/// <summary>
/// Assign MMFF Symbolic atom types. The symbolic type can be accessed with
/// <see cref="IAtomType.AtomTypeName"/>. An atom of unknown type is assigned the
/// symbolic type <c>"UNK"</c>.
/// All atoms, including hydrogens must be explicitly represented.
/// </summary>
/// <param name="mol">molecule</param>
/// <returns>all atoms had a type assigned</returns>
public virtual bool AssignAtomTypes(IAtomContainer mol)
{
// preconditions need explicit hydrogens
foreach (var atom in mol.Atoms)
{
if (atom.ImplicitHydrogenCount == null || atom.ImplicitHydrogenCount > 0)
{
throw new ArgumentException("Hydrogens must be explicit nodes, each must have a zero (non-null) impl H count.");
}
}
// conversion to faster data structures
var edgeMap = EdgeToBondMap.WithSpaceFor(mol);
var adjList = GraphUtil.ToAdjList(mol, edgeMap);
mol.SetProperty(MMFF_ADJLIST_CACHE, adjList);
mol.SetProperty(MMFF_EDGEMAP_CACHE, edgeMap);
var aromBonds = new HashSet <IBond>();
var oldArom = GetAromatics(mol);
// note: for MMFF we need to remove current aromatic flags for type
// assignment (they are restored after)
foreach (var chemObj in oldArom)
{
chemObj.IsAromatic = false;
}
var atomTypes = mmffAtomTyper.SymbolicTypes(mol, adjList, edgeMap, aromBonds);
bool hasUnkType = false;
for (int i = 0; i < mol.Atoms.Count; i++)
{
if (atomTypes[i] == null)
{
mol.Atoms[i].AtomTypeName = "UNK";
hasUnkType = true;
}
else
{
mol.Atoms[i].AtomTypeName = atomTypes[i];
}
}
// restore aromatic flags and mark the MMFF aromatic bonds
foreach (var chemObj in oldArom)
{
chemObj.IsAromatic = true;
}
foreach (var bond in aromBonds)
{
bond.SetProperty(MMFF_AROM, true);
}
return(!hasUnkType);
}
public void HydrogenCountMustBeDefined()
{
var container = CDK.Builder.NewAtomContainer();
container.Atoms.Add(new Atom("C"));
container.Atoms.Add(new Atom("H"));
container.Atoms.Add(new Atom("H"));
container.Atoms.Add(new Atom("H"));
container.Atoms.Add(new Atom("H"));
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Single);
container.AddBond(container.Atoms[0], container.Atoms[2], BondOrder.Single);
container.AddBond(container.Atoms[0], container.Atoms[3], BondOrder.Single);
container.AddBond(container.Atoms[0], container.Atoms[4], BondOrder.Single);
container.Atoms[0].ImplicitHydrogenCount = null;
Instance.SymbolicTypes(container);
}
public override string[] Assign(IAtomContainer container)
{
return(Instance.SymbolicTypes(container));
}