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MolecularFormulaManipulatorTest.java
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MolecularFormulaManipulatorTest.java
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/* $Revision$ $Author$ $Date$
*
* 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.tools.manipulator;
import java.io.IOException;
import java.util.List;
import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.formula.MolecularFormula;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesParser;
/**
* Checks the functionality of the MolecularFormulaManipulator.
*
* @cdk.module test-formula
*/
public class MolecularFormulaManipulatorTest extends CDKTestCase {
private final static IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
private IsotopeFactory ifac;
/**
* Constructor for the MolecularFormulaManipulatorTest object.
*
*/
public MolecularFormulaManipulatorTest(){
super();
try {
ifac = IsotopeFactory.getInstance(builder);
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetAtomCount_IMolecularFormula() {
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C") );
formula.addIsotope( builder.newIsotope("H") ,3);
Assert.assertEquals(2, formula.getIsotopeCount());
Assert.assertEquals(4, MolecularFormulaManipulator.getAtomCount(formula));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetElementCount_IMolecularFormula_IElement() {
IMolecularFormula formula = new MolecularFormula();
IIsotope carb = builder.newIsotope("C");
IIsotope flu = builder.newIsotope("F");
IIsotope h1 = builder.newIsotope("H");
IIsotope h2 = builder.newIsotope("H");
h2.setExactMass(2.014101778);
formula.addIsotope( carb ,2);
formula.addIsotope( flu );
formula.addIsotope( h1 ,3);
formula.addIsotope( h2 ,4);
Assert.assertEquals(10, MolecularFormulaManipulator.getAtomCount(formula));
Assert.assertEquals(4, formula.getIsotopeCount());
Assert.assertEquals(3, formula.getIsotopeCount(h1));
Assert.assertEquals(4, formula.getIsotopeCount(h2));
Assert.assertEquals(2, MolecularFormulaManipulator.getElementCount(formula,builder.newElement(carb)));
Assert.assertEquals(1, MolecularFormulaManipulator.getElementCount(formula,builder.newElement(flu)));
Assert.assertEquals(7, MolecularFormulaManipulator.getElementCount(formula,builder.newElement(h1)));
}
/**
* A unit test suite for JUnit. Not null.
*
* @return The test suite
*/
@Test
public void testGetIsotopes_IMolecularFormula_IElement() {
IMolecularFormula formula = new MolecularFormula();
IIsotope carb = builder.newIsotope("C");
IIsotope flu = builder.newIsotope("F");
IIsotope h1 = builder.newIsotope("H");
IIsotope h2 = builder.newIsotope("H");
h2.setExactMass(2.014101778);
formula.addIsotope( carb ,1);
formula.addIsotope( flu );
formula.addIsotope( h1 ,1);
formula.addIsotope( h2 ,2);
List<IIsotope> isotopes = MolecularFormulaManipulator.getIsotopes(formula, builder.newElement("H"));
Assert.assertEquals(2,isotopes.size());
}
/**
* A unit test suite for JUnit. Not null.
*
* @return The test suite
*/
@Test
public void testContainsElement_IMolecularFormula_IElement() {
IMolecularFormula formula = new MolecularFormula();
IIsotope carb = builder.newIsotope("C");
IIsotope flu = builder.newIsotope("F");
IIsotope h1 = builder.newIsotope("H");
IIsotope h2 = builder.newIsotope("H");
h2.setExactMass(2.014101778);
formula.addIsotope( carb ,1);
formula.addIsotope( flu );
formula.addIsotope( h1 ,1);
formula.addIsotope( h2 ,2);
Assert.assertTrue(MolecularFormulaManipulator.containsElement(formula, builder.newElement("C")));
Assert.assertTrue(MolecularFormulaManipulator.containsElement(formula, builder.newElement("H")));
Assert.assertTrue(MolecularFormulaManipulator.containsElement(formula, builder.newElement("F")));
}
/**
* A unit test suite for JUnit. Not null.
