IsotopeContainer isotope = pattern.getIsotope(i);
IsotopeContainer isotope = pattern.getIsotope(i);
IsotopeContainer isotope = pattern.getIsotope(i);
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testGetIsotope_int() { IsotopePattern isoP = new IsotopePattern(); IsotopeContainer iso1 = new IsotopeContainer(); isoP.setMonoIsotope(iso1); IsotopeContainer iso2 = new IsotopeContainer(); isoP.addIsotope(iso2); Assert.assertEquals(iso1, isoP.getIsotope(0)); Assert.assertEquals(iso2, isoP.getIsotope(1)); }
/** * A unit test for JUnit: Isotopes of the n-Carbone. * * @return Description of the Return Value */ @Test public void testCalculateIsotopesnCarbono() { // RESULTS ACCORDING PAGE: http://www2.sisweb.com/mstools/isotope.htm double[] massResults = {120.000000, 121.003360, 122.006709}; double[] abundResults = {1.00, .108, 0.005}; IMolecularFormula molFor = new MolecularFormula(); molFor.addIsotope(builder.newInstance(IIsotope.class, "C"), 10); IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.0010); IsotopePattern isoPattern = isotopeGe.getIsotopes(molFor); Assert.assertEquals(3, isoPattern.getNumberOfIsotopes()); Assert.assertEquals(massResults[0], isoPattern.getIsotope(0).getMass(), 0.01); Assert.assertEquals(massResults[1], isoPattern.getIsotope(1).getMass(), 0.01); Assert.assertEquals(massResults[2], isoPattern.getIsotope(2).getMass(), 0.01); Assert.assertEquals(abundResults[0], isoPattern.getIsotope(0).getIntensity(), 0.01); Assert.assertEquals(abundResults[1], isoPattern.getIsotope(1).getIntensity(), 0.01); Assert.assertEquals(abundResults[2], isoPattern.getIsotope(2).getIntensity(), 0.01); }
Assert.assertEquals(massResults[0], isoPattern.getIsotope(0).getMass(), 0.01); Assert.assertEquals(massResults[1], isoPattern.getIsotope(1).getMass(), 0.01); Assert.assertEquals(massResults[2], isoPattern.getIsotope(2).getMass(), 0.01); Assert.assertEquals(massResults[3], isoPattern.getIsotope(3).getMass(), 0.01); Assert.assertEquals(massResults[4], isoPattern.getIsotope(4).getMass(), 0.01); Assert.assertEquals(massResults[5], isoPattern.getIsotope(5).getMass(), 0.01); Assert.assertEquals(abundResults[0], isoPattern.getIsotope(0).getIntensity(), 0.01); Assert.assertEquals(abundResults[1], isoPattern.getIsotope(1).getIntensity(), 0.01); Assert.assertEquals(abundResults[2], isoPattern.getIsotope(2).getIntensity(), 0.01); Assert.assertEquals(abundResults[3], isoPattern.getIsotope(3).getIntensity(), 0.01); Assert.assertEquals(abundResults[4], isoPattern.getIsotope(4).getIntensity(), 0.01); Assert.assertEquals(abundResults[5], isoPattern.getIsotope(5).getIntensity(), 0.01);
/** * A unit test for JUnit: Isotopes of the Bromine. * * @return Description of the Return Value */ @Test public void testCalculateIsotopesAllBromine() { // RESULTS ACCORDING PAGE: http://www2.sisweb.com/mstools/isotope.htm double[] massResults = {157.836669, 159.834630, 161.832580}; double[] abundResults = {.512, 1.00, .487}; IMolecularFormula molFor = new MolecularFormula(); molFor.addIsotope(builder.newInstance(IIsotope.class, "Br")); molFor.addIsotope(builder.newInstance(IIsotope.class, "Br")); IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(.1); IsotopePattern isoPattern = isotopeGe.getIsotopes(molFor); Assert.assertEquals(3, isoPattern.getNumberOfIsotopes()); Assert.assertEquals(massResults[0], isoPattern.getIsotope(0).getMass(), 0.01); Assert.assertEquals(massResults[1], isoPattern.getIsotope(1).getMass(), 0.01); Assert.assertEquals(massResults[2], isoPattern.getIsotope(2).getMass(), 0.01); Assert.assertEquals(abundResults[0], isoPattern.getIsotope(0).getIntensity(), 0.01); Assert.assertEquals(abundResults[1], isoPattern.getIsotope(1).getIntensity(), 0.01); Assert.assertEquals(abundResults[2], isoPattern.getIsotope(2).getIntensity(), 0.01); }
