public void testItShouldChangeItsSymbolWhenGivenAValidNewOne() {
Molecule molecule = new DefaultMolecule();
Atom atom = molecule.addAtom("C");
atom.setSymbol("O");
assertEquals("O", atom.getSymbol());
}
public void testItShouldReportValenceTwoForAPrimaryDoubleBondTerminal() {
Molecule molecule = new DefaultMolecule();
Atom c1 = molecule.addAtom("C");
Atom c2 = molecule.addAtom("C");
molecule.connect(c1, c2, 2);
assertEquals(2, c1.getValence());
}
public void testItShouldThrowWhenSettingAnIllegalAtomLabel() {
Molecule molecule = new DefaultMolecule();
Atom atom = molecule.addAtom("C");
try {
atom.setSymbol("bailout");
fail();
} catch (IllegalStateException e) {
}
}
public void testItShouldUpdateItsCoordinatesWhenMoved() {
Molecule molecule = new DefaultMolecule();
Atom atom = molecule.addAtom("C");
atom.move(100, 100, 0);
assertEquals(100d, atom.getX());
assertEquals(100d, atom.getY());
assertEquals(0d, atom.getZ());
}
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 void testItShouldThrowWhenIllegalRadicalIsSet() {
Molecule molecule = new DefaultMolecule();
Atom atom = molecule.addAtom("O");
try {
atom.setRadical(-1);
fail();
} catch (IllegalStateException ignore) {
}
try {
atom.setRadical(4);
fail();
} catch (IllegalStateException ignore) {
}
}
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 void testItShouldReportValenceFourForAQuaternaryCarbon() {
Molecule molecule = new DefaultMolecule();
Atom c1 = molecule.addAtom("C");
Atom c2 = molecule.addAtom("C");
Atom c3 = molecule.addAtom("C");
Atom c4 = molecule.addAtom("C");
Atom c5 = molecule.addAtom("C");
molecule.connect(c1, c2, 1);
molecule.connect(c1, c3, 1);
molecule.connect(c1, c4, 1);
molecule.connect(c1, c5, 1);
assertEquals(4, c1.getValence());
}