*
* @return The test suite
*/
@Test
public void testGetString_IMolecularFormula_Empty() {
String stringMF = MolecularFormulaManipulator.getString(new MolecularFormula());
Assert.assertNotNull(stringMF);
Assert.assertEquals("",stringMF);
}
/**
* A unit test suite for JUnit. Not null.
*
* @return The test suite
*/
@Test
public void testGetString_IMolecularFormula_arrayString_boolean() {
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"), 2);
formula.addIsotope(builder.newIsotope("H"), 2);
Assert.assertEquals("C2H2",MolecularFormulaManipulator.getString(formula));
String[] newOrder = new String[2];
newOrder[0] = "H";
newOrder[1] = "C";
Assert.assertEquals("H2C2",MolecularFormulaManipulator.getString(formula,newOrder,true));
}
/**
* A unit test suite for JUnit. Not null.
*
* @return The test suite
*/
@Test
public void testPutInOrder_arrayString_IMolecularFormula() {
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"), 2);
formula.addIsotope(builder.newIsotope("H"), 2);
String[] newOrder = new String[2];
newOrder[0] = "H";
newOrder[1] = "C";
List<IIsotope> list = MolecularFormulaManipulator.putInOrder(newOrder, formula);
Assert.assertEquals("H",list.get(0).getSymbol());
Assert.assertEquals("C",list.get(1).getSymbol());
newOrder = new String[2];
newOrder[0] = "C";
newOrder[1] = "H";
list = MolecularFormulaManipulator.putInOrder(newOrder, formula);
Assert.assertEquals("C",list.get(0).getSymbol());
Assert.assertEquals("H",list.get(1).getSymbol());
}
/**
* A unit test suite for JUnit. Not null.
*
* @return The test suite
*/
@Test
public void testGetString__String_IMolecularFormula() {
Assert.assertNotNull(MolecularFormulaManipulator.getMolecularFormula("C10H16", new MolecularFormula()));
Assert.assertNotNull(MolecularFormulaManipulator.getMolecularFormula("C10H16", builder));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetString_IMolecularFormula() {
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C"),10);
mf1.addIsotope(builder.newIsotope("H"),16);
Assert.assertEquals("C10H16", MolecularFormulaManipulator.getString(mf1));
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newAtom("H"),16);
mf2.addIsotope(builder.newAtom("C"),10);
Assert.assertEquals("C10H16", MolecularFormulaManipulator.getString(mf2));
Assert.assertEquals(MolecularFormulaManipulator.getString(mf2), MolecularFormulaManipulator.getString(mf1));
}
/**
* @cdk.bug 2276507
*/
@Test
public void testBug2276507() {
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C"), 1);
mf1.addIsotope(builder.newIsotope("H"), 4);
Assert.assertEquals("CH4", MolecularFormulaManipulator.getString(mf1));
}
/**
*
*/
@Test
public void testGetString_IMolecularFormula_boolean() {
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C"), 1);
mf1.addIsotope(builder.newIsotope("H"), 4);
Assert.assertEquals("C1H4", MolecularFormulaManipulator.getString(mf1,true));
}
@Test
public void testGetString_Isotopes() {
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C",12),9);
mf1.addIsotope(builder.newIsotope("C",13),1);
mf1.addIsotope(builder.newIsotope("H"),16);
Assert.assertEquals("C10H16", MolecularFormulaManipulator.getString(mf1));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetMolecularFormula_String_IChemObjectBuilder() {
IMolecularFormula molecularFormula = MolecularFormulaManipulator.getMolecularFormula("C10H16", builder);
Assert.assertEquals(26, MolecularFormulaManipulator.getAtomCount(molecularFormula));
