/** * Clones this IsotopePattern object and its content. * * @return The cloned object */ @Override public Object clone() throws CloneNotSupportedException { IsotopePattern isoClone = new IsotopePattern(); IsotopeContainer isoHighest = getMonoIsotope(); for (IsotopeContainer isoContainer : isotopeCList) { if (isoHighest.equals(isoContainer)) isoClone.setMonoIsotope((IsotopeContainer) isoContainer.clone()); else isoClone.addIsotope((IsotopeContainer) isoContainer.clone()); } isoClone.setCharge(getCharge()); return isoClone; } }
/** * Sets the parameters attribute of the IsotopePatternRule object. * * @param params The new parameters value * @throws CDKException Description of the Exception * * @see #getParameters */ @Override public void setParameters(Object[] params) throws CDKException { if (params.length != 2) throw new CDKException("IsotopePatternRule expects two parameter"); if (!(params[0] instanceof List)) throw new CDKException("The parameter one must be of type List<Double[]>"); if (!(params[1] instanceof Double)) throw new CDKException("The parameter two must be of type Double"); pattern = new IsotopePattern(); for (double[] listISO : (List<double[]>) params[0]) { pattern.addIsotope(new IsotopeContainer(listISO[0], listISO[1])); } is.seTolerance((Double) params[1]); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testAddIsotope_IsotopeContainer() { IsotopePattern isoP = new IsotopePattern(); isoP.addIsotope(new IsotopeContainer()); Assert.assertNotNull(isoP); }
isoNormalized.setMonoIsotope(icClone); else isoNormalized.addIsotope(icClone);
if (isopattern.getIsotopes().get(i).getIntensity() >= (minIntensity)) { IsotopeContainer container = new IsotopeContainer(isopattern.getIsotopes().get(i)); sortedIsoPattern.addIsotope(container);
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testGetIsotopes() { IsotopePattern isoP = new IsotopePattern(); IsotopeContainer iso1 = new IsotopeContainer(); isoP.setMonoIsotope(iso1); IsotopeContainer iso2 = new IsotopeContainer(); isoP.addIsotope(iso2); Assert.assertEquals(iso1, isoP.getIsotopes().get(0)); Assert.assertEquals(iso2, isoP.getIsotopes().get(1)); }
current = new IsotopePattern(); for (IsotopeContainer container : additional) current.addIsotope(container); } else { for (IsotopeContainer container : current.getIsotopes()) { current.addIsotope(container);
/** * 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); }
/** * Junit test * * @throws Exception */ @Test public void testSortByIntensity_IsotopePattern() { IsotopePattern spExp = new IsotopePattern(); spExp.setMonoIsotope(new IsotopeContainer(157.07503, 0.0001)); spExp.addIsotope(new IsotopeContainer(156.07770, 1)); spExp.addIsotope(new IsotopeContainer(157.08059, 0.0003)); spExp.addIsotope(new IsotopeContainer(158.08135, 0.002)); spExp.setCharge(1); IsotopePattern isoNorma = IsotopePatternManipulator.sortByIntensity(spExp); List<IsotopeContainer> listISO = isoNorma.getIsotopes(); Assert.assertEquals(156.07770, isoNorma.getMonoIsotope().getMass(), 0.00001); Assert.assertEquals(156.07770, listISO.get(0).getMass(), 0.00001); Assert.assertEquals(158.08135, listISO.get(1).getMass(), 0.00001); Assert.assertEquals(157.08059, listISO.get(2).getMass(), 0.00001); Assert.assertEquals(157.07503, listISO.get(3).getMass(), 0.00001); Assert.assertEquals(1, isoNorma.getMonoIsotope().getIntensity(), 0.00001); Assert.assertEquals(1, listISO.get(0).getIntensity(), 0.00001); Assert.assertEquals(0.002, listISO.get(1).getIntensity(), 0.00001); Assert.assertEquals(0.0003, listISO.get(2).getIntensity(), 0.001); Assert.assertEquals(0.0001, listISO.get(3).getIntensity(), 0.00001); Assert.assertEquals(1, isoNorma.getCharge(), 0.00001); }
