/** {@inheritDoc} */
protected void encounterVertexAgain(V vertex, E edge) {
super.encounterVertexAgain(vertex, edge);
int i;
if (root != null) {
// For rooted detection, the path must either
// double back to the root, or to a node of a cycle
// which has already been detected.
if (vertex.equals(root)) {
i = 0;
} else if ((cycleSet != null) && cycleSet.contains(vertex)) {
i = 0;
} else {
return;
}
} else {
i = path.indexOf(vertex);
}
if (i > -1) {
if (cycleSet == null) {
// we're doing yes/no cycle detection
throw new CycleDetectedException();
} else {
for (; i < path.size(); ++i) {
cycleSet.add(path.get(i));
}
}
}
}
/** Calculate the shortest paths (not done per default) */
private void lazyCalculatePaths() {
// already we have calculated it once.
if (paths != null) {
return;
}
lazyCalculateMatrix();
Map<VertexPair<V>, GraphPath<V, E>> sps = new HashMap<VertexPair<V>, GraphPath<V, E>>();
int n = vertices.size();
nShortestPaths = 0;
for (int i = 0; i < n; i++) {
V v_i = vertices.get(i);
for (int j = 0; j < n; j++) {
// don't count this.
if (i == j) {
continue;
}
V v_j = vertices.get(j);
GraphPath<V, E> path = getShortestPathImpl(v_i, v_j);
// we got a path
if (path != null) {
sps.put(new VertexPair<V>(v_i, v_j), path);
nShortestPaths++;
}
}
}
this.paths = sps;
}
/**
* @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);
}
}
public void testNonSimplePath() {
List<Integer> vertexList = Arrays.asList(0, 1, 2, 3, 2, 3, 4);
List<DefaultEdge> edgeList = new ArrayList<>();
for (int i = 0; i < vertexList.size() - 1; i++)
edgeList.add(completeGraph.getEdge(vertexList.get(i), vertexList.get(i + 1)));
GraphPath<Integer, DefaultEdge> p1 = new GraphWalk<>(completeGraph, 0, 4, edgeList, 10);
assertEquals(0, p1.getStartVertex().intValue());
assertEquals(4, p1.getEndVertex().intValue());
assertEquals(vertexList, p1.getVertexList());
assertEquals(edgeList.size(), p1.getLength());
assertEquals(10.0, p1.getWeight());
GraphPath<Integer, DefaultEdge> p2 = new GraphWalk<>(completeGraph, vertexList, 10);
assertEquals(0, p2.getStartVertex().intValue());
assertEquals(4, p2.getEndVertex().intValue());
assertEquals(edgeList, p2.getEdgeList());
assertEquals(edgeList.size(), p2.getLength());
assertEquals(10.0, p2.getWeight());
}
/** Calculates the matrix of all shortest paths, but does not populate the paths map. */
private void lazyCalculateMatrix() {
if (d != null) {
// already done
return;
}
int n = vertices.size();
// init the backtrace matrix
backtrace = new int[n][n];
for (int i = 0; i < n; i++) {
Arrays.fill(backtrace[i], -1);
}
// initialize matrix, 0
d = new double[n][n];
for (int i = 0; i < n; i++) {
Arrays.fill(d[i], Double.POSITIVE_INFINITY);
}
// initialize matrix, 1
for (int i = 0; i < n; i++) {
d[i][i] = 0.0;
}
// initialize matrix, 2
Set<E> edges = graph.edgeSet();
for (E edge : edges) {
V v1 = graph.getEdgeSource(edge);
V v2 = graph.getEdgeTarget(edge);
int v_1 = vertices.indexOf(v1);
int v_2 = vertices.indexOf(v2);
d[v_1][v_2] = graph.getEdgeWeight(edge);
if (!(graph instanceof DirectedGraph<?, ?>)) {
d[v_2][v_1] = graph.getEdgeWeight(edge);
}
}
// run fw alg
for (int k = 0; k < n; k++) {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
double ik_kj = d[i][k] + d[k][j];
if (ik_kj < d[i][j]) {
d[i][j] = ik_kj;
backtrace[i][j] = k;
}
}
}
}
}
/** {@inheritDoc} */
protected V provideNextVertex() {
V v = super.provideNextVertex();
// backtrack
for (int i = path.size() - 1; i >= 0; --i) {
if (graph.containsEdge(path.get(i), v)) {
break;
}
path.remove(i);
}
path.add(v);
return v;
}
/**
* @return the diameter (longest of all the shortest paths) computed for the graph. If the graph
* is vertexless, return 0.0.
