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IsotopePatternGeneratorTest.java
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IsotopePatternGeneratorTest.java
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/* Copyright (C) 2007 Miguel Rojasch <miguelrojasch@users.sf.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.formula;
import org.junit.Assert;
import org.junit.Ignore;
import org.junit.Test;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
/**
* Checks the functionality of the IsotopePatternGenerator.
*
* @cdk.module test-formula
*
* @author Miguel Rojas
* @cdk.created 2007-03-01
*/
public class IsotopePatternGeneratorTest extends CDKTestCase {
private final static IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
/**
* Constructor for the IsotopePatternGeneratorTest object
*
*/
public IsotopePatternGeneratorTest() {
super();
}
/**
* A unit test for JUnit.
*
* @return Description of the Return Value
*/
@Test
public void testIsotopePatternGenerator() {
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator();
Assert.assertNotNull(isotopeGe);
}
/**
* A unit test for JUnit.
*
* @return Description of the Return Value
*/
@Test
public void testIsotopePatternGenerator_double() {
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator();
Assert.assertNotNull(isotopeGe);
}
/**
* A unit test for JUnit:
*
* @return Description of the Return Value
*/
@Test
public void testGetIsotopes_IMolecularFormula() {
IMolecularFormula molFor = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula("C41H79N8O3P1", builder);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(.1);
IsotopePattern isos = isotopeGe.getIsotopes(molFor);
Assert.assertEquals(2, isos.getNumberOfIsotopes(), 0.001);
}
/**
* A unit test for JUnit:
*
* @return Description of the Return Value
*/
@Test
public void testGetIsotopes_IMolecularFormula_withoutONE() {
IMolecularFormula molFor = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula("C41H79N8O3P", builder);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(.01);
IsotopePattern isos = isotopeGe.getIsotopes(molFor);
Assert.assertEquals(6, isos.getNumberOfIsotopes(), 0.001);
}
/**
* A unit test for JUnit: Isotopes of the Bromine.
*
* @return Description of the Return Value
*/
@Test
public void testGetIsotopes1() {
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());
}
/**
* 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);
}
/**
* 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);
}
/**
* A unit test for JUnit.
*
* @return Description of the Return Value
*/
@Test
public void testCalculateIsotopesOrthinine() {
// RESULTS ACCORDING PAGE: http://www2.sisweb.com/mstools/isotope.htm
double[] massResults = {133.097720, 134.094750, 134.101079, 134.103990, 135.101959, 135.104430};
double[] abundResults = {1.00, .006, .054, 0.002, 0.004, 0.001};
IMolecularFormula molFor = new MolecularFormula();
molFor.addIsotope(builder.newInstance(IIsotope.class, "C"), 5);
molFor.addIsotope(builder.newInstance(IIsotope.class, "H"), 13);
molFor.addIsotope(builder.newInstance(IIsotope.class, "N"), 2);
molFor.addIsotope(builder.newInstance(IIsotope.class, "O"), 2);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.0010);
IsotopePattern isoPattern = isotopeGe.getIsotopes(molFor);
Assert.assertEquals(6, 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(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);
}
/**
* @cdk.bug 3273205
*/
@Test
public void testCalculateIsotopesMn() {
IMolecularFormula molFor = new MolecularFormula();
molFor.addIsotope(builder.newInstance(IIsotope.class, "Mn"), 1);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.001);
IsotopePattern isoPattern = isotopeGe.getIsotopes(molFor);
Assert.assertEquals(1, isoPattern.getNumberOfIsotopes());
}
/**
* 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);
}
/**
* Calculate isotopes for C20H30Fe2P2S4Cl4 (in CDK 1.5.12, this call
* sometimes returns 34 and sometimes 35 isotopes, non-deterministically).
*/
@Ignore("Non-deterministic test value is bad! This likely depends on our current isotope data which is also bad.")
public void testCalculateIsotopesC20H30Fe2P2S4Cl4() {
IMolecularFormula molFor = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula("C20H30Fe2P2S4Cl4", builder);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(.01);
IsotopePattern isos = isotopeGe.getIsotopes(molFor);
Assert.assertEquals(35, isos.getNumberOfIsotopes());
}
@Test
public void testGeneratorSavesState() {
IsotopePatternGenerator isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mf1 = MolecularFormulaManipulator.getMolecularFormula("C6H12O6", builder);
IsotopePattern ip1 = isogen.getIsotopes(mf1);
Assert.assertEquals(1, ip1.getNumberOfIsotopes());
IMolecularFormula mf2 = MolecularFormulaManipulator.getMolecularFormula("C6H12O6", builder);
IsotopePattern ip2 = isogen.getIsotopes(mf2);
Assert.assertEquals(1, ip2.getNumberOfIsotopes());
}
@Test
public void testGetIsotopes_IMolecularFormula_Charged() {
IsotopePatternGenerator isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mfPositive = MolecularFormulaManipulator.getMolecularFormula("C6H12O6Na", 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());
}
}