/// <summary>
/// Gets the fragments from a target matching a set of query fragments.
/// </summary>
/// <remarks>
/// This method returns a list of lists. Each list contains the atoms of the target <see cref="IAtomContainer"/>
/// that arise in the mapping of bonds in the target molecule to the bonds in the query fragment.
/// The query fragments should be constructed
/// using the <see cref="QueryAtomContainerCreator.CreateAnyAtomAnyBondContainer(IAtomContainer, bool)"/> method of the <see cref="QueryAtomContainerCreator"/>
/// CDK class, since we are only interested in connectivity and not actual atom or bond type information.
/// </remarks>
/// <param name="atomContainer">The target <see cref="IAtomContainer"/></param>
/// <param name="queries">An array of query fragments</param>
/// <returns>A list of lists, each list being the atoms that match the query fragments</returns>
public static List <List <int> > GetFragments(IAtomContainer atomContainer, QueryAtomContainer[] queries)
{
var universalIsomorphismTester = new UniversalIsomorphismTester();
var uniqueSubgraphs = new List <List <int> >();
foreach (var query in queries)
{
IReadOnlyList <IReadOnlyList <RMap> > subgraphMaps = null;
try
{
// we get the list of bond mappings
subgraphMaps = universalIsomorphismTester.GetSubgraphMaps(atomContainer, query).ToReadOnlyList();
}
catch (CDKException e)
{
Console.Error.WriteLine(e.StackTrace);
}
if (subgraphMaps == null)
{
continue;
}
if (!subgraphMaps.Any())
{
continue;
}
// get the atom paths in the unique set of bond maps
uniqueSubgraphs.AddRange(GetUniqueBondSubgraphs(subgraphMaps, atomContainer));
}
// lets run a check on the length of each returned fragment and delete
// any that don't match the length of out query fragments. Note that since
// sometimes a fragment might be a ring, it will have number of atoms
// equal to the number of bonds, where as a fragment with no rings
// will have number of atoms equal to the number of bonds+1. So we need to check
// fragment size against all unique query sizes - I get lazy and don't check
// unique query sizes, but the size of each query
var ret = new List <List <int> >(uniqueSubgraphs.Count);
foreach (var fragment in uniqueSubgraphs)
{
foreach (var query in queries)
{
if (fragment.Count == query.Atoms.Count)
{
ret.Add(fragment);
break;
}
}
}
return(ret);
}
/// <summary>
/// Determine the number of amino acids groups the supplied <see cref="IAtomContainer"/>.
/// </summary>
/// <returns>the number of aromatic atoms of this AtomContainer</returns>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
var results = new List <int>(substructureSet.Count);
var universalIsomorphismTester = new UniversalIsomorphismTester();
foreach (var substructure in substructureSet)
{
var maps = universalIsomorphismTester.GetSubgraphMaps(container, substructure);
results.Add(maps.Count());
}
return(new Result(results));
}
public void TestSFBug1708336()
{
var atomContainer = builder.NewAtomContainer();
atomContainer.Atoms.Add(builder.NewAtom("C"));
atomContainer.Atoms.Add(builder.NewAtom("C"));
atomContainer.Atoms.Add(builder.NewAtom("N"));
atomContainer.AddBond(atomContainer.Atoms[0], atomContainer.Atoms[1], BondOrder.Single);
atomContainer.AddBond(atomContainer.Atoms[1], atomContainer.Atoms[2], BondOrder.Single);
var query = new QueryAtomContainer();
if (!Smarts.Parse(query, "C*C"))
{
Assert.Fail(Smarts.GetLastErrorMessage());
}
var list = uiTester.GetSubgraphMaps(atomContainer, query);
Assert.IsTrue(list.Count() == 0);
}