*/
public double getDiameter() {
lazyCalculateMatrix();
if (Double.isNaN(diameter)) {
diameter = 0.0;
int n = vertices.size();
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
if (!Double.isInfinite(d[i][j]) && d[i][j] > diameter) {
diameter = d[i][j];
}
}
}
}
return diameter;
}
private GraphPath<V, E> getShortestPathImpl(V a, V b) {
int v_a = vertices.indexOf(a);
int v_b = vertices.indexOf(b);
List<E> edges = new ArrayList<E>();
shortestPathRecur(edges, v_a, v_b);
// no path, return null
if (edges.size() < 1) {
return null;
}
double weight = 0.;
for (E e : edges) {
weight += graph.getEdgeWeight(e);
}
GraphPathImpl<V, E> path = new GraphPathImpl<V, E>(graph, a, b, edges, weight);
return path;
}
/**
* Reads the geometry and connectivity.
*
* @param filename the location of the gjf file
*/
public GJFfile(String filename) {
super(filename);
// read geometry
String name = "";
List<Atom> contents = new ArrayList<>();
SimpleWeightedGraph<Atom, DefaultWeightedEdge> connectivity =
new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
int blanks = 0;
boolean lastBlank = false;
boolean inGeometryBlock = false;
for (List<String> line : fileContents) {
// keep track of how many blanks we have seen
if (line.size() == 1 && line.get(0).length() == 0) {
if (lastBlank == false) {
blanks++;
lastBlank = true;
}
continue;
} else lastBlank = false;
// read the metadata
if (blanks == 1) {
for (String s : line) {
String[] fields = s.split("@");
if (fields.length != 3) continue;
String identifier = fields[1].toLowerCase();
String value = fields[2];
// System.out.println(s);
// System.out.println(identifier + " : " + value);
if (identifier.equals("o1")) O1Number = Integer.parseInt(value);
else if (identifier.equals("o2")) O2Number = Integer.parseInt(value);
else if (identifier.equals("n3")) N3Number = Integer.parseInt(value);
else if (identifier.equals("cl1")) Cl1Number = Integer.parseInt(value);
else if (identifier.equals("su2")) Su2Number = Integer.parseInt(value);
else if (identifier.equals("ol3")) Ol3Number = Integer.parseInt(value);
else if (identifier.equals("mem")) mem = Integer.parseInt(value);
else if (identifier.equals("nprocshared")) nprocshared = Integer.parseInt(value);
else if (identifier.equals("method")) method = value;
else if (identifier.equals("basis")) basis = value;
else System.out.println("unrecognized entry: " + s);
}
continue;
} else if (blanks != 2) continue;
// deal with the charge and multiplicity card (by ignoring it)
if (line.size() == 2 && inGeometryBlock == false) {
inGeometryBlock = true;
continue;
}
if (line.size() != 4 && inGeometryBlock == false)
throw new IllegalArgumentException(
"unexpected text in geometry block in " + filename + ":\n" + line.toString());
// create atom
// tinker atom types will be nonsense, of course
Atom newAtom =
new Atom(
line.get(0),
new Vector3D(
Double.parseDouble(line.get(1)),
Double.parseDouble(line.get(2)),
Double.parseDouble(line.get(3))),
1);
contents.add(newAtom);
connectivity.addVertex(newAtom);
}
// read connectivity
blanks = 0;
lastBlank = false;
for (List<String> line : fileContents) {
// read the fourth block of text
if (line.size() == 1 && line.get(0).length() == 0) {
if (lastBlank == false) {
blanks++;
lastBlank = true;
}
continue;
} else lastBlank = false;
// only read connectivity lines
if (blanks != 3) continue;
Atom fromAtom = contents.get(Integer.parseInt(line.get(0)) - 1);
for (int i = 1; i < line.size(); i += 2) {
int toAtomIndex = Integer.parseInt(line.get(i)) - 1;
Atom toAtom = contents.get(toAtomIndex);
double bondOrder = Double.parseDouble(line.get(i + 1));
DefaultWeightedEdge thisEdge = connectivity.addEdge(fromAtom, toAtom);
connectivity.setEdgeWeight(thisEdge, bondOrder);
}
}
// create the molecule
molecule = new Molecule(name, contents, connectivity, 0.0);
}
