/**
* Recognise the cyclic carbohydrate projections.
*
* @param projections the types of projections to recognise
* @return recognised stereocenters
*/
List<IStereoElement> recognise(Set<Projection> projections) {
if (!projections.contains(Projection.Haworth) && !projections.contains(Projection.Chair))
return Collections.emptyList();
List<IStereoElement> elements = new ArrayList<IStereoElement>();
RingSearch ringSearch = new RingSearch(container, graph);
for (int[] isolated : ringSearch.isolated()) {
if (isolated.length < 5 || isolated.length > 7) continue;
int[] cycle = Arrays.copyOf(GraphUtil.cycle(graph, isolated), isolated.length);
Point2d[] points = coordinatesOfCycle(cycle, container);
Turn[] turns = turns(points);
WoundProjection projection = WoundProjection.ofTurns(turns);
if (!projections.contains(projection.projection)) continue;
// ring is not aligned correctly for haworth
if (projection.projection == Projection.Haworth && !checkHaworthAlignment(points)) continue;
final Point2d horizontalXy = horizontalOffset(points, turns, projection.projection);
// near vertical, should also flag as potentially ambiguous
if (1 - Math.abs(horizontalXy.y) < QUART_CARDINALITY_THRESHOLD) continue;
int[] above = cycle.clone();
int[] below = cycle.clone();
if (!assignSubstituents(cycle, above, below, projection, horizontalXy)) continue;
elements.addAll(newTetrahedralCenters(cycle, above, below, projection));
}
return elements;
}
/**
* Create a predicate to match components for the provided query and target. The target is
* converted to an adjacency list ({@link GraphUtil#toAdjList(IAtomContainer)}) and the query
* components extracted from the property {@link #KEY} in the query.
*
* @param query query structure
* @param target target structure
*/
public ComponentGrouping(IAtomContainer query, IAtomContainer target) {
this(query, GraphUtil.toAdjList(target));
}