/** * {@inheritDoc} */ @Override public IAtom newAtom() { return new Atom(); }
@Test public void testNewAtomImplicitHydrogenCount() { Assert.assertNull(new Atom("C").getImplicitHydrogenCount()); Assert.assertNull(new Atom("*").getImplicitHydrogenCount()); Assert.assertNull(new Atom("H").getImplicitHydrogenCount()); Assert.assertNull(new Atom("D").getImplicitHydrogenCount()); Assert.assertNull(new Atom("T").getImplicitHydrogenCount()); } }
public String toString() { StringBuffer stringContent = new StringBuffer(64); stringContent.append("Atom(").append(hashCode()); if (getSymbol() != null) { stringContent.append(", S:").append(getSymbol()); if (getImplicitHydrogenCount() != null) { stringContent.append(", H:").append(getImplicitHydrogenCount()); if (getStereoParity() != null) { stringContent.append(", SP:").append(getStereoParity()); if (getPoint2d() != null) { stringContent.append(", 2D:[").append(getPoint2d()).append(']'); if (getPoint3d() != null) { stringContent.append(", 3D:[").append(getPoint3d()).append(']'); if (getFractionalPoint3d() != null) { stringContent.append(", F3D:[").append(getFractionalPoint3d()); if (getCharge() != null) { stringContent.append(", C:").append(getCharge());
/** * Clones this atom object and its content. * * @return The cloned object */ @Override public IAtom clone() throws CloneNotSupportedException { Object clone = super.clone(); if (point2d != null) { ((Atom) clone).setPoint2d(new Point2d(point2d.x, point2d.y)); } if (point3d != null) { ((Atom) clone).setPoint3d(new Point3d(point3d.x, point3d.y, point3d.z)); } if (fractionalPoint3d != null) { ((Atom) clone).setFractionalPoint3d(new Point3d(fractionalPoint3d.x, fractionalPoint3d.y, fractionalPoint3d.z)); } return (IAtom) clone; }
IAtomContainer mol = new AtomContainer(); Atom[] atoms = new Atom[] { new Atom("C"), new Atom("F"), new Atom("N"), new Atom("O"), }; atoms[0].setPoint3d(new Point3d(0, 0, -10)); atoms[1].setPoint3d(new Point3d(0, 1, -10)); atoms[2].setPoint3d(new Point3d(-1, -1, -10)); atoms[3].setPoint3d(new Point3d(1, -1, -10)); mol.setAtoms(atoms); mol.addBond(0, 1, IBond.Order.SINGLE); Point3d p = atoms[i].getPoint3d(); atoms[i].setPoint3d(new Point3d(p.x, p.y, p.z + 20));
@Test public void writeLeadingZero() throws IOException, CDKException { IAtomContainer mol = new AtomContainer(); Atom atom = new Atom("C"); atom.setPoint2d(new Point2d(0.5, 1.2)); mol.addAtom(atom); assertThat(writeToStr(mol), CoreMatchers.containsString("0.5 1.2")); }
/** * Clones this atom object and its content. * * @return The cloned object */ @Override public IAtom clone() throws CloneNotSupportedException { Object clone = super.clone(); if (point2d != null) { ((Atom) clone).setPoint2d(new Point2d(point2d.x, point2d.y)); } if (point3d != null) { ((Atom) clone).setPoint3d(new Point3d(point3d.x, point3d.y, point3d.z)); } if (fractionalPoint3d != null) { ((Atom) clone).setFractionalPoint3d(new Point3d(fractionalPoint3d.x, fractionalPoint3d.y, fractionalPoint3d.z)); } return (IAtom) clone; }
/** * {@inheritDoc} */ @Override public IAtom newAtom() { return new Atom(); }
public String toString() { StringBuffer stringContent = new StringBuffer(64); stringContent.append("Atom(").append(hashCode()); if (getSymbol() != null) { stringContent.append(", S:").append(getSymbol()); if (getImplicitHydrogenCount() != null) { stringContent.append(", H:").append(getImplicitHydrogenCount()); if (getStereoParity() != null) { stringContent.append(", SP:").append(getStereoParity()); if (getPoint2d() != null) { stringContent.append(", 2D:[").append(getPoint2d()).append(']'); if (getPoint3d() != null) { stringContent.append(", 3D:[").append(getPoint3d()).append(']'); if (getFractionalPoint3d() != null) { stringContent.append(", F3D:[").append(getFractionalPoint3d()); if (getCharge() != null) { stringContent.append(", C:").append(getCharge());
@Override public IChemObject newTestObject() { return new Atom(); } });
static IAtom atom(String symb, int h) { IAtom atom = new org.openscience.cdk.silent.Atom(symb); atom.setImplicitHydrogenCount(h); return atom; } }
static IAtom atomAt(String symb, Point2d p) { IAtom atom = new Atom(symb); atom.setPoint2d(p); return atom; }
static IAtom atom(String symbol, int hCount) { IAtom atom = new Atom(symbol); atom.setImplicitHydrogenCount(hCount); return atom; } }
static IAtom atom(String symbol, int hCount) { IAtom atom = new Atom(symbol); atom.setImplicitHydrogenCount(hCount); return atom; }
@Test(expected = NullPointerException.class) public void testConstructor_Container_Null() { new ShortestPaths(null, new Atom()); }
@Test(expected = IllegalArgumentException.class) public void testConstructor_Container_MissingAtom() { new ShortestPaths(TestMoleculeFactory.makeBenzene(), new Atom()); }
/** InChI=1/C2H6O.H2O/c1-2-3;/h3H,2H2,1H3;1H2 */ static IAtomContainer ethylAlcoholHydrate() { IAtomContainer m = new AtomContainer(); m.addAtom(new Atom("O")); m.addAtom(new Atom("C")); m.addAtom(new Atom("C")); m.addAtom(new Atom("O")); m.addBond(1, 2, IBond.Order.SINGLE); m.addBond(2, 3, IBond.Order.SINGLE); return m; }
@BeforeClass public static void setUp() { setTestObjectBuilder(new ITestObjectBuilder() { @Override public IChemObject newTestObject() { return new Atom(); } }); }