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Merge branch 'egon/369-14x-inchiCleaning' into cdk-1.4.x
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@@ -9,3 +9,4 @@ cdk-valencycheck.jar | |
| cdk-test.jar | ||
| cdk-inchi.jar | ||
| cdk-smiles.jar | ||
| cdk-silent.jar | ||
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146 changes: 146 additions & 0 deletions
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src/test/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java
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| /* Copyright (C) 2006 Sam Adams <sea36@users.sf.net> | ||
| * 2007 Rajarshi Guha <rajarshi.guha@gmail.com> | ||
| * 2010,2012 Egon Willighagen <egonw@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.inchi; | ||
|
|
||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
|
|
||
| import net.sf.jniinchi.INCHI_OPTION; | ||
| import net.sf.jniinchi.INCHI_RET; | ||
|
|
||
| import org.junit.Assert; | ||
| import org.junit.Test; | ||
| import org.openscience.cdk.Atom; | ||
| import org.openscience.cdk.AtomContainer; | ||
| import org.openscience.cdk.DefaultChemObjectBuilder; | ||
| import org.openscience.cdk.exception.CDKException; | ||
| import org.openscience.cdk.interfaces.IAtom; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
|
|
||
| /** | ||
| * @cdk.module test-inchi | ||
| */ | ||
| public class InChIGeneratorFactoryTest { | ||
|
|
||
| @Test | ||
| public void testGetInstance() throws CDKException { | ||
| InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance(); | ||
| Assert.assertNotNull(factory); | ||
| } | ||
|
|
||
| /** | ||
| * Because we are not setting any options, we get an Standard InChI. | ||
| */ | ||
| @Test public void testGetInChIGenerator_IAtomContainer() throws Exception { | ||
| IAtomContainer ac = new AtomContainer(); | ||
| IAtom a = new Atom("Cl"); | ||
| a.setImplicitHydrogenCount(1); | ||
| ac.addAtom(a); | ||
| InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(ac); | ||
| Assert.assertEquals(gen.getReturnStatus(), INCHI_RET.OKAY); | ||
| Assert.assertEquals("InChI=1S/ClH/h1H", gen.getInchi()); | ||
| } | ||
|
|
||
| /** | ||
| * Because we are setting an options, we get a non-standard InChI. | ||
| */ | ||
| @Test public void testGetInChIGenerator_IAtomContainer_String() throws Exception { | ||
| IAtomContainer ac = new AtomContainer(); | ||
| IAtom a = new Atom("Cl"); | ||
| a.setImplicitHydrogenCount(1); | ||
| ac.addAtom(a); | ||
| InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(ac, "FixedH"); | ||
| Assert.assertEquals(gen.getReturnStatus(), INCHI_RET.OKAY); | ||
| Assert.assertEquals("InChI=1/ClH/h1H", gen.getInchi()); | ||
| } | ||
|
|
||
| /** | ||
| * Because we are setting no option, we get a Standard InChI. | ||
| */ | ||
| @Test public void testGetInChIGenerator_IAtomContainer_NullString() throws Exception { | ||
| IAtomContainer ac = new AtomContainer(); | ||
| IAtom a = new Atom("Cl"); | ||
| a.setImplicitHydrogenCount(1); | ||
| ac.addAtom(a); | ||
| InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(ac, (String)null); | ||
| Assert.assertEquals(gen.getReturnStatus(), INCHI_RET.OKAY); | ||
| Assert.assertEquals("InChI=1S/ClH/h1H", gen.getInchi()); | ||
| } | ||
|
|
||
| /** | ||
| * Because we are setting an options, we get a non-standard InChI. | ||
| */ | ||
| @Test public void testGetInChIGenerator_IAtomContainer_List() throws Exception { | ||
| IAtomContainer ac = new AtomContainer(); | ||
| IAtom a = new Atom("Cl"); | ||
| a.setImplicitHydrogenCount(1); | ||
| ac.addAtom(a); | ||
| List<INCHI_OPTION> options = new ArrayList<INCHI_OPTION>(); | ||
| options.add(INCHI_OPTION.FixedH); | ||
| InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(ac, options); | ||
| Assert.assertEquals(gen.getReturnStatus(), INCHI_RET.OKAY); | ||
| Assert.assertEquals("InChI=1/ClH/h1H", gen.getInchi()); | ||
| } | ||
|
|
||
| /** | ||
| * Because we are setting an options, we get a non-standard InChI. | ||
| */ | ||
| @Test(expected=IllegalArgumentException.class) | ||
| public void testGetInChIGenerator_IAtomContainer_NullList() throws Exception { | ||
| IAtomContainer ac = new AtomContainer(); | ||
| IAtom a = new Atom("Cl"); | ||
| a.setImplicitHydrogenCount(1); | ||
| ac.addAtom(a); | ||
| InChIGeneratorFactory.getInstance().getInChIGenerator(ac, (List<INCHI_OPTION>)null); | ||
| } | ||
|
|
||
| @Test | ||
| public void testGetInChIToStructure_String_IChemObjectBuilder() throws CDKException { | ||
| InChIToStructure parser = InChIGeneratorFactory.getInstance().getInChIToStructure( | ||
| "InChI=1/ClH/h1H", DefaultChemObjectBuilder.getInstance() | ||
| ); | ||
| Assert.assertNotNull(parser); | ||
| } | ||
|
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| @Test(expected=IllegalArgumentException.class) | ||
| public void testGetInChIToStructure_String_IChemObjectBuilder_NullString() throws CDKException { | ||
| InChIGeneratorFactory.getInstance().getInChIToStructure( | ||
| "InChI=1/ClH/h1H", DefaultChemObjectBuilder.getInstance(), (String)null | ||
| ); | ||
| } | ||
|
|
||
| @Test(expected=IllegalArgumentException.class) | ||
| public void testGetInChIToStructure_String_IChemObjectBuilder_NullList() throws CDKException { | ||
| InChIGeneratorFactory.getInstance().getInChIToStructure( | ||
| "InChI=1/ClH/h1H", DefaultChemObjectBuilder.getInstance(), (List<String>)null | ||
| ); | ||
| } | ||
|
|
||
| /** | ||
| * No options set. | ||
| */ | ||
| @Test public void testGetInChIToStructure_String_IChemObjectBuilder_List() throws CDKException { | ||
| InChIToStructure parser = InChIGeneratorFactory.getInstance().getInChIToStructure( | ||
| "InChI=1/ClH/h1H", DefaultChemObjectBuilder.getInstance(), new ArrayList<String>() | ||
| ); | ||
| Assert.assertNotNull(parser); | ||
| } | ||
| } |
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