/** * {@inheritDoc} */ @Override public Integer getMassNumber() { return atom.getMassNumber(); }
/** * {@inheritDoc} */ @Override public Integer getMassNumber() { return atom.getMassNumber(); }
@Override /** {@inheritDoc} */ protected int getIntLabel(int vertexIndex) { IAtom atom = molecule.getAtom(vertexIndex); return atom.getMassNumber(); }
private boolean isMajorIsotope(IAtom atom) { if (atom.getMassNumber() == null) return false; try { IIsotope major = Isotopes.getInstance().getMajorIsotope(atom.getSymbol()); return major != null && major.getMassNumber().equals(atom.getMassNumber()); } catch (IOException ex) { return false; } }
@Test public void testMassNumber() { IAtom atom = mock(IAtom.class); IAtomContainer container = mock(IAtomContainer.class); AtomEncoder encoder = BasicAtomEncoder.MASS_NUMBER; when(atom.getMassNumber()).thenReturn(12); assertThat(encoder.encode(atom, container), is(12)); verify(atom, times(1)).getMassNumber(); verifyNoMoreInteractions(atom, container); }
@Test public void massDiff_c13() throws Exception { IAtom atom = reader.readAtomFast(" 7.8089 -1.3194 0.0000 C 1 0 0 0 0 0 0 0 0 0 0 0", builder, 1); assertThat(atom.getMassNumber(), is(13)); }
@Test public void testHasIsotope() { Expr expr = new Expr(HAS_ISOTOPE); IAtom atom = mock(IAtom.class); when(atom.getMassNumber()).thenReturn(null); assertFalse(expr.matches(atom)); when(atom.getMassNumber()).thenReturn(12); assertTrue(expr.matches(atom)); }
private Integer getMassNumber(ILigand ligand) { Integer massNumber = ligand.getLigandAtom().getMassNumber(); if (massNumber != null) return massNumber; if (factory == null) return 0; return factory.getMajorIsotope(ligand.getLigandAtom().getSymbol()).getMassNumber(); }
@Test public void nullMassNumber() { IAtomContainer container = mock(IAtomContainer.class); IAtom atom = mock(IAtom.class); when(atom.getAtomicNumber()).thenReturn(6); when(atom.getMassNumber()).thenReturn(null); when(atom.getImplicitHydrogenCount()).thenReturn(0); when(atom.getFormalCharge()).thenReturn(0); AtomSymbol atomSymbol = atomGenerator.generateSymbol(container, atom, HydrogenPosition.Left, new RendererModel()); List<Shape> shapes = atomSymbol.getOutlines(); assertThat(shapes.size(), is(1)); }
@Test public void testIsotopeT() { Expr expr = new Expr(ISOTOPE, 13); IAtom atom = mock(IAtom.class); when(atom.getMassNumber()).thenReturn(13); assertTrue(expr.matches(atom)); }
@Test public void testIsotopeF() { Expr expr = new Expr(ISOTOPE, 12); IAtom atom = mock(IAtom.class); when(atom.getMassNumber()).thenReturn(13); assertFalse(expr.matches(atom)); }
@Test public void seaborgiumAbsMass() throws Exception { try (InputStream in = getClass().getResourceAsStream("seaborgium_abs.mol"); MDLV2000Reader mdlr = new MDLV2000Reader(in, Mode.STRICT)) { IAtomContainer mol = mdlr.read(new AtomContainer()); assertThat(mol.getAtom(0).getMassNumber(), is(261)); } }
@Test public void testMassDiff() throws Exception { String mdl = "deuterium.mol\n" + "\n" + "\n" + " 1 0 0 0 0 1\n" + " 0.0000 0.0000 0.0000 H +1 0 0 0 0\n"; try (MDLReader reader = new MDLReader(new StringReader(mdl), Mode.STRICT)) { IAtomContainer mol = reader.read(new AtomContainer()); IAtom atom = mol.getAtom(0); Assert.assertEquals(1, atom.getAtomicNumber().intValue()); Assert.assertEquals(2, atom.getMassNumber().intValue()); } }
public void setMassNumber(IAtom atom, int massNumber) { if (getUndoRedoFactory() != null && getUndoRedoHandler() != null) { IUndoRedoable undoredo = getUndoRedoFactory().getChangeIsotopeEdit( atom, atom.getMassNumber(), massNumber, "Change Atomic Mass to " + massNumber); getUndoRedoHandler().postEdit(undoredo); } atom.setMassNumber(massNumber); structurePropertiesChanged(); }
@Test public void configureDoesNotSetMajorIsotope() throws Exception { IAtom atom = new Atom("CH4"); Isotopes isotopes = Isotopes.getInstance(); IIsotope major = isotopes.getMajorIsotope(atom.getSymbol()); assertThat(major, is(notNullValue())); assertThat(major.getMassNumber(), is(12)); isotopes.configure(atom); assertThat(atom.getMassNumber(), is(nullValue())); }
@Test public void testExpectedValues() throws Exception { IAtom hydrogen = new ImmutableHydrogen(); Assert.assertEquals("H", hydrogen.getSymbol()); Assert.assertEquals(1, hydrogen.getAtomicNumber().intValue()); Assert.assertEquals(1, hydrogen.getMassNumber().intValue()); }
@Test public void carbon_13() { IAtom a = g2c.toCDKAtom(AtomBuilder.aliphatic(Element.Carbon).hydrogens(4).isotope(13).build(), 4); assertThat(a.getMassNumber(), is(13)); }
@Test public void testOverwriteStaticValues() throws Exception { IAtom hydrogen = new ImmutableHydrogen(); hydrogen.setSymbol("C"); hydrogen.setAtomicNumber(12); hydrogen.setMassNumber(13); Assert.assertEquals("H", hydrogen.getSymbol()); Assert.assertEquals(1, hydrogen.getAtomicNumber().intValue()); Assert.assertEquals(1, hydrogen.getMassNumber().intValue()); }
@Test public void testMassNumber() throws Exception { String cmlString = "<molecule id='m1'><atomArray><atom id='a1' elementType='C' isotopeNumber='12'/></atomArray></molecule>"; IChemFile chemFile = parseCMLString(cmlString); IAtomContainer mol = checkForSingleMoleculeFile(chemFile); Assert.assertEquals(1, mol.getAtomCount()); IAtom atom = mol.getAtom(0); Assert.assertEquals("C", atom.getSymbol()); Assert.assertEquals(12, atom.getMassNumber().intValue()); }
@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()); }