Assert.assertEquals(2, molecularFormula.getIsotopeCount());
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetMolecularFormula_String_IMolecularFormula() {
IMolecularFormula mf1 = new MolecularFormula();
mf1.addIsotope(builder.newIsotope("C"),10);
mf1.addIsotope(builder.newIsotope("H"),16);
Assert.assertEquals(26, MolecularFormulaManipulator.getAtomCount(mf1));
Assert.assertEquals(2, mf1.getIsotopeCount());
IMolecularFormula mf2 = MolecularFormulaManipulator.getMolecularFormula("C11H17",mf1);
Assert.assertEquals(54, MolecularFormulaManipulator.getAtomCount(mf2));
Assert.assertEquals(2, mf2.getIsotopeCount());
}
@Test
public void testGetMajorIsotopeMolecularFormula_String_IChemObjectBuilder() throws Exception {
IMolecularFormula mf2 = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula("C11H17", builder);
Assert.assertEquals(28, MolecularFormulaManipulator.getAtomCount(mf2));
Assert.assertEquals(2, mf2.getIsotopeCount());
IIsotope carbon = IsotopeFactory.getInstance(builder).getMajorIsotope("C");
IIsotope hydrogen = IsotopeFactory.getInstance(builder).getMajorIsotope("H");
double totalMass = carbon.getExactMass()*11;
totalMass += hydrogen.getExactMass()*17;
Assert.assertEquals(totalMass, MolecularFormulaManipulator.getTotalExactMass(mf2), 0.0000001);
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testRemoveElement_IMolecularFormula_IElement() {
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"),1);
IIsotope fl = builder.newIsotope("F");
IIsotope hy2 = builder.newIsotope("H");
IIsotope hy1 = builder.newIsotope("H");
hy2.setExactMass(2.014101778);
formula.addIsotope(fl,1);
formula.addIsotope(hy1,2);
formula.addIsotope(hy2,1);
Assert.assertEquals(4, formula.getIsotopeCount());
formula = MolecularFormulaManipulator.removeElement(formula,builder.newElement("F"));
Assert.assertEquals(3, formula.getIsotopeCount());
Assert.assertEquals(4, MolecularFormulaManipulator.getAtomCount(formula));
formula = MolecularFormulaManipulator.removeElement(formula,builder.newElement("H"));
Assert.assertEquals(1, MolecularFormulaManipulator.getAtomCount(formula));
Assert.assertEquals(1, formula.getIsotopeCount());
}
/**
* A unit test suite for JUnit. Test total Exact Mass.
*
*/
@Test
public void testGetTotalExactMass_IMolecularFormula() throws Exception{
IMolecularFormula formula = new MolecularFormula();
IIsotope carb = builder.newIsotope("C");
carb.setExactMass(12.00);
IIsotope cl = builder.newIsotope("Cl");
cl.setExactMass(34.96885268);
formula.addIsotope(carb);
formula.addIsotope(cl);
double totalExactMass = MolecularFormulaManipulator.getTotalExactMass(formula);
Assert.assertEquals(46.96885268,totalExactMass,0.000001);
}
/**
* A unit test suite for JUnit. Test total Exact Mass.
*
* @throws IOException
* @throws ClassNotFoundException
* @throws CDKException
*/
@Test
public void testGetTotalExactMassWithCharge_IMolecularFormula() throws Exception{
IMolecularFormula formula = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula("CH5O", builder);
double totalExactMass = MolecularFormulaManipulator.getTotalExactMass(formula);
Assert.assertEquals(33.034040,totalExactMass,0.0001);
formula.setCharge(1);
double totalExactMass2 = MolecularFormulaManipulator.getTotalExactMass(formula);
Assert.assertEquals(33.03349,totalExactMass2,0.0001);
}
/**
* A unit test suite for JUnit. Test total Exact Mass.
