/** * {@inheritDoc} */ @Override public Point3d getFractionalPoint3d() { return atom.getFractionalPoint3d(); }
/** * {@inheritDoc} */ @Override public Point3d getFractionalPoint3d() { return atom.getFractionalPoint3d(); }
private void mapFractionalCoordsToCML(CMLAtom cmlAtom, IAtom cdkAtom) { if (cdkAtom.getFractionalPoint3d() != null) { cmlAtom.setXFract(cdkAtom.getFractionalPoint3d().x); cmlAtom.setYFract(cdkAtom.getFractionalPoint3d().y); cmlAtom.setZFract(cdkAtom.getFractionalPoint3d().z); } }
/** * Method to test the clone() method */ @Test public void testClone_FractionalPoint3d() throws Exception { IAtom atom = (IAtom) newChemObject(); atom.setFractionalPoint3d(new Point3d(2, 3, 4)); IAtom clone = (IAtom) atom.clone(); Assert.assertEquals(clone.getFractionalPoint3d().x, 2.0, 0.001); }
@Test public void testFractional3D() throws Exception { String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2' xFract='0.0 0.1' yFract='1.2 1.3' zFract='2.1 2.5'/></molecule>"; IChemFile chemFile = parseCMLString(cmlString); IAtomContainer mol = checkForSingleMoleculeFile(chemFile); Assert.assertEquals(2, mol.getAtomCount()); Assert.assertNull(mol.getAtom(0).getPoint3d()); Assert.assertNull(mol.getAtom(1).getPoint3d()); Assert.assertNotNull(mol.getAtom(0).getFractionalPoint3d()); Assert.assertNotNull(mol.getAtom(1).getFractionalPoint3d()); }
@Test public void testFractional3D() throws Exception { String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2' xFract='0.0 0.1' yFract='1.2 1.3' zFract='2.1 2.5'/></molecule>"; IChemFile chemFile = parseCMLString(cmlString); IAtomContainer mol = checkForSingleMoleculeFile(chemFile); Assert.assertEquals(2, mol.getAtomCount()); Assert.assertNull(mol.getAtom(0).getPoint3d()); Assert.assertNull(mol.getAtom(1).getPoint3d()); Assert.assertNotNull(mol.getAtom(0).getFractionalPoint3d()); Assert.assertNotNull(mol.getAtom(1).getFractionalPoint3d()); }
/** * 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() { IAtom a = new DebugAtom("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()); }
/** * Method to test the Atom(String symbol, javax.vecmath.Point3d point3D) method. */ @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_String_Point3d() { Point3d point3d = new Point3d(1.0, 2.0, 3.0); IAtom a = new Atom("C", point3d); Assert.assertEquals("C", a.getSymbol()); Assert.assertEquals(point3d, a.getPoint3d()); Assert.assertNull(a.getPoint2d()); Assert.assertNull(a.getFractionalPoint3d()); }
/** * Method to test the Atom(String symbol, javax.vecmath.Point3d point3D) method. */ @Test public void testAtom_String_Point3d() { Point3d point3d = new Point3d(1.0, 2.0, 3.0); IAtom a = new Atom("C", point3d); Assert.assertEquals("C", a.getSymbol()); Assert.assertEquals(point3d, a.getPoint3d()); Assert.assertNull(a.getPoint2d()); Assert.assertNull(a.getFractionalPoint3d()); }
@Test public void testAtom_Ca2plus() { IAtom a = new Atom("Ca+2"); Assert.assertEquals("Ca", a.getSymbol()); Assert.assertEquals((Integer) 20, a.getAtomicNumber()); Assert.assertEquals(null, a.getImplicitHydrogenCount()); Assert.assertEquals(Integer.valueOf(+2), a.getFormalCharge()); Assert.assertNull(a.getPoint2d()); Assert.assertNull(a.getPoint3d()); Assert.assertNull(a.getFractionalPoint3d()); }
@Test public void testAtomFract3D() throws Exception { IAtomContainer mol = new AtomContainer(); Atom atom = new Atom("N"); Point3d p3d = new Point3d(0.3, 0.4, 0.9); atom.setFractionalPoint3d(p3d); mol.addAtom(atom); IAtomContainer roundTrippedMol = CMLRoundTripTool.roundTripMolecule(convertor, mol); Assert.assertEquals(1, roundTrippedMol.getAtomCount()); IAtom roundTrippedAtom = roundTrippedMol.getAtom(0); assertEquals(atom.getFractionalPoint3d(), roundTrippedAtom.getFractionalPoint3d(), 0.00001); }
@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_CH3_direct() { IAtom a = new Atom(6, 3); Assert.assertEquals("C", a.getSymbol()); 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()); }
@Test public void testAtom_NH4plus_direct() { IAtom a = new Atom(7, 4, +1); 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_Cl_direct() { IAtom a = new Atom(17); Assert.assertEquals("Cl", a.getSymbol()); Assert.assertEquals((Integer) 17, a.getAtomicNumber()); Assert.assertEquals((Integer) 0, a.getImplicitHydrogenCount()); Assert.assertEquals((Integer) 0, 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()); }