MolecularFormulaManipulator { public static String getHTML(IMolecularFormula formula) { return getHTML(formula, true, true); }  static int getAtomCount(IMolecularFormula formula); static int getElementCount(IMolecularFormula formula, IElement element); static int getElementCount(IMolecularFormula formula, IIsotope isotope); static int getElementCount(IMolecularFormula formula, String symbol); static List<IIsotope> getIsotopes(IMolecularFormula formula, IElement element); static List<IElement> elements(IMolecularFormula formula); static boolean containsElement(IMolecularFormula formula, IElement element); static IMolecularFormula removeElement(IMolecularFormula formula, IElement element); static String getString(IMolecularFormula formula, String[] orderElements,
                                   boolean setOne); static String getString(IMolecularFormula formula, String[] orderElements,
                                   boolean setOne, boolean setMassNumber); static String getString(IMolecularFormula formula); static String getString(IMolecularFormula formula, boolean setOne); static String getString(IMolecularFormula formula, boolean setOne, boolean setMassNumber); static List<IIsotope> putInOrder(String[] orderElements, IMolecularFormula formula); @Deprecated static String getHillString(IMolecularFormula formula); static String getHTML(IMolecularFormula formula); static String getHTML(IMolecularFormula formula, boolean chargeB, boolean isotopeB); static String getHTML(IMolecularFormula formula, String[] orderElements, boolean showCharge, boolean showIsotopes); static IMolecularFormula getMolecularFormula(String stringMF, IChemObjectBuilder builder); static IMolecularFormula getMajorIsotopeMolecularFormula(String stringMF, IChemObjectBuilder builder); static IMolecularFormula getMolecularFormula(String stringMF, IMolecularFormula formula); @Deprecated static double getTotalExactMass(IMolecularFormula formula); static double getTotalMassNumber(IMolecularFormula formula); static double getMass(IMolecularFormula mf, int flav); static double getMass(IMolecularFormula mf); @Deprecated static double getNaturalExactMass(IMolecularFormula formula); @Deprecated static double getMajorIsotopeMass(IMolecularFormula formula); static double getTotalNaturalAbundance(IMolecularFormula formula); static double getDBE(IMolecularFormula formula); static IMolecularFormula getMolecularFormula(IAtomContainer atomContainer); static IMolecularFormula getMolecularFormula(IAtomContainer atomContainer, IMolecularFormula formula); static IAtomContainer getAtomContainer(IMolecularFormula formula); static IAtomContainer getAtomContainer(IMolecularFormula formula, IAtomContainer atomContainer); static IAtomContainer getAtomContainer(String formulaString, IChemObjectBuilder builder); static String[] generateOrderEle(); static boolean compare(IMolecularFormula formula1, IMolecularFormula formula2); static List<IElement> getHeavyElements(IMolecularFormula formula); static String simplifyMolecularFormula(String formula); static boolean adjustProtonation(IMolecularFormula mf, int hcnt); static IMolecularFormula getMostAbundant(IMolecularFormula mf); static IMolecularFormula getMostAbundant(IAtomContainer mol); static final int MolWeight; static final int MolWeightIgnoreSpecified; static final int MonoIsotopic; static final int MostAbundant; static final Comparator<IIsotope> NAT_ABUN_COMP; }
@Test public void testGetHTML_IMolecularFormula() { MolecularFormula formula = new MolecularFormula(); formula.addIsotope(builder.newInstance(IIsotope.class, "C"), 8); formula.addIsotope(builder.newInstance(IIsotope.class, "H"), 10); formula.addIsotope(builder.newInstance(IIsotope.class, "Cl"), 2); formula.addIsotope(builder.newInstance(IIsotope.class, "O"), 2); Assert.assertEquals("C<sub>8</sub>H<sub>10</sub>Cl<sub>2</sub>O<sub>2</sub>", MolecularFormulaManipulator.getHTML(formula)); }
@Test public void htmlFormulaDoesNotAddSubscriptForSingleElements() { MolecularFormula formula = new MolecularFormula(); formula.addIsotope(builder.newInstance(IIsotope.class, "C"), 1); formula.addIsotope(builder.newInstance(IIsotope.class, "H"), 4); Assert.assertEquals("CH<sub>4</sub>", MolecularFormulaManipulator.getHTML(formula)); }
@Test public void testGetHTML_IMolecularFormula_boolean_boolean() { MolecularFormula formula = new MolecularFormula(); formula.addIsotope(builder.newInstance(IIsotope.class, "C"), 10); Assert.assertEquals("C<sub>10</sub>", MolecularFormulaManipulator.getHTML(formula, true, false)); formula.setCharge(1); Assert.assertEquals("C<sub>10</sub><sup>+</sup>", MolecularFormulaManipulator.getHTML(formula, true, false)); formula.setCharge(formula.getCharge() - 2); Assert.assertEquals("C<sub>10</sub><sup>–</sup>", MolecularFormulaManipulator.getHTML(formula, true, false)); }
@Test public void nullIsotopeLabels() { MolecularFormula formula = new MolecularFormula(); formula.addIsotope(builder.newInstance(IIsotope.class, "C"), 10); Assert.assertEquals("C<sub>10</sub>", MolecularFormulaManipulator.getHTML(formula, true, false)); formula.setCharge(1); Assert.assertEquals("C<sub>10</sub><sup>+</sup>", MolecularFormulaManipulator.getHTML(formula, true, true)); formula.setCharge(formula.getCharge() - 2); Assert.assertEquals("C<sub>10</sub><sup>–</sup>", MolecularFormulaManipulator.getHTML(formula, true, true)); }
@Test public void testGetHTML_IMolecularFormula_arrayString_boolean_boolean() { IMolecularFormula formula = new MolecularFormula(); formula.addIsotope(builder.newInstance(IIsotope.class, "C"), 2); formula.addIsotope(builder.newInstance(IIsotope.class, "H"), 2); String[] newOrder = new String[2]; newOrder[0] = "H"; newOrder[1] = "C"; Assert.assertEquals("H<sub>2</sub>C<sub>2</sub>", MolecularFormulaManipulator.getHTML(formula, newOrder, false, false)); }
@Test public void testGetHTML_IMolecularFormulaWithIsotope() { MolecularFormula formula = new MolecularFormula(); formula.addIsotope(ifac.getMajorIsotope("C"), 2); formula.addIsotope(ifac.getMajorIsotope("H"), 6); Assert.assertEquals("<sup>12</sup>C<sub>2</sub><sup>1</sup>H<sub>6</sub>", MolecularFormulaManipulator.getHTML(formula, false, true)); }
@Test public void testGetHTML_IMolecularFormulaWithIsotopeAndCharge() { MolecularFormula formula = new MolecularFormula(); formula.addIsotope(ifac.getMajorIsotope("C"), 2); formula.addIsotope(ifac.getMajorIsotope("H"), 6); formula.setCharge(1); Assert.assertEquals("<sup>12</sup>C<sub>2</sub><sup>1</sup>H<sub>6</sub><sup>+</sup>", MolecularFormulaManipulator.getHTML(formula, true, true)); }