/** * {@inheritDoc} */ @Override public Point3d getPoint3d() { return atom.getPoint3d(); }
@Override public String toString() { return ("<" + atom.getPoint3d().x + "," + atom.getPoint3d().y + "," + atom.getPoint3d().z + ">"); } }
private double calculateSquareDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2) { double distance; double tmp; Point3d firstPoint = atom1.getPoint3d(); Point3d secondPoint = atom2.getPoint3d(); tmp = firstPoint.distance(secondPoint); distance = tmp * tmp; return distance; }
private void map3DCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom) { if (cdkAtom.getPoint3d() != null) { cmlAtom.setX3(cdkAtom.getPoint3d().x); cmlAtom.setY3(cdkAtom.getPoint3d().y); cmlAtom.setZ3(cdkAtom.getPoint3d().z); } }
public static void project2D(IAtomContainer container, HashMap<IAtom, Point2d> renderingCoordinates) { for (int i = 0; i < container.getAtomCount(); i++) { IAtom atom = container.getAtom(i); if (atom.getPoint3d() != null) { atom.setPoint2d(new Point2d(atom.getPoint3d().x, atom.getPoint3d().y)); renderingCoordinates.put(atom, new Point2d(atom.getPoint3d().x, atom.getPoint3d().y)); } else { // should throw an exception } } } }
public static void project2D(IAtomContainer container) { for (int i = 0; i < container.getAtomCount(); i++) { IAtom atom = container.getAtom(i); if (atom.getPoint3d() != null) { atom.setPoint2d(new Point2d(atom.getPoint3d().x, atom.getPoint3d().y)); } else { // should throw an exception } } }
private Point3d[] getCoordinateList(IAtomContainer atomContainer) { Point3d[] tmp = new Point3d[atomContainer.getAtomCount()]; for (int i = 0; i < atomContainer.getAtomCount(); i++) { IAtom atom = atomContainer.getAtom(i); if (atom.getPoint3d() == null) throw new IllegalArgumentException("Molecule must have 3D coordinates"); tmp[i] = new Point3d(atom.getPoint3d()); } return tmp; }
private static void set3D(IAtomContainer container, int index, IAtom[] atoms) { if ((container.getAtom(index)).getPoint3d() != null) { atoms[index].setPoint3d(new Point3d(container.getAtom(index).getPoint3d())); } }
private static void set3D(IAtomContainer container, int index, IAtom[] atoms) { if ((container.getAtom(index)).getPoint3d() != null) { atoms[index].setPoint3d(new Point3d(container.getAtom(index).getPoint3d())); } }
private double[] calculateDistanceBetweenAtomAndBond(IAtom proton, IBond theBond) { Point3d middlePoint = theBond.get3DCenter(); Point3d protonPoint = proton.getPoint3d(); double[] values = new double[4]; values[0] = middlePoint.distance(protonPoint); values[1] = middlePoint.x; values[2] = middlePoint.y; values[3] = middlePoint.z; return values; }
private double[] calculateDistanceBetweenAtomAndBond(IAtom proton, IBond theBond) { Point3d middlePoint = theBond.get3DCenter(); Point3d protonPoint = proton.getPoint3d(); double[] values = new double[4]; values[0] = middlePoint.distance(protonPoint); values[1] = middlePoint.x; values[2] = middlePoint.y; values[3] = middlePoint.z; return values; }
private int getNumberOfDimensions(IAtomContainer mol) { for (IAtom atom : mol.atoms()) { if (atom.getPoint3d() != null) return 3; else if (atom.getPoint2d() != null) return 2; } return 0; }
private int getNumberOfDimensions(IAtomContainer mol) { for (IAtom atom : mol.atoms()) { if (atom.getPoint3d() != null && !forceWriteAs2DCoords.isSet()) return 3; else if (atom.getPoint2d() != null) return 2; } return 0; }
@Test public void readCoordinates() throws Exception { IAtom atom = reader.readAtomFast(" 7.8089 -1.3194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0", builder, 1); assertThat(atom.getPoint3d().x, is(closeTo(7.8089, 0.5))); assertThat(atom.getPoint3d().y, is(closeTo(-1.3194, 0.5))); assertThat(atom.getPoint3d().z, is(closeTo(0.0d, 0.5))); }
@Test public void testCoordinates3D() throws Exception { String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2' x3='0.0 0.1' y3='1.2 1.3' z3='2.1 2.5'/></molecule>"; IChemFile chemFile = parseCMLString(cmlString); IAtomContainer mol = checkForSingleMoleculeFile(chemFile); Assert.assertEquals(2, mol.getAtomCount()); Assert.assertNull(mol.getAtom(0).getPoint2d()); Assert.assertNull(mol.getAtom(1).getPoint2d()); Assert.assertNotNull(mol.getAtom(0).getPoint3d()); Assert.assertNotNull(mol.getAtom(1).getPoint3d()); }
/** * Method to test the Atom(String symbol) method. */ @Test public void testAtom_String() { IAtom a = new Atom("C"); Assert.assertEquals("C", a.getSymbol()); Assert.assertNull(a.getPoint2d()); Assert.assertNull(a.getPoint3d()); Assert.assertNull(a.getFractionalPoint3d()); }
@Test public void testDebugAtom_String_Point3d() { Point3d point3d = new Point3d(1.0, 2.0, 3.0); IAtom a = new DebugAtom("C", point3d); Assert.assertEquals("C", a.getSymbol()); Assert.assertEquals(point3d, a.getPoint3d()); Assert.assertNull(a.getPoint2d()); Assert.assertNull(a.getFractionalPoint3d()); }
@Test public void testAtom_String_Point2d() { Point2d point2d = new Point2d(1.0, 2.0); IAtom a = new Atom("C", point2d); Assert.assertEquals("C", a.getSymbol()); Assert.assertEquals(point2d, a.getPoint2d()); Assert.assertNull(a.getPoint3d()); Assert.assertNull(a.getFractionalPoint3d()); }
@Test public void testAtom_NH4plus() { IAtom a = new Atom("NH4+"); Assert.assertEquals("N", a.getSymbol()); Assert.assertEquals((Integer) 7, a.getAtomicNumber()); Assert.assertEquals((Integer) 4, a.getImplicitHydrogenCount()); Assert.assertEquals((Integer) 1, a.getFormalCharge()); Assert.assertNull(a.getPoint2d()); Assert.assertNull(a.getPoint3d()); Assert.assertNull(a.getFractionalPoint3d()); }
@Test public void testAtom_13CH3() { IAtom a = new Atom("13CH3"); Assert.assertEquals("C", a.getSymbol()); Assert.assertEquals((Integer) 13, a.getMassNumber()); Assert.assertEquals((Integer) 6, a.getAtomicNumber()); Assert.assertEquals((Integer) 3, a.getImplicitHydrogenCount()); Assert.assertEquals((Integer) 0, a.getFormalCharge()); Assert.assertNull(a.getPoint2d()); Assert.assertNull(a.getPoint3d()); Assert.assertNull(a.getFractionalPoint3d()); }