/* * $Id: BasicMoleculeTests.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 org.junit.*; public class BasicMoleculeTests extends GraphMolTest { private ROMol mol1; @Before public void setUp() { String smiles="c1ccccc1"; mol1 = RWMol.MolFromSmiles(smiles); } @Test public void testBasics() { assertEquals(6,mol1.getNumAtoms()); assertEquals(6,mol1.getNumBonds()); } @Test public void testSmilesWrite() { String smi = mol1.MolToSmiles(); assertEquals(smi,smi,"c1ccccc1"); } @Test public void testAtoms() { assertEquals( mol1.getAtomWithIdx(0).getAtomicNum(),6); assertFalse(mol1.hasAtomBookmark(1)); mol1.setAtomBookmark(mol1.getAtomWithIdx(0),1); assertTrue(mol1.hasAtomBookmark(1)); } @Test public void testBonds() { assertEquals(Bond.BondType.AROMATIC,mol1.getBondWithIdx(0).getBondType()); } @Test public void testReactionBasics() { ChemicalReaction rxn; rxn=ChemicalReaction.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]"); assertEquals(2,rxn.getNumReactantTemplates()); assertEquals(1,rxn.getNumProductTemplates()); ROMol r1,r2; r1=RWMol.MolFromSmiles("CC(=O)O"); r2=RWMol.MolFromSmiles("ClCN"); assertEquals(4,r1.getNumAtoms()); assertEquals(3,r2.getNumAtoms()); ROMol_Vect rs= new ROMol_Vect(2); rs.set(0,r1); rs.set(1,r2); ROMol_Vect_Vect ps; ps=rxn.runReactants(rs); assertFalse(ps.isEmpty()); assertEquals(1,ps.size()); assertFalse(ps.get(0).isEmpty()); assertEquals(1,ps.get(0).size()); assertEquals(4,r1.getNumAtoms()); assertEquals(3,r2.getNumAtoms()); assertEquals(6,ps.get(0).get(0).getNumAtoms()); } @Test public void testSubstruct1() { ROMol p; Match_Vect mv; p = RWMol.MolFromSmarts("c"); assertTrue(mol1.hasSubstructMatch(p)); mv=mol1.getSubstructMatch(p); assertEquals(1,mv.size()); assertEquals(0,mv.get(0).getFirst()); assertEquals(0,mv.get(0).getSecond()); } @Test public void testSubstruct2() { ROMol p; Match_Vect mv; p = RWMol.MolFromSmarts("C"); assertFalse(mol1.hasSubstructMatch(p)); mv=mol1.getSubstructMatch(p); assertEquals(0,mv.size()); } @Test public void testSubstruct3() { ROMol p; Match_Vect mv; ROMol m2; m2 = RWMol.MolFromSmiles("NC(=O)CC"); p = RWMol.MolFromSmarts("CN"); mv=m2.getSubstructMatch(p); assertEquals(2,mv.size()); assertEquals(0,mv.get(0).getFirst()); assertEquals(1,mv.get(0).getSecond()); assertEquals(1,mv.get(1).getFirst()); assertEquals(0,mv.get(1).getSecond()); } @Test public void testSubstruct4() { ROMol p; Match_Vect_Vect mvv; ROMol m2; m2 = RWMol.MolFromSmiles("NC(=O)CC"); p = RWMol.MolFromSmarts("CN"); mvv=m2.getSubstructMatches(p); assertEquals(1,mvv.size()); assertEquals(2,mvv.get(0).size()); assertEquals(0,mvv.get(0).get(0).getFirst()); assertEquals(1,mvv.get(0).get(0).getSecond()); assertEquals(1,mvv.get(0).get(1).getFirst()); assertEquals(0,mvv.get(0).get(1).getSecond()); } @Test public void testSubstruct5() { ROMol p; Match_Vect_Vect mvv; ROMol m2; m2 = RWMol.MolFromSmiles("NC(=O)NCC"); p = RWMol.MolFromSmarts("[$(C=O)]N"); mvv=m2.getSubstructMatches(p); assertEquals(2,mvv.size()); assertEquals(2,mvv.get(0).size()); assertEquals(0,mvv.get(0).get(0).getFirst()); assertEquals(1,mvv.get(0).get(0).getSecond()); assertEquals(1,mvv.get(0).get(1).getFirst()); assertEquals(0,mvv.get(0).get(1).getSecond()); assertEquals(2,mvv.get(1).size()); assertEquals(0,mvv.get(1).get(0).getFirst()); assertEquals(1,mvv.get(1).get(0).getSecond()); assertEquals(1,mvv.get(1).get(1).getFirst()); assertEquals(3,mvv.get(1).get(1).getSecond()); } @Test public void testFingerprints1() { ROMol m1,m2; m1 = RWMol.MolFromSmiles("C1=CC=CC=C1"); m2 = RWMol.MolFromSmiles("C1=CC=CC=N1"); ExplicitBitVect fp1,fp2; fp1=RDKFuncs.RDKFingerprintMol(m1); fp2=RDKFuncs.RDKFingerprintMol(m1); assertEquals( 0.0,RDKFuncs.TanimotoSimilarity(fp1,fp2),1.0); fp2=RDKFuncs.RDKFingerprintMol(m2); assertTrue(RDKFuncs.TanimotoSimilarity(fp1,fp2)<1.0); assertTrue(RDKFuncs.TanimotoSimilarity(fp1,fp2)>0.0); } @Test public void testFingerprints2() { ROMol m1,m2; m1 = RWMol.MolFromSmiles("C1=CC=CC=C1"); m2 = RWMol.MolFromSmiles("C1=CC=CC=N1"); SparseIntVectu32 fp1,fp2; fp1=RDKFuncs.MorganFingerprintMol(m1,2); fp2=RDKFuncs.MorganFingerprintMol(m1,2); assertEquals(0.0,RDKFuncs.DiceSimilarity(fp1,fp2),1.0); fp2=RDKFuncs.MorganFingerprintMol(m2,2); assertTrue(RDKFuncs.DiceSimilarity(fp1,fp2)<1.0); assertTrue(RDKFuncs.DiceSimilarity(fp1,fp2)>0.0); UInt_Pair_Vect v1=fp1.getNonzero(); assertTrue(v1.size()>0); UInt_Pair_Vect v2=fp2.getNonzero(); assertTrue(v2.size()>0); assertTrue(v2.size()>v1.size()); } @Test public void testErrorHandling_BadParse() { ROMol m1 = RWMol.MolFromSmiles("C1CC"); assertEquals(null,m1); } @Test(expected=MolSanitizeException.class) public void testErrorHandling_BadKekulize() { RWMol.MolFromSmiles("c1cc1"); } @Test(expected=MolSanitizeException.class) public void testErrorHandling_BadKekulize2() { RWMol mol=RWMol.MolFromSmiles("c1cc1",0,false); RDKFuncs.sanitizeMol(mol); } @Test public void testErrorHandling_BadKekulize3() { RWMol mol=RWMol.MolFromSmiles("c1cc1",0,false); int ops=SanitizeFlags.SANITIZE_ALL.swigValue(); int failedAt=RDKFuncs.sanitizeMol(mol,ops); assertEquals(failedAt,SanitizeFlags.SANITIZE_KEKULIZE.swigValue()); ops ^= SanitizeFlags.SANITIZE_KEKULIZE.swigValue(); failedAt=RDKFuncs.sanitizeMol(mol,ops); assertEquals(failedAt,0); } @Test public void testAddAtomsAndBonds() { RWMol mol = new RWMol(); assertEquals(mol.getNumBonds(),0); Atom carbon = new Atom(6); mol.addAtom(carbon,false); mol.addAtom(carbon,false); assertEquals(mol.getNumAtoms(),2); Bond single = new Bond(Bond.BondType.SINGLE); single.setOwningMol(mol); single.setBeginAtomIdx(1); single.setEndAtomIdx(0); mol.addBond(single); assertEquals(mol.getNumBonds(),1); assertEquals(mol.getBondWithIdx(0).getBeginAtomIdx(),1); assertEquals(mol.getBondWithIdx(0).getEndAtomIdx(),0); // the molecule has copied the bond, so if we change it, there's // no impact on the molecule itself: single.setBeginAtomIdx(0); single.setEndAtomIdx(1); assertEquals(mol.getBondWithIdx(0).getBeginAtomIdx(),1); assertEquals(mol.getBondWithIdx(0).getEndAtomIdx(),0); } /* @Test -- the contents of this test now in UnitTestPickling, testIssue219 public void testConformer(){ } */ public static void main(String args[]) { org.junit.runner.JUnitCore.main("org.RDKit.BasicMoleculeTests"); } }