*
* @throws IOException
* @throws ClassNotFoundException
* @throws CDKException
*/
@Test
public void testGetTotalExactMassWithChargeNeg_IMolecularFormula() throws IOException, ClassNotFoundException, CDKException{
IMolecularFormula formula = MolecularFormulaManipulator.getMajorIsotopeMolecularFormula("H2PO4", builder);
formula.setCharge(-1);
double totalExactMass2 = MolecularFormulaManipulator.getTotalExactMass(formula);
Assert.assertEquals(96.96961875390926,totalExactMass2,0.0001);
}
@Test
public void testGetNaturalExactMass_IMolecularFormula() throws Exception {
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"));
formula.addIsotope(builder.newIsotope("Cl"));
double expectedMass = 0.0;
expectedMass += IsotopeFactory.getInstance(builder).getNaturalMass(builder.newElement("C"));
expectedMass += IsotopeFactory.getInstance(builder).getNaturalMass(builder.newElement("Cl"));
double totalExactMass = MolecularFormulaManipulator.getNaturalExactMass(formula);
Assert.assertEquals(expectedMass, totalExactMass, 0.000001);
}
@Test
public void testGetTotalMassNumber_IMolecularFormula() throws Exception {
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"));
formula.addIsotope(builder.newIsotope("O"));
double totalExactMass = MolecularFormulaManipulator.getTotalMassNumber(formula);
Assert.assertEquals(28, totalExactMass, 0.000001);
}
@Test
public void testGetMajorIsotopeMass_IMolecularFormula() throws Exception {
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"));
formula.addIsotope(builder.newIsotope("H"), 4);
double expectedMass = 0.0;
expectedMass += IsotopeFactory.getInstance(builder).getMajorIsotope("C").getExactMass();
expectedMass += 4.0*IsotopeFactory.getInstance(builder).getMajorIsotope("H").getExactMass();
double totalExactMass = MolecularFormulaManipulator.getMajorIsotopeMass(formula);
Assert.assertEquals(expectedMass, totalExactMass, 0.000001);
}
/**
* A unit test suite for JUnit. Test total Exact Mass. It is
* necessary to have added the corresponding isotope before to calculate
* the exact mass.
*
*/
@Test
public void testBug_1944604() throws Exception{
IMolecularFormula formula = new MolecularFormula();
IIsotope carb = builder.newIsotope("C");
formula.addIsotope(carb);
Assert.assertEquals("C1",MolecularFormulaManipulator.getString(formula,true));
double totalExactMass = MolecularFormulaManipulator.getTotalExactMass(formula);
Assert.assertEquals(12.0,totalExactMass,0.000001);
}
/**
* A unit test suite for JUnit. Test total natural abundance.
*
*/
@Test
public void testGetTotalNaturalAbundance_IMolecularFormula() throws Exception{
IMolecularFormula formula = new MolecularFormula();
IIsotope carb = builder.newIsotope("C");
carb.setNaturalAbundance(98.93);
IIsotope cl = builder.newIsotope("Cl");
cl.setNaturalAbundance(75.78);
formula.addIsotope(carb);
formula.addIsotope(cl);
double totalAbudance = MolecularFormulaManipulator.getTotalNaturalAbundance(formula);
Assert.assertEquals(0.74969154,totalAbudance,0.000001);
}
/**
* A unit test suite for JUnit. Test total natural abundance.
