public void setMolecule(Molecule molecule) {
GeometryTools.translateAllPositive(molecule);
GeometryTools.center(
molecule, new Dimension(renderer.getCanvas().getWidth(), renderer.getCanvas().getHeight()));
this.molecule = molecule;
calcAverageBondLength();
renderer.paintNewMolecule(molecule);
// renderer.getTransformer().dumpMatrix();
}
public void calcAverageBondLength() {
double total = 0;
for (int i = 0; i < molecule.countBonds(); i++) {
Bond bond = molecule.getBond(i);
total +=
GeometryTools.calcDistance(
new Point2D(bond.getSource().getX(), bond.getSource().getY()),
new Point2D(bond.getTarget().getX(), bond.getTarget().getY()));
}
renderer.getRendererModel().setDefaultBondLength(total / molecule.countBonds());
}
public Atom getClosestAtom(Point2D graphCord) {
Atom closestAtom = null;
double closestDistance = Double.MAX_VALUE;
for (int i = 0; i < molecule.countAtoms(); i++) {
Atom currentAtom = molecule.getAtom(i);
Point2D currentPointGraph =
realCordToGraphCord(new Point2D(currentAtom.getX(), currentAtom.getY()));
double distance = GeometryTools.calcDistance(graphCord, currentPointGraph);
if (distance <= renderer.getRendererModel().getAtomRadius() && distance < closestDistance) {
closestAtom = currentAtom;
closestDistance = distance;
}
}
return closestAtom;
}
public Bond getClosestBond(Point2D graphCord) {
Bond closestBond = null;
double closestDistance = Double.MAX_VALUE;
for (int i = 0; i < molecule.countBonds(); i++) {
Bond currentBond = molecule.getBond(i);
Point2D currentCenterGraph =
realCordToGraphCord(
new Point2D(
(currentBond.getSource().getX() + currentBond.getTarget().getX()) / 2,
(currentBond.getSource().getY() + currentBond.getTarget().getY()) / 2));
double distance = GeometryTools.calcDistance(graphCord, currentCenterGraph);
if (distance <= renderer.getRendererModel().getAtomRadius() && distance < closestDistance) {
closestBond = currentBond;
closestDistance = distance;
}
}
return closestBond;
}
public Point2D graphCordToRealCord(Point2D graphCord) {
return renderer.getTransformer().inverseTransform(graphCord, null);
}
public Point2D realCordToGraphCord(Point2D realCord) {
return renderer.getTransformer().transform(realCord, null);
}
public void zoomInOut(double factor) {
renderer.getRendererModel().setZoomFactor(renderer.getRendererModel().getZoomFactor() * factor);
renderer.paintNewMolecule(molecule);
}
public void refreshView() {
renderer.paintMolecule(molecule);
}