/// <summary>
/// Perform a SMARTS match and check whether the query is present in the target molecule.
/// <para>This function simply
/// checks whether the query pattern matches the specified molecule. However the function will also, internally, save
/// the mapping of query atoms to the target molecule</para>
/// </summary>
/// <param name="atomContainer">The target moleculoe</param>
/// <param name="forceInitialization">If true, then the molecule is initialized (ring perception, aromaticity etc). If
/// false, the molecule is only initialized if it is different (in terms of object
/// reference) than one supplied in a previous call to this method.</param>
/// <returns>true if the pattern is found in the target molecule, false otherwise</returns>
/// <exception cref="CDKException">if there is an error in ring, aromaticity or isomorphism perception</exception>
/// <seealso cref="GetMatchingAtoms"/>
/// <seealso cref="MatchesCount"/>
/// <seealso cref="Matches(IAtomContainer)"/>
public bool Matches(IAtomContainer atomContainer, bool forceInitialization)
{
if (this.atomContainer == atomContainer)
{
if (forceInitialization)
{
InitializeMolecule();
}
}
else
{
this.atomContainer = atomContainer;
InitializeMolecule();
}
// lets see if we have a single atom query
if (query.Atoms.Count == 1)
{
// lets get the query atom
var queryAtom = (IQueryAtom)query.Atoms[0];
mappings = new List <int[]>();
for (int i = 0; i < atomContainer.Atoms.Count; i++)
{
if (queryAtom.Matches(atomContainer.Atoms[i]))
{
mappings.Add(new int[] { i });
}
}
}
else
{
mappings = Ullmann.FindSubstructure(query).MatchAll(atomContainer)
.Where(n => new SmartsStereoMatch(query, atomContainer).Apply(n))
.ToList();
}
return(mappings.Count != 0);
}
void Main()
{
IAtomContainer queryStructure = null;
IChemObjectSet <IAtomContainer> ms = null;
{
#region 1
IAtomContainer query = queryStructure;
Pattern pattern = Ullmann.FindSubstructure(query);
int hits = 0;
foreach (var m in ms)
{
if (pattern.Matches(m))
{
hits++;
}
}
#endregion
}
{
#region 2
IAtomContainer query = queryStructure;
Pattern pattern = Ullmann.FindSubstructure(query);
int hits = 0;
foreach (var m in ms)
{
int[] match = pattern.Match(m);
if (match.Length > 0)
{
hits++;
}
}
#endregion
}
}
public override Pattern Create(IAtomContainer container)
{
return(Ullmann.FindSubstructure(container));
}