*
*/
@Test
public void testGetTotalNaturalAbundance_IMolecularFormula2() throws Exception{
IMolecularFormula formula1 = new MolecularFormula();
IIsotope br1 = builder.newIsotope("Br");
br1.setNaturalAbundance(49.31);
IIsotope br2 = builder.newIsotope("Br");
br2.setNaturalAbundance(50.69);
formula1.addIsotope(br1);
formula1.addIsotope(br2);
Assert.assertEquals(2,formula1.getIsotopeCount(),0.000001);
double totalAbudance = MolecularFormulaManipulator.getTotalNaturalAbundance(formula1);
Assert.assertEquals(0.24995235,totalAbudance,0.000001);
}
@Test
public void testGetTotalNaturalAbundance_IMolecularFormula3() throws Exception{
IMolecularFormula formula2 = new MolecularFormula();
IIsotope br1 = builder.newIsotope("Br");
br1.setNaturalAbundance(50.69);
IIsotope br2 = builder.newIsotope("Br");
br2.setNaturalAbundance(50.69);
formula2.addIsotope(br1);
formula2.addIsotope(br2);
Assert.assertEquals(1,formula2.getIsotopeCount(),0.000001);
double totalAbudance = MolecularFormulaManipulator.getTotalNaturalAbundance(formula2);
Assert.assertEquals(0.25694761,totalAbudance,0.000001);
}
@Test
public void testGetTotalNaturalAbundance_IMolecularFormula4() throws Exception{
IMolecularFormula formula2 = new MolecularFormula();
IIsotope br1 = builder.newIsotope("Br");
br1.setNaturalAbundance(50.69);
formula2.addIsotope(br1);
formula2.addIsotope(br1);
Assert.assertEquals(1,formula2.getIsotopeCount());
double totalAbudance = MolecularFormulaManipulator.getTotalNaturalAbundance(formula2);
Assert.assertEquals(0.25694761,totalAbudance,0.000001);
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetDBE_IMolecularFormula()throws Exception{
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"),10);
formula.addIsotope(builder.newIsotope("H"),22);
Assert.assertEquals(0.0,MolecularFormulaManipulator.getDBE(formula), 0.01);
formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"),10);
formula.addIsotope(builder.newIsotope("H"),16);
Assert.assertEquals(3.0,MolecularFormulaManipulator.getDBE(formula), 0.01);
formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"),10);
formula.addIsotope(builder.newIsotope("H"),16);
formula.addIsotope(builder.newIsotope("O"));
Assert.assertEquals(3.0,MolecularFormulaManipulator.getDBE(formula), 0.01);
formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"),10);
formula.addIsotope(builder.newIsotope("H"),19);
formula.addIsotope(builder.newIsotope("N"));
Assert.assertEquals(2.0,MolecularFormulaManipulator.getDBE(formula), 0.01);
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetHTML_IMolecularFormula() {
MolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"),8);
formula.addIsotope(builder.newIsotope("H"),10);
formula.addIsotope(builder.newIsotope("Cl"),2);
formula.addIsotope(builder.newIsotope("O"),2);
Assert.assertEquals("C<sub>8</sub>H<sub>10</sub>O<sub>2</sub>Cl<sub>2</sub>", MolecularFormulaManipulator.getHTML(formula));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetHTML_IMolecularFormula_boolean_boolean() {
MolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"),10);
Assert.assertEquals("C<sub>10</sub>", MolecularFormulaManipulator.getHTML(formula,true,false));
formula.setCharge(1);
Assert.assertEquals("C<sub>10</sub><sup>1+</sup>", MolecularFormulaManipulator.getHTML(formula,true,false));
formula.setCharge(formula.getCharge() - 2);
Assert.assertEquals("C<sub>10</sub><sup>1-</sup>", MolecularFormulaManipulator.getHTML(formula,true,false));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetHTML_IMolecularFormulaWhitIsotope() {
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));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetHTML_IMolecularFormulaWhitIsotopeAndCharge() {
