/**
* @param graph the graph to be ordered
* @param orderByDegree should the vertices be ordered by their degree. This speeds up the VF2
* algorithm.
* @param cacheEdges if true, the class creates a adjacency matrix and two arrays for incoming and
* outgoing edges for fast access.
*/
public GraphOrdering(Graph<V, E> graph, boolean orderByDegree, boolean cacheEdges) {
this.graph = graph;
this.cacheEdges = cacheEdges;
List<V> vertexSet = new ArrayList<>(graph.vertexSet());
if (orderByDegree) {
java.util.Collections.sort(vertexSet, new GeneralVertexDegreeComparator<>(graph));
}
vertexCount = vertexSet.size();
mapVertexToOrder = new HashMap<>();
mapOrderToVertex = new ArrayList<>(vertexCount);
if (cacheEdges) {
outgoingEdges = new int[vertexCount][];
incomingEdges = new int[vertexCount][];
adjMatrix = new Boolean[vertexCount][vertexCount];
}
Integer i = 0;
for (V vertex : vertexSet) {
mapVertexToOrder.put(vertex, i++);
mapOrderToVertex.add(vertex);
}
}
/**
* be careful: there's no check against an invalid vertexNumber
*
* @param vertexNumber the number identifying the vertex v
* @return v
*/
public V getVertex(int vertexNumber) {
return mapOrderToVertex.get(vertexNumber);
}
public String toString(Molecule molecule) {
// write header
String returnString =
String.format(
"%%mem=%dGB\n%%nprocshared=%d\n#p geom=connect %s/genecp empiricaldispersion=gd3bj opt\n",
mem, nprocshared, method);
returnString += "\ntitle\n\n0 1\n";
// write geometry
returnString = returnString + molecule.getGJFstring() + "\n";
// initialize some variables
Atom fromAtom = null;
Atom toAtom = null;
Integer fromAtomNumber = 0;
Integer toAtomNumber = 0;
Double bondOrder = 0.0;
DefaultWeightedEdge thisEdge = null;
// read connectivity data into parallel arrays
ArrayList<Integer> fromAtoms = new ArrayList<Integer>();
ArrayList<Integer> toAtoms = new ArrayList<Integer>();
ArrayList<Double> bondOrders = new ArrayList<Double>();
ArrayList<Boolean> visited = new ArrayList<Boolean>();
for (DefaultWeightedEdge e : molecule.connectivity.edgeSet()) {
fromAtom = molecule.connectivity.getEdgeSource(e);
fromAtomNumber = molecule.contents.indexOf(fromAtom) + 1;
toAtom = molecule.connectivity.getEdgeTarget(e);
toAtomNumber = molecule.contents.indexOf(toAtom) + 1;
bondOrder = molecule.connectivity.getEdgeWeight(e);
fromAtoms.add(fromAtomNumber);
toAtoms.add(toAtomNumber);
bondOrders.add(bondOrder);
visited.add(false);
}
// write connectivity data
for (int i = 0; i < molecule.contents.size(); i++) {
returnString = returnString + (i + 1) + " ";
for (int j = 0; j < fromAtoms.size(); j++) {
if (fromAtoms.get(j) == i + 1 && visited.get(j) == false) {
returnString =
returnString + toAtoms.get(j) + " " + String.format("%.1f ", bondOrders.get(j));
visited.set(j, true);
}
if (toAtoms.get(j) == i + 1 && visited.get(j) == false) {
returnString =
returnString + fromAtoms.get(j) + " " + String.format("%.1f ", bondOrders.get(j));
visited.set(j, true);
}
}
returnString = returnString + "\n";
}
// write footer
returnString += String.format("\n@%s\n\n", basis);
return returnString;
}