/* * $Id: DescriptorTests.java 131 2011-01-20 22:01:29Z ebakke $ * * Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc. * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are * met: * * * Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * * Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * Neither the name of Novartis Institutes for BioMedical Research Inc. * nor the names of its contributors may be used to endorse or promote * products derived from this software without specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ package org.RDKit; import static org.junit.Assert.*; import java.io.*; import java.util.*; import org.junit.*; public class DescriptorTests extends GraphMolTest { private File dataFile; public class DescriptorTestEntry { String smi; double clogp; double mr; int lineNo; public DescriptorTestEntry(int lineNo, String[] line) { this.lineNo = lineNo; smi = line[0].trim(); clogp = Double.parseDouble(line[1].trim()); mr = Double.parseDouble(line[2].trim()); } } public List readData(String fn) throws Exception { List data = new ArrayList(); int lineNo = 0; BufferedReader reader = new BufferedReader(new FileReader(fn)); String line; // Skip the header try { reader.readLine(); while ((line = reader.readLine()) != null) { lineNo += 1; if (line.length() > 0 && !line.startsWith("#")) { String[] splitL = line.split("\t"); if (splitL.length == 3) data.add(new DescriptorTestEntry(lineNo, splitL)); } } } finally { reader.close(); } return data; } @Before public void setUp() { File base = getRdBase(); dataFile = new File(base, "rdkit" + File.separator + "Chem" + File.separator + "test_data" + File.separator + "Crippen.csv"); } @Test public void testLogP() throws Exception { List data = readData(dataFile.getPath()); for (DescriptorTestEntry item : data) { ROMol mol = RWMol.MolFromSmiles(item.smi); Double_Pair calcProps = RDKFuncs.calcCrippenDescriptors(mol); assertEquals("cLogp on " + item.smi, item.clogp, calcProps.getFirst(), defaultDoubleTol); assertEquals("mr on " + item.smi, item.mr, calcProps.getSecond(), defaultDoubleTol); } } @Test public void testRepeat() throws Exception { List data = readData(dataFile.getPath()); for (DescriptorTestEntry item : data) { ROMol mol = RWMol.MolFromSmiles(item.smi); Double_Pair calcProps = RDKFuncs.calcCrippenDescriptors(mol); assertEquals("cLogp on " + item.smi, item.clogp, calcProps.getFirst(), defaultDoubleTol); assertEquals("mr on " + item.smi, item.mr, calcProps.getSecond(), defaultDoubleTol); } } @Test public void testIssue80() { ROMol m = RWMol.MolFromSmiles("CCOC"); double ref = RDKFuncs.calcCrippenDescriptors(m).getFirst(); double probe = RDKFuncs.calcCrippenDescriptors(m).getFirst(); assertEquals(ref, probe, 0.0); } @Test public void testIssue1749494() { ROMol m1 = RWMol.MolFromSmiles("[*]CC"); double v = RDKFuncs.calcCrippenDescriptors(m1).getFirst(); assertEquals( 0.9739,v,defaultDoubleTol); } @Test public void testDescriptors1() { ROMol m1,m2,m3; m1 = RWMol.MolFromSmiles("C1=CC=CC=C1"); m2 = RWMol.MolFromSmiles("C1=CC=CC=N1"); m3 = RWMol.MolFromSmiles("C1=CC=CC=C1CC(=O)O"); long tmp; tmp=RDKFuncs.calcNumHBA(m1); assertEquals(tmp,0); tmp=RDKFuncs.calcNumHBA(m2); assertEquals(tmp,1); tmp=RDKFuncs.calcNumHBA(m3); assertEquals(tmp,1); tmp=RDKFuncs.calcNumHBD(m1); assertEquals(tmp,0); tmp=RDKFuncs.calcNumHBD(m2); assertEquals(tmp,0); tmp=RDKFuncs.calcNumHBD(m3); assertEquals(tmp,1); tmp=RDKFuncs.calcLipinskiHBA(m1); assertEquals(tmp,0); tmp=RDKFuncs.calcLipinskiHBA(m2); assertEquals(tmp,1); tmp=RDKFuncs.calcLipinskiHBA(m3); assertEquals(tmp,2); tmp=RDKFuncs.calcLipinskiHBD(m1); assertEquals(tmp,0); tmp=RDKFuncs.calcLipinskiHBD(m2); assertEquals(tmp,0); tmp=RDKFuncs.calcLipinskiHBD(m3); assertEquals(tmp,1); } @Test