public static IEnumerable <string> GetAllIDs(IChemModel chemModel)
{
if (chemModel.Id != null)
{
yield return(chemModel.Id);
}
var crystal = chemModel.Crystal;
if (crystal != null)
{
foreach (var e in AtomContainerManipulator.GetAllIDs(crystal))
{
yield return(e);
}
}
var moleculeSet = chemModel.MoleculeSet;
if (moleculeSet != null)
{
foreach (var e in MoleculeSetManipulator.GetAllIDs(moleculeSet))
{
yield return(e);
}
}
var reactionSet = chemModel.ReactionSet;
if (reactionSet != null)
{
foreach (var e in ReactionSetManipulator.GetAllIDs(reactionSet))
{
yield return(e);
}
}
yield break;
}
public static IEnumerable <string> GetAllIDs(IReaction reaction)
{
if (reaction.Id != null)
{
yield return(reaction.Id);
}
var reactants = reaction.Reactants;
for (int i = 0; i < reactants.Count; i++)
{
var mol = reactants[i];
foreach (var id in AtomContainerManipulator.GetAllIDs(mol))
{
yield return(id);
}
}
var products = reaction.Products;
for (int i = 0; i < products.Count; i++)
{
var mol = products[i];
foreach (var id in AtomContainerManipulator.GetAllIDs(mol))
{
yield return(id);
}
}
yield break;
}
public static IEnumerable <string> GetAllIDs <T>(IChemObjectSet <T> set) where T : IAtomContainer
{
if (set != null)
{
if (set.Id != null)
{
yield return(set.Id);
}
foreach (var atomContainer in set)
{
foreach (var id in AtomContainerManipulator.GetAllIDs(atomContainer))
{
yield return(id);
}
}
}
yield break;
}
public void TestNoDuplicateCreation()
{
var mol = new AtomContainer();
Atom atom1 = new Atom("C")
{
Id = "a1"
};
Atom atom2 = new Atom("C");
mol.Atoms.Add(atom2);
mol.Atoms.Add(atom1);
IDCreator.CreateIDs(mol);
Assert.AreEqual("a2", atom2.Id);
var ids = AtomContainerManipulator.GetAllIDs(mol);
Assert.AreEqual(3, ids.Count());
}
public void TestKeepingIDs()
{
var mol = new AtomContainer();
Atom atom = new Atom("C")
{
Id = "atom1"
};
mol.Atoms.Add(atom);
IDCreator.CreateIDs(mol);
Assert.AreEqual("atom1", atom.Id);
Assert.IsNotNull(mol.Id);
var ids = AtomContainerManipulator.GetAllIDs(mol);
Assert.AreEqual(2, ids.Count());
}
/// <summary>
/// Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2
/// scheme often used in CML.
/// </summary>
/// <seealso cref="CreateIDs(IChemObject)"/>
private static void CreateIDsForAtomContainer(IAtomContainer container, List <string> tabuList)
{
if (tabuList == null)
{
tabuList = AtomContainerManipulator.GetAllIDs(container).ToList();
}
if (null == container.Id)
{
// generate new ID and remember it
atomContainerCount = SetId(ATOMCONTAINER_PREFIX, atomContainerCount, container, tabuList);
}
// the tabu list for the container should force singularity
// within a container only!
var internalTabuList = AtomContainerManipulator.GetAllIDs(container).ToList();
if (policy == UniquePolicy.Object)
{
// start atom and bond indices within a container set always from 1
atomCount = 0;
bondCount = 0;
}
else
{
internalTabuList = tabuList;
}
foreach (var atom in container.Atoms)
{
if (null == atom.Id)
{
atomCount = SetId(ATOM_PREFIX, atomCount, atom, internalTabuList);
}
}
foreach (var bond in container.Bonds)
{
if (null == bond.Id)
{
bondCount = SetId(BOND_PREFIX, bondCount, bond, internalTabuList);
}
}
}
public void TestCreateIDs_IChemObject()
{
var mol = new AtomContainer();
Atom atom1 = new Atom("C");
Atom atom2 = new Atom("C");
mol.Atoms.Add(atom1);
mol.Atoms.Add(atom2);
Bond bond = new Bond(atom1, atom2);
mol.Bonds.Add(bond);
IDCreator.CreateIDs(mol);
Assert.AreEqual("a1", atom1.Id);
Assert.AreEqual("b1", bond.Id);
var ids = AtomContainerManipulator.GetAllIDs(mol);
Assert.AreEqual(4, ids.Count());
}