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>1+</sup>", MolecularFormulaManipulator.getHTML(formula,true,true));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetMolecularFormula_IAtomContainer(){
IAtomContainer ac = builder.newAtomContainer();
ac.addAtom(builder.newAtom("C"));
ac.addAtom(builder.newAtom("C"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
IMolecularFormula mf1 = MolecularFormulaManipulator.getMolecularFormula(ac);
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newIsotope("C"),2);
mf2.addIsotope(builder.newIsotope("H"),4);
Assert.assertEquals(MolecularFormulaManipulator.getAtomCount(mf2), MolecularFormulaManipulator.getAtomCount(mf1));
Assert.assertEquals(mf2.getIsotopeCount(), mf1.getIsotopeCount());
IElement elemC = builder.newElement("C");
IElement elemH = builder.newElement("H");
Assert.assertEquals(mf2.getIsotopeCount(builder.newIsotope(elemC)), mf1.getIsotopeCount(builder.newIsotope(elemC)));
Assert.assertEquals(mf2.getIsotopeCount(builder.newIsotope(elemH)), mf1.getIsotopeCount(builder.newIsotope(elemH)));
Assert.assertEquals(MolecularFormulaManipulator.getElementCount(mf2, elemC), MolecularFormulaManipulator.getElementCount(mf1,elemC));
Assert.assertEquals(MolecularFormulaManipulator.getElementCount(mf2, elemH), MolecularFormulaManipulator.getElementCount(mf1,elemH));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetMolecularFormula_IAtomContainer_withCharge(){
IAtomContainer ac = builder.newAtomContainer();
ac.addAtom(builder.newAtom("C"));
ac.getAtom(0).setFormalCharge(1);
ac.addAtom(builder.newAtom("C"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
IMolecularFormula mf1 = MolecularFormulaManipulator.getMolecularFormula(ac);
Assert.assertEquals(1, mf1.getCharge(),0.000);
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetMolecularFormula_IAtomContainer_IMolecularFormula(){
IAtomContainer ac = builder.newAtomContainer();
ac.addAtom(builder.newAtom("C"));
ac.addAtom(builder.newAtom("C"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
IMolecularFormula mf1 = MolecularFormulaManipulator.getMolecularFormula(ac,new MolecularFormula());
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newIsotope("C"),2);
mf2.addIsotope(builder.newIsotope("H"),4);
Assert.assertEquals(MolecularFormulaManipulator.getAtomCount(mf2), MolecularFormulaManipulator.getAtomCount(mf1));
Assert.assertEquals(mf2.getIsotopeCount(), mf1.getIsotopeCount());
IElement elemC = builder.newElement("C");
IElement elemH = builder.newElement("H");
Assert.assertEquals(mf2.getIsotopeCount(builder.newIsotope(elemC)), mf1.getIsotopeCount(builder.newIsotope(elemC)));
Assert.assertEquals(mf2.getIsotopeCount(builder.newIsotope(elemH)), mf1.getIsotopeCount(builder.newIsotope(elemH)));
Assert.assertEquals(MolecularFormulaManipulator.getElementCount(mf2, elemC), MolecularFormulaManipulator.getElementCount(mf1,elemC));
Assert.assertEquals(MolecularFormulaManipulator.getElementCount(mf2, elemH), MolecularFormulaManipulator.getElementCount(mf1,elemH));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetMolecularFormula_IAtomContainerIMolecularFormula_2(){
IAtomContainer ac = builder.newAtomContainer();
ac.addAtom(builder.newAtom("C"));
ac.addAtom(builder.newAtom("C"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
IMolecularFormula mf0 = new MolecularFormula();
mf0.addIsotope(builder.newIsotope("C"),2);
mf0.addIsotope(builder.newIsotope("H"),5);
IMolecularFormula mf1 = MolecularFormulaManipulator.getMolecularFormula(ac,mf0);
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newIsotope("C"),4);
mf2.addIsotope(builder.newIsotope("H"),9);
Assert.assertEquals(MolecularFormulaManipulator.getAtomCount(mf2), MolecularFormulaManipulator.getAtomCount(mf1));