public void testDescriptors2() { ROMol m1,m2; m1 = RWMol.MolFromSmiles("C1=CC=CC=C1"); m2 = RWMol.MolFromSmiles("C1=CC=CC=N1"); double tmp; tmp=RDKFuncs.calcMolLogP(m1); assertEquals(tmp,1.687,0.001); tmp=RDKFuncs.calcMolLogP(m2); assertEquals(tmp,1.082,0.001); tmp=RDKFuncs.calcMolMR(m1); assertEquals(tmp,26.442,0.001); tmp=RDKFuncs.calcMolMR(m2); assertEquals(tmp,24.237,0.001); } @Test public void testDescriptors3() { ROMol m1,m2,m3; m1 = RWMol.MolFromSmiles("C1=CC=CC=C1"); m2 = RWMol.MolFromSmiles("C1=CC=CC=N1"); m3 = RWMol.MolFromSmiles("C1=CC=CC=C1CC(=O)O"); double tmp; tmp=RDKFuncs.calcTPSA(m1); assertEquals(tmp,0,0.01); tmp=RDKFuncs.calcTPSA(m2); assertEquals(tmp,12.89,0.01); tmp=RDKFuncs.calcTPSA(m3); assertEquals(tmp,37.30,0.01); } @Test public void testVSADescriptors() { ROMol m1,m2,m3; m1 = RWMol.MolFromSmiles("CO"); m2 = RWMol.MolFromSmiles("CCO"); Double_Vect v; v = RDKFuncs.calcSlogP_VSA(m1); assertEquals(v.get(0),0.0,0.001); assertEquals(v.get(1),12.216,0.001); v = RDKFuncs.calcSlogP_VSA(m2); assertEquals(v.get(0),0.0,0.001); assertEquals(v.get(1),11.713,0.001); assertEquals(v.get(4),6.924,0.001); v = RDKFuncs.calcSMR_VSA(m1); assertEquals(v.get(0),5.106,0.001); assertEquals(v.get(1),0.0,0.001); assertEquals(v.get(5),7.110,0.001); v = RDKFuncs.calcSMR_VSA(m2); assertEquals(v.get(0),5.106,0.001); assertEquals(v.get(4),6.924,0.001); assertEquals(v.get(5),6.607,0.001); v = RDKFuncs.calcPEOE_VSA(m1); assertEquals(v.get(0),5.106,0.001); assertEquals(v.get(7),7.110,0.001); assertEquals(v.get(5),0.000,0.001); v = RDKFuncs.calcPEOE_VSA(m2); assertEquals(v.get(0),5.106,0.001); assertEquals(v.get(6),6.924,0.001); assertEquals(v.get(7),6.607,0.001); } @Test public void testMW() { ROMol m1; m1 = RWMol.MolFromSmiles("C"); assertEquals(16.043,RDKFuncs.calcAMW(m1),0.001); assertEquals(16.031,RDKFuncs.calcExactMW(m1),0.001); } @Test public void testMolFormula() { ROMol m1; m1 = RWMol.MolFromSmiles("C([2H])([3H])O"); assertEquals("CH4O",RDKFuncs.calcMolFormula(m1)); assertEquals("CH2DTO",RDKFuncs.calcMolFormula(m1,true)); assertEquals("CH2[2H][3H]O",RDKFuncs.calcMolFormula(m1,true,false)); } @Test public void testMolFormula2() { ROMol m1; m1 = RWMol.MolFromSmiles("C[13C]([2H])([3H])O"); assertEquals("C2H6O",RDKFuncs.calcMolFormula(m1)); assertEquals("C[13C]H4DTO",RDKFuncs.calcMolFormula(m1,true)); assertEquals("C[13C]H4[2H][3H]O",RDKFuncs.calcMolFormula(m1,true,false)); } @Test public void testConnectivityDescriptors1() { ROMol m1; m1 = RWMol.MolFromSmiles("c1ccccc1O"); double tmp; tmp=RDKFuncs.calcChi0v(m1); assertEquals(tmp,3.834,0.01); tmp=RDKFuncs.calcChi1v(m1); assertEquals(tmp,2.134,0.01); tmp=RDKFuncs.calcChi2v(m1); assertEquals(tmp,1.336,0.01); tmp=RDKFuncs.calcChi3v(m1); assertEquals(tmp,0.756,0.01); tmp=RDKFuncs.calcChi4v(m1); assertEquals(tmp,0.428,0.01); tmp=RDKFuncs.calcChiNv(m1,4); assertEquals(tmp,0.428,0.01); tmp=RDKFuncs.calcChi0n(m1); assertEquals(tmp,3.834,0.01); tmp=RDKFuncs.calcChi1n(m1); assertEquals(tmp,2.134,0.01); tmp=RDKFuncs.calcChi2n(m1); assertEquals(tmp,1.336,0.01); tmp=RDKFuncs.calcChi3n(m1); assertEquals(tmp,0.756,0.01); tmp=RDKFuncs.calcChi4n(m1); assertEquals(tmp,0.428,0.01); tmp=RDKFuncs.calcChiNn(m1,4); assertEquals(tmp,0.428,0.01); } @Test public void testConnectivityDescriptors2() { ROMol m1; double tmp; m1 = RWMol.MolFromSmiles("C12CC2C3CC13"); tmp=RDKFuncs.calcKappa1(m1); assertEquals(tmp,2.344,0.01); m1 = RWMol.MolFromSmiles("CC(C)C1CCC(C)CCC1"); tmp=RDKFuncs.calcKappa2(m1); assertEquals(tmp,4.133,0.01); m1 = RWMol.MolFromSmiles("CC(C)C1CCC(C)CCC1"); tmp=RDKFuncs.calcKappa3(m1); assertEquals(tmp,2.844,0.01); } public static void main(String args[]) { org.junit.runner.JUnitCore.main("org.RDKit.DescriptorTests"); } }