/** * A unit test for JUnit: Isotopes of the Iodemethylidyne. * * @return Description of the Return Value */ @Test public void testCalculateIsotopesIodemethylidyne() { // RESULTS ACCORDING PAGE: http://www2.sisweb.com/mstools/isotope.htm double[] massResults = {138.904480, 139.907839}; double[] abundResults = {1.00, .011}; IMolecularFormula molFor = new MolecularFormula(); molFor.addIsotope(builder.newInstance(IIsotope.class, "C")); molFor.addIsotope(builder.newInstance(IIsotope.class, "I")); Assert.assertEquals(2, molFor.getIsotopeCount()); IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(.01); IsotopePattern isoPattern = isotopeGe.getIsotopes(molFor); Assert.assertEquals(2, isoPattern.getNumberOfIsotopes()); Assert.assertEquals(massResults[0], isoPattern.getIsotope(0).getMass(), 0.01); Assert.assertEquals(massResults[1], isoPattern.getIsotope(1).getMass(), 0.01); Assert.assertEquals(abundResults[0], isoPattern.getIsotope(0).getIntensity(), 0.01); Assert.assertEquals(abundResults[1], isoPattern.getIsotope(1).getIntensity(), 0.01); }
@Test public void testGetIsotopes_IMolecularFormula_deprotonate() { IsotopePatternGenerator isogen = new IsotopePatternGenerator(.1); IMolecularFormula mf1 = MolecularFormulaManipulator.getMolecularFormula("C6H12O6", builder); MolecularFormulaManipulator.adjustProtonation(mf1, -1); IsotopePattern ip1 = isogen.getIsotopes(mf1); Assert.assertEquals(1, ip1.getNumberOfIsotopes()); isogen = new IsotopePatternGenerator(.1); IMolecularFormula mf2 = MolecularFormulaManipulator.getMolecularFormula("C6H11O6", builder); IsotopePattern ip2 = isogen.getIsotopes(mf2); Assert.assertEquals(1, ip2.getNumberOfIsotopes()); Assert.assertEquals(ip1.getIsotope(0).getMass(), ip2.getIsotope(0).getMass(), 0.001); }
/** * Calculate isotopes for C10000 (failed in CDK 1.5.12). */ @Test public void testCalculateIsotopesC10000() { IMolecularFormula molFor = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula("C10000", builder); IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(.1); IsotopePattern isos = isotopeGe.getIsotopes(molFor); Assert.assertEquals(44, isos.getNumberOfIsotopes()); for (int i = 0; i < isos.getNumberOfIsotopes(); i++) Assert.assertTrue(isos.getIsotope(i).getMass() > 120085); }
@Test public void testGetIsotopes_IMolecularFormula_Charged() { IsotopePatternGenerator isogen = new IsotopePatternGenerator(.1); IMolecularFormula mfPositive = MolecularFormulaManipulator.getMolecularFormula("C6H11O6Na", builder); mfPositive.setCharge(1); IsotopePattern ip1 = isogen.getIsotopes(mfPositive); Assert.assertEquals(1, ip1.getNumberOfIsotopes()); isogen = new IsotopePatternGenerator(.1); IMolecularFormula mfNeutral = MolecularFormulaManipulator.getMolecularFormula("C6H12O6Na", builder); mfNeutral.setCharge(0); IsotopePattern ip2 = isogen.getIsotopes(mfNeutral); Assert.assertEquals(1, ip2.getNumberOfIsotopes()); Assert.assertNotEquals(ip1.getIsotope(0).getMass(), ip2.getIsotope(0).getMass()); }