Assert.assertEquals(mf2.getIsotopeCount(), mf1.getIsotopeCount());
IElement elemC = builder.newElement("C");
IElement elemH = builder.newElement("H");
Assert.assertEquals(mf2.getIsotopeCount(builder.newIsotope(elemC)), mf1.getIsotopeCount(builder.newIsotope(elemC)));
Assert.assertEquals(mf2.getIsotopeCount(builder.newIsotope(elemH)), mf1.getIsotopeCount(builder.newIsotope(elemH)));
Assert.assertEquals(MolecularFormulaManipulator.getElementCount(mf2, elemC), MolecularFormulaManipulator.getElementCount(mf1,elemC));
Assert.assertEquals(MolecularFormulaManipulator.getElementCount(mf2, elemH), MolecularFormulaManipulator.getElementCount(mf1,elemH));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetAtomContainer_IMolecularFormula(){
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newIsotope("C"),2);
mf2.addIsotope(builder.newIsotope("H"),4);
IAtomContainer ac = MolecularFormulaManipulator.getAtomContainer(mf2);
Assert.assertEquals(6, ac.getAtomCount());
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testGetAtomContainer_IMolecularFormula_IAtomContainer(){
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newIsotope("C"),2);
mf2.addIsotope(builder.newIsotope("H"),4);
IAtomContainer ac = MolecularFormulaManipulator.getAtomContainer(mf2,builder.newAtomContainer());
Assert.assertEquals(6, ac.getAtomCount());
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testMolecularFormulaIAtomContainer_to_IAtomContainer2(){
IAtomContainer ac = builder.newAtomContainer();
ac.addAtom(builder.newAtom("C"));
ac.addAtom(builder.newAtom("C"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
ac.addAtom(builder.newAtom("H"));
IMolecularFormula mf2 = new MolecularFormula();
mf2.addIsotope(builder.newIsotope("C"),2);
mf2.addIsotope(builder.newIsotope("H"),4);
IAtomContainer ac2 = MolecularFormulaManipulator.getAtomContainer(mf2,builder.newAtomContainer());
Assert.assertEquals(ac2.getAtomCount(), ac2.getAtomCount());
Assert.assertEquals(ac2.getAtom(0).getSymbol(),ac2.getAtom(0).getSymbol());
Assert.assertEquals(ac2.getAtom(5).getSymbol(),ac2.getAtom(5).getSymbol());
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testElements_IMolecularFormula(){
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"),1);
formula.addIsotope(builder.newIsotope("H"),2);
IIsotope br1 = builder.newIsotope("Br");
br1.setNaturalAbundance(50.69);
formula.addIsotope(br1);
IIsotope br2 = builder.newIsotope("Br");
br2.setNaturalAbundance(50.69);
formula.addIsotope(br2);
List<IElement> elements = MolecularFormulaManipulator.elements(formula);
Assert.assertEquals(5, MolecularFormulaManipulator.getAtomCount(formula));
Assert.assertEquals(3, elements.size());
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testCompare_Charge(){
IMolecularFormula formula1 = new MolecularFormula();
formula1.addIsotope(builder.newIsotope("C"),1);
formula1.addIsotope(builder.newIsotope("H"),2);
IMolecularFormula formula2 = new MolecularFormula();
formula2.addIsotope(builder.newIsotope("C"),1);
formula2.addIsotope(builder.newIsotope("H"),2);
IMolecularFormula formula3 = new MolecularFormula();
formula3.addIsotope(builder.newIsotope("C"),1);
formula3.addIsotope(builder.newIsotope("H"),2);
formula3.setCharge(0);
Assert.assertTrue(MolecularFormulaManipulator.compare(formula1, formula2));
Assert.assertFalse(MolecularFormulaManipulator.compare(formula1, formula3));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testCompare_NumberIsotope(){
IMolecularFormula formula1 = new MolecularFormula();
formula1.addIsotope(builder.newIsotope("C"),1);
formula1.addIsotope(builder.newIsotope("H"),2);
IMolecularFormula formula2 = new MolecularFormula();
formula2.addIsotope(builder.newIsotope("C"),1);
