/** {@inheritDoc} */ @Override public Point2d getPoint2d() { Point2d point2d = super.getPoint2d(); if (point2d == null) { logger.debug("Getting point2d: null"); } else { logger.debug("Getting point2d: x=" + point2d.x + ", y=" + point2d.y); } return point2d; }
stringContent.append(", SP:").append(getStereoParity()); if (getPoint2d() != null) { stringContent.append(", 2D:[").append(getPoint2d()).append(']');
stringContent.append(", SP:").append(getStereoParity()); if (getPoint2d() != null) { stringContent.append(", 2D:[").append(getPoint2d()).append(']');
@Test public void testTranslateAllPositive_IAtomContainer_HashMap() { Atom atom1 = new Atom("C"); atom1.setPoint2d(new Point2d(-1, -1)); Atom atom2 = new Atom("C"); atom2.setPoint2d(new Point2d(1, 0)); IAtomContainer ac = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class); ac.addAtom(atom1); ac.addAtom(atom2); GeometryUtil.translateAllPositive(ac); Assert.assertEquals(atom1.getPoint2d().x, 0.0, 0.01); Assert.assertEquals(atom1.getPoint2d().y, 0.0, 0.01); Assert.assertEquals(atom2.getPoint2d().x, 2.0, 0.01); Assert.assertEquals(atom2.getPoint2d().y, 1.0, 0.01); }
@Test public void testRotate_IAtomContainer_Point2d_double() { Atom atom1 = new Atom("C"); atom1.setPoint2d(new Point2d(1, 1)); Atom atom2 = new Atom("C"); atom2.setPoint2d(new Point2d(1, 0)); IAtomContainer ac = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class); ac.addAtom(atom1); ac.addAtom(atom2); GeometryUtil.rotate(ac, new Point2d(0, 0), Math.PI / 2); Assert.assertEquals(atom1.getPoint2d().x, -1, .2); Assert.assertEquals(atom1.getPoint2d().y, 1, .2); Assert.assertEquals(atom2.getPoint2d().x, 0, .2); Assert.assertEquals(atom2.getPoint2d().y, 1, .2); atom2.setPoint2d(new Point2d(0, 0)); GeometryUtil.rotate(ac, new Point2d(0, 0), Math.PI); Assert.assertFalse(Double.isNaN(atom2.getPoint2d().x)); Assert.assertFalse(Double.isNaN(atom2.getPoint2d().y)); }
dichloromethane.addBond(new Bond(carbon, cl2)); Assert.assertNull(h1.getPoint2d()); Assert.assertNull(h2.getPoint2d()); assertEquals(carbonPos, carbon.getPoint2d(), 0.01); assertEquals(cl1Pos, cl1.getPoint2d(), 0.01); assertEquals(cl2Pos, cl2.getPoint2d(), 0.01); Assert.assertNotNull(h1.getPoint2d()); Assert.assertNotNull(h2.getPoint2d());
@Test public void testAtom2D() throws Exception { IAtomContainer mol = new AtomContainer(); Atom atom = new Atom("N"); Point2d p2d = new Point2d(1.3, 1.4); atom.setPoint2d(p2d); mol.addAtom(atom); IAtomContainer roundTrippedMol = CMLRoundTripTool.roundTripMolecule(convertor, mol); Assert.assertEquals(1, roundTrippedMol.getAtomCount()); IAtom roundTrippedAtom = roundTrippedMol.getAtom(0); assertEquals(atom.getPoint2d(), roundTrippedAtom.getPoint2d(), 0.00001); }
@Test public void testAtom2DAnd3D() throws Exception { IAtomContainer mol = new AtomContainer(); Atom atom = new Atom("N"); Point2d p2d = new Point2d(1.3, 1.4); atom.setPoint2d(p2d); Point3d p3d = new Point3d(1.3, 1.4, 0.9); atom.setPoint3d(p3d); mol.addAtom(atom); IAtomContainer roundTrippedMol = CMLRoundTripTool.roundTripMolecule(convertor, mol); Assert.assertEquals(1, roundTrippedMol.getAtomCount()); IAtom roundTrippedAtom = roundTrippedMol.getAtom(0); assertEquals(atom.getPoint2d(), roundTrippedAtom.getPoint2d(), 0.00001); assertEquals(atom.getPoint3d(), roundTrippedAtom.getPoint3d(), 0.00001); }