/** Sets up all parameters with target Graph target */
public MoleculeParameters(Molecule target) {
// automatically set initial individuals size range
int vertices = target.getVerticesSize();
verticesInterval.set(Math.max(2, vertices / 2), vertices * 2);
cyclesInterval.set(0, target.getNumberOfCycles() * 2);
// insure that all possible vertex and edge types are in initial population in roughly equal
// quantities
java.util.Hashtable elements = new java.util.Hashtable();
for (VertexIterator v = target.getVertexIterator(); v.more(); v.next()) {
String s = v.vertex().toString();
if (!elements.containsKey(s)) {
elements.put(s, s);
try {
provider.add((Vertex) v.vertex().clone());
} catch (CloneNotSupportedException e) {
Error.fatal("can't clone vertex: " + e);
}
}
}
for (EdgeIterator e = target.getEdgeIterator(); e.more(); e.next()) {
String s = e.edge().toString();
if (!elements.containsKey(s)) {
elements.put(s, s);
try {
provider.add((Edge) e.edge().clone());
} catch (CloneNotSupportedException ee) {
Error.fatal("can't clone edge: " + ee);
}
}
}
setParameters(target);
}
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;
}
public static void main(String[] args) {
JFrame frame = new JFrame();
Molecule molecule = new Molecule("H");
SiteType[] type = new SiteType[Colors.COLORARRAY.length];
for (int i = 0; i < type.length; i++) {
type[i] = new SiteType(molecule, "Type " + i);
type[i].setRadius(1 + 0.5 * (i % 3));
type[i].setColor(Colors.COLORARRAY[i]);
molecule.addType(type[i]);
}
Site[] site = new Site[3 * type.length];
for (int i = 0; i < site.length; i++) {
site[i] = new Site(molecule, type[i % type.length]);
site[i].setX(30 * Math.cos(2 * Math.PI * i / site.length));
site[i].setY(30 * Math.sin(2 * Math.PI * i / site.length));
site[i].setZ(6);
site[i].setLocation(SystemGeometry.INSIDE);
molecule.addSite(site[i]);
}
Link[] link = new Link[site.length - 1];
for (int i = 0; i < link.length; i++) {
link[i] = new Link(site[i], site[i + 1]);
molecule.addLink(link[i]);
}
DrawPanel3D panel3d = new DrawPanel3D(molecule);
DrawPanel3DPanel panel = new DrawPanel3DPanel(panel3d);
Container c = frame.getContentPane();
c.add(panel);
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame.setLocationRelativeTo(null);
frame.setSize(600, 400);
frame.setVisible(true);
}
private Position checkRailPos(Position curpos, Position newPos, Molecule molecule) {
// TODO Auto-generated method stub
double a1 = curpos.getX();
double b1 = curpos.getY();
double c1 = curpos.getZ();
double a2 = newPos.getX();
double b2 = newPos.getY();
double c2 = newPos.getZ();
for (MicroTubule mt : listOfMicroTubule) {
double r = mt.getRadiusMicroTubule();
Position plusend = mt.getPlusEndCentre();
Position minusend = mt.getMinusEndCentre();
double x1 = plusend.getX();
double y1 = plusend.getY();
double z1 = plusend.getZ();
double x2 = minusend.getX();
double y2 = minusend.getY();
double z2 = minusend.getZ();
double l = x2 - x1;
double m = y2 - y1;
double n = z2 - z1;
double a =
Math.pow(n * (b2 - b1) - m * (c2 - c1), 2)
+ Math.pow(l * (c2 - c1) - n * (a2 - a1), 2)
+ Math.pow(m * (a2 - a1) - l * (b2 - b1), 2);
double b =
(n * (b2 - b1) - m * (c2 - c1)) * (n * (b1 - y1) - m * (c1 - z1))
+ (l * (c2 - c1) - n * (a2 - a1)) * (l * (c1 - z1) - n * (a1 - x1))
+ (m * (a2 - a1) - l * (b2 - b1)) * (m * (a1 - x1) - l * (b1 - y1));
double c =
Math.pow(n * (b1 - y1) - m * (c1 - z1), 2)
+ Math.pow(l * (c1 - z1) - n * (a1 - x1), 2)
+ Math.pow(m * (a1 - x1) - l * (b1 - y1), 2)
- r * r * (l * l + m * m + n * n);
double det = -1;
if ((det = b * b - a * c) >= 0) {
double t1 = (Math.sqrt(det) - b) / a;
Position pos1 = new Position(a1 + t1 * (a2 - a1), b1 + t1 * (b2 - b1), c1 + t1 * (c2 - c1));
double t2 = -(Math.sqrt(det) + b) / a;
Position pos2 = new Position(a1 + t2 * (a2 - a1), b1 + t2 * (b2 - b1), c1 + t2 * (c2 - c1));
double dist1 = Double.MAX_VALUE;
double dist2 = Double.MAX_VALUE;
if (t1 > 0
&& t1 <= 1
&& Math.sqrt(Math.pow(pos1.getDistance(plusend), 2) - r * r)
<= plusend.getDistance(minusend)
&& Math.sqrt(Math.pow(pos1.getDistance(minusend), 2) - r * r)
<= plusend.getDistance(minusend)) {
dist1 = pos1.getDistance(curpos);
}
if (t2 > 0
&& t2 <= 1
&& Math.sqrt(Math.pow(pos2.getDistance(plusend), 2) - r * r)
<= plusend.getDistance(minusend)
&& Math.sqrt(Math.pow(pos2.getDistance(minusend), 2) - r * r)
<= plusend.getDistance(minusend)) {
dist2 = pos2.getDistance(curpos);
}
if (dist1 <= dist2 && dist1 != Double.MAX_VALUE) {
molecule.setCurrentMicrotubule(mt);
return pos1;
