>
/// <param name="container"><see cref="IAtomContainer"/> to which the chiral atom belongs.</param>
/// <param name="cdkChirality"><see cref="ITetrahedralChirality"/> object specifying the chirality.</param>
public LigancyFourChirality(IAtomContainer container, ITetrahedralChirality cdkChirality)
{
this.ChiralAtom = cdkChirality.ChiralAtom;
var ligandAtoms = cdkChirality.Ligands;
this.ligands = new List <ILigand>(ligandAtoms.Count);
var visitedAtoms = new VisitedAtoms();
foreach (var ligandAtom in ligandAtoms)
{
// ITetrahedralChirality stores a implicit hydrogen as the central atom
if (ligandAtom == ChiralAtom)
{
this.ligands.Add(new ImplicitHydrogenLigand(container, visitedAtoms, ChiralAtom));
}
else
{
this.ligands.Add(new Ligand(container, visitedAtoms, ChiralAtom, ligandAtom));
}
}
this.Stereo = cdkChirality.Stereo;
}
/// <summary>
/// Adds all atoms from the <paramref name="visitedAtoms"/> list to the current list.
/// </summary>
/// <param name="visitedAtoms">the <see cref="VisitedAtoms"/> from which all atoms are added</param>
public void Visited(VisitedAtoms visitedAtoms)
{
visitedItems.AddRange(visitedAtoms.visitedItems);
}
public void TestConstructor()
{
VisitedAtoms visited = new VisitedAtoms();
Assert.IsNotNull(visited);
}