/** * Junit test * * @throws Exception */ @Test public void testSortAndNormalizedByIntensity_IsotopePattern() { IsotopePattern spExp = new IsotopePattern(); spExp.addIsotope(new IsotopeContainer(157.07503, 0.0002)); spExp.setMonoIsotope(new IsotopeContainer(156.07770, 2)); spExp.addIsotope(new IsotopeContainer(158.08135, 0.004)); spExp.addIsotope(new IsotopeContainer(157.08059, 0.0006)); spExp.setCharge(1); IsotopePattern isoNorma = IsotopePatternManipulator.sortAndNormalizedByIntensity(spExp); List<IsotopeContainer> listISO = isoNorma.getIsotopes(); Assert.assertEquals(156.07770, isoNorma.getMonoIsotope().getMass(), 0.00001); Assert.assertEquals(156.07770, listISO.get(0).getMass(), 0.00001); Assert.assertEquals(158.08135, listISO.get(1).getMass(), 0.00001); Assert.assertEquals(157.08059, listISO.get(2).getMass(), 0.00001); Assert.assertEquals(157.07503, listISO.get(3).getMass(), 0.00001); Assert.assertEquals(1, isoNorma.getMonoIsotope().getIntensity(), 0.00001); Assert.assertEquals(1, listISO.get(0).getIntensity(), 0.00001); Assert.assertEquals(0.002, listISO.get(1).getIntensity(), 0.00001); Assert.assertEquals(0.0003, listISO.get(2).getIntensity(), 0.00001); Assert.assertEquals(0.0001, listISO.get(3).getIntensity(), 0.00001); Assert.assertEquals(1, isoNorma.getCharge(), 0.001); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testGetNumberOfIsotopes() { IsotopePattern isoP = new IsotopePattern(); IsotopeContainer iso1 = new IsotopeContainer(); isoP.setMonoIsotope(iso1); IsotopeContainer iso2 = new IsotopeContainer(); isoP.addIsotope(iso2); Assert.assertEquals(2, isoP.getNumberOfIsotopes()); }
/** * 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); }
/** * Junit test * * @throws Exception */ @Test public void testNormalize_IsotopePattern() { IsotopePattern spExp = new IsotopePattern(); spExp.setMonoIsotope(new IsotopeContainer(156.07770, 2)); spExp.addIsotope(new IsotopeContainer(157.08059, 0.0006)); spExp.addIsotope(new IsotopeContainer(157.07503, 0.0002)); spExp.addIsotope(new IsotopeContainer(158.08135, 0.004)); spExp.setCharge(1); IsotopePattern isoNorma = IsotopePatternManipulator.normalize(spExp); List<IsotopeContainer> listISO = isoNorma.getIsotopes(); Assert.assertEquals(1, isoNorma.getMonoIsotope().getIntensity(), 0.00001); Assert.assertEquals(1, listISO.get(0).getIntensity(), 0.00001); Assert.assertEquals(0.0003, listISO.get(1).getIntensity(), 0.00001); Assert.assertEquals(0.0001, listISO.get(2).getIntensity(), 0.00001); Assert.assertEquals(0.002, listISO.get(3).getIntensity(), 0.00001); Assert.assertEquals(156.07770, isoNorma.getMonoIsotope().getMass(), 0.00001); Assert.assertEquals(156.07770, listISO.get(0).getMass(), 0.00001); Assert.assertEquals(157.08059, listISO.get(1).getMass(), 0.00001); Assert.assertEquals(157.07503, listISO.get(2).getMass(), 0.00001); Assert.assertEquals(158.08135, listISO.get(3).getMass(), 0.00001); Assert.assertEquals(1, isoNorma.getCharge(), 0.00001); }
public void testSortByMass_IsotopePattern() { IsotopePattern spExp = new IsotopePattern(); spExp.addIsotope(new IsotopeContainer(157.07503, 0.0002)); spExp.setMonoIsotope(new IsotopeContainer(156.07770, 2)); spExp.addIsotope(new IsotopeContainer(158.08135, 0.004)); spExp.addIsotope(new IsotopeContainer(157.08059, 0.0006)); spExp.setCharge(1);
/** * 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); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testClone() throws Exception { 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)); spExp.setCharge(1); IsotopePattern clone = (IsotopePattern) spExp.clone(); Assert.assertEquals(156.07770, clone.getMonoIsotope().getMass(), 0.001); Assert.assertEquals(156.07770, clone.getIsotopes().get(0).getMass(), 0.001); Assert.assertEquals(157.07503, clone.getIsotopes().get(1).getMass(), 0.001); Assert.assertEquals(157.08059, clone.getIsotopes().get(2).getMass(), 0.001); Assert.assertEquals(158.08135, clone.getIsotopes().get(3).getMass(), 0.001); Assert.assertEquals(1, clone.getMonoIsotope().getIntensity(), 0.001); Assert.assertEquals(1, clone.getIsotopes().get(0).getIntensity(), 0.001); Assert.assertEquals(0.0004, clone.getIsotopes().get(1).getIntensity(), 0.001); Assert.assertEquals(0.0003, clone.getIsotopes().get(2).getIntensity(), 0.001); Assert.assertEquals(0.002, clone.getIsotopes().get(3).getIntensity(), 0.001); Assert.assertEquals(1, clone.getCharge(), 0.001); }
/** * 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)); }