formula2.addIsotope(builder.newIsotope("H"),2);
IMolecularFormula formula3 = new MolecularFormula();
formula3.addIsotope(builder.newIsotope("C"),1);
formula3.addIsotope(builder.newIsotope("H"),3);
Assert.assertTrue(MolecularFormulaManipulator.compare(formula1, formula2));
Assert.assertFalse(MolecularFormulaManipulator.compare(formula1, formula3));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testCompare_IMolecularFormula_IMolecularFormula(){
IMolecularFormula formula1 = new MolecularFormula();
formula1.addIsotope(builder.newIsotope("C"),1);
formula1.addIsotope(builder.newIsotope("H"),2);
IMolecularFormula formula2 = new MolecularFormula();
formula2.addIsotope(builder.newIsotope("C"),1);
formula2.addIsotope(builder.newIsotope("H"),2);
IMolecularFormula formula3 = new MolecularFormula();
formula3.addIsotope(builder.newIsotope("C"),1);
IIsotope hyd = builder.newIsotope("H");
hyd.setExactMass(2.002334234);
formula3.addIsotope(hyd,2);
Assert.assertTrue(MolecularFormulaManipulator.compare(formula1, formula2));
Assert.assertFalse(MolecularFormulaManipulator.compare(formula1, formula3));
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test public void testGetHeavyElements_IMolecularFormula() {
IMolecularFormula formula = new MolecularFormula();
formula.addIsotope(builder.newIsotope("C"),10);
formula.addIsotope(builder.newIsotope("H"),16);
Assert.assertEquals(1, MolecularFormulaManipulator.getHeavyElements(formula).size());
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test public void testGetHeavyElements_IMolecularFormula_2() {
IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula("CH3OH", builder);
Assert.assertEquals(2, MolecularFormulaManipulator.getHeavyElements(formula).size());
}
/**
* A unit test suite for JUnit. Not null.
*
* @return The test suite
*/
@Test
public void testGenerateOrderEle() {
String[] listElements = new String[]{
"C", "H", "O", "N", "Si", "P", "S", "F", "Cl",
"Br", "I", "Sn", "B", "Pb", "Tl", "Ba", "In", "Pd",
"Pt", "Os", "Ag", "Zr", "Se", "Zn", "Cu", "Ni", "Co",
"Fe", "Cr", "Ti", "Ca", "K", "Al", "Mg", "Na", "Ce",
"Hg", "Au", "Ir", "Re", "W", "Ta", "Hf", "Lu", "Yb",
"Tm", "Er", "Ho", "Dy", "Tb", "Gd", "Eu", "Sm", "Pm",
"Nd", "Pr", "La", "Cs", "Xe", "Te", "Sb", "Cd", "Rh",
"Ru", "Tc", "Mo", "Nb", "Y", "Sr", "Rb", "Kr", "As",
"Ge", "Ga", "Mn", "V", "Sc", "Ar", "Ne", "Be", "Li",
"Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac",
"Th", "Pa", "U", "Np", "Pu","R"};
String[] listGenerated = MolecularFormulaManipulator.generateOrderEle();
Assert.assertEquals(listElements.length,listGenerated.length);
for(int i = 0 ; i < listElements.length; i++)
Assert.assertEquals(listElements[i],listGenerated[i]);
}
/**
* A unit test suite for JUnit. Not null.
* TODO: REACT: Introduce method
*
* @return The test suite
* @cdk.bug 2672696
*/
@Test
public void testGetHillString_IMolecularFormula() {
IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula("CH3OH", builder);
String listGenerated = MolecularFormulaManipulator.getHillString(formula);
Assert.assertEquals("CH4O", listGenerated);
formula = MolecularFormulaManipulator.getMolecularFormula("CH3CH2Br", builder);
listGenerated = MolecularFormulaManipulator.getHillString(formula);
Assert.assertEquals("C2H5Br", listGenerated);
formula = MolecularFormulaManipulator.getMolecularFormula("HCl", builder);
listGenerated = MolecularFormulaManipulator.getHillString(formula);
Assert.assertEquals("ClH", listGenerated);
formula = MolecularFormulaManipulator.getMolecularFormula("HBr", builder);
listGenerated = MolecularFormulaManipulator.getHillString(formula);
Assert.assertEquals("BrH", listGenerated);
}
/**
* @cdk.bug 1944604
* @throws InvalidSmilesException