/** * Constructor for the IsotopePatternRule object. */ public IsotopePatternRule() { isotopeGe = new IsotopePatternGenerator(0.01); is = new IsotopePatternSimilarity(); is.seTolerance(toleranceMass); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testIsotopePatternSimilarity() { IsotopePatternSimilarity is = new IsotopePatternSimilarity(); Assert.assertNotNull(is); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testSeTolerance_double() { IsotopePatternSimilarity is = new IsotopePatternSimilarity(); is.seTolerance(0.001); Assert.assertNotNull(is); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testGetTolerance() { IsotopePatternSimilarity is = new IsotopePatternSimilarity(); is.seTolerance(0.001); Assert.assertEquals(0.001, is.getTolerance(), 0.000001); }
/** * Real example. Lipid PC * * @throws Exception */ @Test public void testExperiment() { IsotopePattern spExp = new IsotopePattern(); spExp.setMonoIsotope(new IsotopeContainer(762.6006, 124118304)); spExp.addIsotope(new IsotopeContainer(763.6033, 57558840)); spExp.addIsotope(new IsotopeContainer(764.6064, 15432262)); spExp.setCharge(1.0); IMolecularFormula formula = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula("C42H85NO8P", SilentChemObjectBuilder.getInstance()); IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.01); IsotopePattern patternIsoPredicted = isotopeGe.getIsotopes(formula); IsotopePatternSimilarity is = new IsotopePatternSimilarity(); double score = is.compare(spExp, patternIsoPredicted); Assert.assertEquals(0.97, score, .01); }
/** * Histidine example * * @throws Exception */ @Test public void testCompare_IsotopePattern_IsotopePattern() { IsotopePatternSimilarity is = new IsotopePatternSimilarity(); IsotopePattern spExp = new IsotopePattern(); spExp.setMonoIsotope(new IsotopeContainer(156.07770, 1)); spExp.addIsotope(new IsotopeContainer(157.07503, 0.0004)); spExp.addIsotope(new IsotopeContainer(157.08059, 0.0003)); spExp.addIsotope(new IsotopeContainer(158.08135, 0.002)); IMolecularFormula formula = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula("C6H10N3O2", builder); IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.1); IsotopePattern patternIsoPredicted = isotopeGe.getIsotopes(formula); IsotopePattern patternIsoNormalize = IsotopePatternManipulator.normalize(patternIsoPredicted); double score = is.compare(spExp, patternIsoNormalize); Assert.assertNotSame(0.0, score); }
/** * Histidine example * * @throws Exception */ @Test public void testSelectingMF() { IsotopePatternSimilarity is = new IsotopePatternSimilarity(); IsotopePattern spExp = new IsotopePattern(); spExp.setCharge(1); spExp.setMonoIsotope(new IsotopeContainer(156.07770, 1)); spExp.addIsotope(new IsotopeContainer(157.07503, 0.0101)); spExp.addIsotope(new IsotopeContainer(157.08059, 0.074)); spExp.addIsotope(new IsotopeContainer(158.08135, 0.0024)); double score = 0; String mfString = ""; String[] listMF = {"C4H8N6O", "C2H12N4O4", "C3H12N2O5", "C6H10N3O2", "CH10N5O4", "C4H14NO5"}; for (int i = 0; i < listMF.length; i++) { IMolecularFormula formula = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula(listMF[i], builder); IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.01); IsotopePattern patternIsoPredicted = isotopeGe.getIsotopes(formula); IsotopePattern patternIsoNormalize = IsotopePatternManipulator.normalize(patternIsoPredicted); double tempScore = is.compare(spExp, patternIsoNormalize); if (score < tempScore) { mfString = MolecularFormulaManipulator.getString(formula); score = tempScore; } } Assert.assertEquals("C6H10N3O2", mfString); }