}
if (dist2 < dist1) {
molecule.setCurrentMicrotubule(mt);
return pos2;
}
}
}
return null;
}
private void simulatePropagation(Molecule molecule, FileWriter... writer) {
String newline = "";
long time = System.nanoTime();
long elapsed = 0;
double runStep = maxSimulationTime;
// boolean reachFlag = false;
boolean onRailFlag = false;
// double distance = distSendReciever!=0?distSendReciever:;
if (maxSimulationStep > 0) {
runStep = maxSimulationStep;
}
try {
Position curpos = molecule.getPosition();
if (probDrail != 0) {
if (!onRailFlag) {
for (MicroTubule mt : listOfMicroTubule) {
Position p = getInitPointOnMicrotubule(mt, curpos);
if (p != null) {
molecule.setCurrentMicrotubule(mt);
molecule.setPosition(p);
onRailFlag = true;
break;
}
}
}
}
while ((elapsed = (maxSimulationStep <= 0) ? (System.nanoTime() - time) : (elapsed + 1))
< (long) runStep) {
curpos = molecule.getPosition();
if (generateOutputFile) {
writer[1].write(newline + curpos.getX() + delim + curpos.getY() + delim + curpos.getZ());
newline = "\n";
}
if (hasReachDestination(curpos)) {
if (maxSimulationStep <= 0) {
molecule.setReachTime(System.nanoTime() - time);
} else {
molecule.setReachTime(elapsed);
}
molecule.setReachFlag(true);
break;
}
if (probDrail != 0) {
if (onRailFlag) {
if (hasDRailed()) {
onRailFlag = false;
System.out.println("off rail");
molecule.setCurrentMicrotubule(null);
Position newPos = new Position();
newPos.setX(
curpos.getX() + molecule.getStepLengthX() * steparr[(int) (Math.random() * 3)]);
newPos.setY(
curpos.getY() + molecule.getStepLengthY() * steparr[(int) (Math.random() * 3)]);
newPos.setZ(
curpos.getZ() + molecule.getStepLengthZ() * steparr[(int) (Math.random() * 3)]);
checkBoundary(newPos);
Position nextPos = checkRailPos(curpos, newPos, molecule);
if (nextPos != null) {
// distance = curpos.getDistance(reciever);
molecule.setPosition(nextPos);
onRailFlag = true;
System.out.println("On Rail");
} else {
molecule.setPosition(newPos);
}
} else {
Position plusend = molecule.getCurrentMicrotubule().getPlusEndCentre();
Position minusend = molecule.getCurrentMicrotubule().getMinusEndCentre();
Position newPos = new Position();
Position perp = new Position();
double x2 = plusend.getX();
double y2 = plusend.getY();
double z2 = plusend.getZ();
double x1 = minusend.getX();
double y1 = minusend.getY();
double z1 = minusend.getZ();
double d = curpos.getX();
double e = curpos.getY();
double f = curpos.getZ();
double t =
((x2 - d) * (x2 - x1) + (y2 - e) * (y2 - y1) + (z2 - f) * (z2 - z1))
/ ((x2 - x1) * (x2 - x1) + (y2 - y1) * (y2 - y1) + (z2 - z1) * (z2 - z1));
perp.setX(d + (x2 - x1) * t);
perp.setY(e + (y2 - y1) * t);
perp.setZ(f + (z2 - z1) * t);
double distance = perp.getDistance(curpos);
curpos.setX(
(velRail * perp.getX() + (distance - velRail) * curpos.getX()) / distance);
curpos.setY(
(velRail * perp.getY() + (distance - velRail) * curpos.getY()) / distance);
curpos.setZ(
(velRail * perp.getZ() + (distance - velRail) * curpos.getZ()) / distance);
// System.out.println(curpos.getX()+","+curpos.getY()+","+curpos.getZ());
// molecule.setPosition(curpos);
}
} else {
Position newPos = new Position();
newPos.setX(
curpos.getX() + molecule.getStepLengthX() * steparr[(int) (Math.random() * 3)]);
newPos.setY(
curpos.getY() + molecule.getStepLengthY() * steparr[(int) (Math.random() * 3)]);
newPos.setZ(
curpos.getZ() + molecule.getStepLengthZ() * steparr[(int) (Math.random() * 3)]);
checkBoundary(newPos);
Position nextPos = checkRailPos(curpos, newPos, molecule);
if (nextPos != null) {
// distance = curpos.getDistance(reciever);
molecule.setPosition(nextPos);
onRailFlag = true;
System.out.println("Gets on Rail");
} else {
molecule.setPosition(newPos);
}
}
} else {
curpos.setX(
curpos.getX() + molecule.getStepLengthX() * steparr[(int) (Math.random() * 3)]);
curpos.setY(
curpos.getY() + molecule.getStepLengthY() * steparr[(int) (Math.random() * 3)]);
curpos.setZ(
curpos.getZ() + molecule.getStepLengthZ() * steparr[(int) (Math.random() * 3)]);
checkBoundary(curpos);
}
if (generateOutputFile) {
writer[1].flush();
}
}
if (generateOutputFile) {
writer[1].flush();
writer[1].close();
}
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
if (molecule.isReachFlag()) {
System.out.println(":) Hooray this molecule reached to destination");
try {
writer[0].write(molecule.getReachTime() + "\n");
writer[0].flush();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
} else System.out.println(":( This molecule couldn't reach its destination");
}
