/// <summary>
/// Adapter to current CDK <see cref="Pattern"/> that takes and iterator of an
/// int[] permutation from the query to the molecule.
/// </summary>
/// <returns>the enumerator</returns>
public IEnumerator <int[]> GetEnumerator()
{
var lstate = new DfState(this);
while (lstate.MatchNext())
{
yield return(lstate.amap);
}
yield break;
}
void Main()
{
IQueryAtomContainer query = null;
IAtomContainer mol = null;
#region
var state = new DfState(query);
state.SetMol(mol);
int count = 0;
foreach (int[] amap in state)
{
// amap is permutation of query to molecule
++count;
}
#endregion
}
/// <summary>
/// Match the pattern at the provided root.
/// </summary>
/// <param name="root">the root atom of the molecule</param>
/// <returns>mappings</returns>
/// <see cref="Mappings"/>
Mappings MatchRoot(IAtom root)
{
CheckCompatibleAPI(root);
var mol = root.Container;
if (query.Atoms.Count > 0 && ((IQueryAtom)query.Atoms[0]).Matches(root))
{
var local = new DfState(state);
local.SetRoot(root);
return(Filter(new Mappings(query, mol, local), query, mol));
}
else
{
return(new Mappings(query, mol, Array.Empty <int[]>()));
}
}
/// <inheritdoc/>
public override Mappings MatchAll(IAtomContainer mol)
{
if (mol.Atoms.Count < query.Atoms.Count)
{
return(new Mappings(query, mol, Array.Empty <int[]>()));
}
if (mol.Atoms.Count > 0)
{
CheckCompatibleAPI(mol.Atoms[0]);
}
var local = new DfState(state);
local.SetMol(mol);
var mappings = new Mappings(query, mol, local);
return(Filter(mappings, query, mol));
}
/// <summary>
/// Copy constructor, if a state has already been prepared the internals
/// can be copied and the separate instance used in a thread-safe manner.
/// </summary>
/// <param name="state">the state</param>
internal DfState(DfState state)
{
// only need shallow copy of the query bonds
this.qbonds = (IQueryBond[])state.qbonds.Clone();
this.query = state.query;
this.numBonds = state.numBonds;
this.numAtoms = state.numAtoms;
this.numMapped = state.numMapped;
this.amap = (int[])state.amap.Clone();
this.avisit = state.avisit != null ? (bool[])state.avisit.Clone() : null;
this.mol = state.mol;
// deep copy of the stack-frame
this.stack = new StackFrame[state.stack.Length];
for (int i = 0; i < stack.Length; i++)
{
this.stack[i] = new StackFrame(state.stack[i]);
}
this.sptr = state.sptr;
}
private DfPattern(IQueryAtomContainer query)
{
this.query = query;
DetermineFilters(query);
state = new DfState(query);
}