1 /* Copyright (C) 2018 Jeffrey Plante (Lhasa Limited) <Jeffrey.Plante@lhasalimited.org> 2 * 3 * This program is free software; you can redistribute it and/or 4 * modify it under the terms of the GNU Lesser General Public License 5 * as published by the Free Software Foundation; either version 2.1 6 * of the License, or (at your option) any later version. 7 * 8 * This program is distributed in the hope that it will be useful, 9 * but WITHOUT ANY WARRANTY; without even the implied warranty of 10 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 11 * GNU Lesser General Public License for more details. 12 * 13 * You should have received a copy of the GNU Lesser General Public License 14 * along with this program; if not, write to the Free Software 15 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. 16 */ 17 package org.openscience.cdk.qsar.descriptors.molecular; 18 19 import static org.junit.Assert.*; 20 21 import java.util.Map; 22 23 import org.junit.Test; 24 import org.openscience.cdk.aromaticity.Aromaticity; 25 import org.openscience.cdk.exception.CDKException; 26 import org.openscience.cdk.interfaces.IAtomContainer; 27 import org.openscience.cdk.qsar.DescriptorSpecification; 28 import org.openscience.cdk.qsar.DescriptorValue; 29 import org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor; 30 import org.openscience.cdk.qsar.result.DoubleResult; 31 import org.openscience.cdk.silent.SilentChemObjectBuilder; 32 import org.openscience.cdk.smiles.SmilesParser; 33 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; 34 35 public class JPlogPDescriptorTest { 36 37 static SmilesParser parser = null; 38 39 @Test testPyridine()40 public void testPyridine() throws CDKException { 41 parser = new SmilesParser(SilentChemObjectBuilder.getInstance()); 42 IAtomContainer struct = parseSmiles("c1ncccc1"); 43 JPlogPDescriptor desc = new JPlogPDescriptor(); 44 DescriptorValue answer = desc.calculate(struct); 45 DoubleResult result = (DoubleResult) answer.getValue(); 46 double output = result.doubleValue(); 47 assertEquals(0.9, output, 0.1); 48 } 49 50 @Test testPropionicAcid()51 public void testPropionicAcid() throws CDKException { 52 parser = new SmilesParser(SilentChemObjectBuilder.getInstance()); 53 IAtomContainer struct = parseSmiles("CCC(=O)O"); 54 JPlogPDescriptor desc = new JPlogPDescriptor(); 55 DescriptorValue answer = desc.calculate(struct); 56 DoubleResult result = (DoubleResult) answer.getValue(); 57 double output = result.doubleValue(); 58 assertEquals(0.3, output, 0.1); 59 } 60 61 @Test testAcetonitrile()62 public void testAcetonitrile() throws CDKException { 63 parser = new SmilesParser(SilentChemObjectBuilder.getInstance()); 64 IAtomContainer struct = parseSmiles("CC#N"); 65 JPlogPDescriptor desc = new JPlogPDescriptor(); 66 DescriptorValue answer = desc.calculate(struct); 67 DoubleResult result = (DoubleResult) answer.getValue(); 68 double output = result.doubleValue(); 69 assertEquals(0.4, output, 0.1); 70 } 71 72 @Test testAniline()73 public void testAniline() throws CDKException { 74 parser = new SmilesParser(SilentChemObjectBuilder.getInstance()); 75 IAtomContainer struct = parseSmiles("Nc1ccccc1"); 76 JPlogPDescriptor desc = new JPlogPDescriptor(); 77 DescriptorValue answer = desc.calculate(struct); 78 DoubleResult result = (DoubleResult) answer.getValue(); 79 double output = result.doubleValue(); 80 assertEquals(1.2, output, 0.1); 81 } 82 83 @Test testFluorobenzene()84 public void testFluorobenzene() throws CDKException { 85 parser = new SmilesParser(SilentChemObjectBuilder.getInstance()); 86 IAtomContainer struct = parseSmiles("Fc1ccccc1"); 87 JPlogPDescriptor desc = new JPlogPDescriptor(); 88 DescriptorValue answer = desc.calculate(struct); 89 DoubleResult result = (DoubleResult) answer.getValue(); 90 double output = result.doubleValue(); 91 assertEquals(2.0, output, 0.1); 92 } 93 94 @Test testSimpleTextFields()95 public void testSimpleTextFields() { 96 JPlogPDescriptor desc = new JPlogPDescriptor(); 97 DescriptorSpecification specification = desc.getSpecification(); 98 String name = desc.getDescriptorNames()[0]; 99 assertEquals("JPlogP developed at Lhasa Limited www.lhasalimited.org", 100 specification.getSpecificationReference()); 101 assertEquals("Jeffrey Plante - Lhasa Limited", specification.getImplementationVendor()); 102 assertEquals("JPLogP", name); 103 assertEquals(1, desc.getParameterNames().length); 104 assertEquals("addImplicitH", desc.getParameterNames()[0]); 105 } 106 107 @Test testGetHologram()108 public void testGetHologram() throws CDKException { 109 JPlogPDescriptor desc = new JPlogPDescriptor(); 110 parser = new SmilesParser(SilentChemObjectBuilder.getInstance()); 111 IAtomContainer molecule = parseSmiles("c1ccccc1"); 112 Map<Integer, Integer> holo = desc.jplogp.getMappedHologram(molecule); 113 assertEquals(2, holo.keySet().size()); 114 assertEquals(6, holo.get(106204).intValue()); 115 } 116 117 118 parseSmiles(String smiles)119 private static IAtomContainer parseSmiles(String smiles) throws CDKException { 120 parser = new SmilesParser(SilentChemObjectBuilder.getInstance()); 121 IAtomContainer molecule = parser.parseSmiles(smiles); 122 AtomContainerManipulator.percieveAtomTypesAndConfigureUnsetProperties(molecule); 123 AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule); 124 Aromaticity.cdkLegacy().apply(molecule); 125 return molecule; 126 } 127 128 } 129