/// <summary>
/// Obtain the chem objects (atoms and bonds) that have 'hit' in the target molecule.
/// </summary>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Isomorphisms.Mappings_Example.cs+ToChemObjects"]/*' />
/// </example>
/// <returns>lazy iterable of chem objects</returns>
public IEnumerable <IChemObject> ToChemObjects()
{
var mapper = new AtomBondMaper(query, target);
foreach (var a in GetMapping(n => mapper.Apply(n)).Select(map => map.Values))
{
foreach (var b in a)
{
yield return(b);
}
}
yield break;
}
/// <summary>
/// Obtain the mapped substructures (atoms/bonds) of the target compound. The atoms
/// and bonds are the same as in the target molecule but there may be less of them.
/// </summary>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Isomorphisms.Mappings_Example.cs+ToSubstructures"]/*' />
/// </example>
/// <returns>lazy iterable of molecules</returns>
public IEnumerable <IAtomContainer> ToSubstructures()
{
var mapper = new AtomBondMaper(query, target);
return(GetMapping(n => mapper.Apply(n)).Select(map =>
{
var submol = target.Builder.NewAtomContainer();
foreach (var atom in query.Atoms)
{
submol.Atoms.Add((IAtom)map[atom]);
}
foreach (var bond in query.Bonds)
{
submol.Bonds.Add((IBond)map[bond]);
}
return submol;
}));
}
/// <summary>
/// Convert the permutations to an atom-atom bond-bond map.
/// </summary>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Isomorphisms.Mappings_Example.cs+ToAtomBondMap"]/*' />
/// </example>
/// <returns>iterable of atom-atom and bond-bond mappings</returns>
public IEnumerable <IReadOnlyDictionary <IChemObject, IChemObject> > ToAtomBondMaps()
{
var map = new AtomBondMaper(query, target);
return(GetMapping(n => map.Apply(n)));
}