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0edde326ac
- Add a couple of tests to avoid similar regressions in the future Co-authored-by: ptosco <paolo.tosco@novartis.com>
266 lines
9.2 KiB
Java
266 lines
9.2 KiB
Java
/*
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*
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* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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package org.RDKit;
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import static org.junit.Assert.*;
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import org.junit.*;
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public class BasicMoleculeTests extends GraphMolTest {
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private ROMol mol1;
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@Before public void setUp() {
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String smiles="c1ccccc1";
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mol1 = RWMol.MolFromSmiles(smiles);
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}
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@Test public void testBasics() {
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assertEquals(6,mol1.getNumAtoms());
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assertEquals(6,mol1.getNumBonds());
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}
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@Test public void testSmilesWrite() {
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String smi = mol1.MolToSmiles();
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assertEquals(smi,smi,"c1ccccc1");
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String smiRDKFuncs = RDKFuncs.MolToSmiles(mol1);
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assertEquals(smiRDKFuncs,smiRDKFuncs,smi);
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}
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@Test public void testAtoms() {
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assertEquals( mol1.getAtomWithIdx(0).getAtomicNum(),6);
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assertFalse(mol1.hasAtomBookmark(1));
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mol1.setAtomBookmark(mol1.getAtomWithIdx(0),1);
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assertTrue(mol1.hasAtomBookmark(1));
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}
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@Test public void testBonds() {
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assertEquals(Bond.BondType.AROMATIC,mol1.getBondWithIdx(0).getBondType());
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}
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@Test public void testReactionBasics() {
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ChemicalReaction rxn;
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rxn=ChemicalReaction.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
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assertEquals(2,rxn.getNumReactantTemplates());
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assertEquals(1,rxn.getNumProductTemplates());
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ROMol r1,r2;
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r1=RWMol.MolFromSmiles("CC(=O)O");
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r2=RWMol.MolFromSmiles("ClCN");
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assertEquals(4,r1.getNumAtoms());
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assertEquals(3,r2.getNumAtoms());
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ROMol_Vect rs= new ROMol_Vect(2);
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rs.set(0,r1);
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rs.set(1,r2);
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ROMol_Vect_Vect ps;
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ps=rxn.runReactants(rs);
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assertFalse(ps.isEmpty());
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assertEquals(1,ps.size());
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assertFalse(ps.get(0).isEmpty());
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assertEquals(1,ps.get(0).size());
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assertEquals(4,r1.getNumAtoms());
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assertEquals(3,r2.getNumAtoms());
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assertEquals(6,ps.get(0).get(0).getNumAtoms());
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}
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@Test public void testSubstruct1() {
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ROMol p;
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Match_Vect mv;
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p = RWMol.MolFromSmarts("c");
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assertTrue(mol1.hasSubstructMatch(p));
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mv=mol1.getSubstructMatch(p);
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assertEquals(1,mv.size());
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assertEquals(0,mv.get(0).getFirst());
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assertEquals(0,mv.get(0).getSecond());
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}
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@Test public void testSubstruct2() {
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ROMol p;
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Match_Vect mv;
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p = RWMol.MolFromSmarts("C");
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assertFalse(mol1.hasSubstructMatch(p));
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mv=mol1.getSubstructMatch(p);
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assertEquals(0,mv.size());
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}
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@Test public void testSubstruct3() {
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ROMol p;
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Match_Vect mv;
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ROMol m2;
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m2 = RWMol.MolFromSmiles("NC(=O)CC");
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p = RWMol.MolFromSmarts("CN");
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mv=m2.getSubstructMatch(p);
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assertEquals(2,mv.size());
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assertEquals(0,mv.get(0).getFirst());
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assertEquals(1,mv.get(0).getSecond());
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assertEquals(1,mv.get(1).getFirst());
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assertEquals(0,mv.get(1).getSecond());
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}
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@Test public void testSubstruct4() {
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ROMol p;
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Match_Vect_Vect mvv;
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ROMol m2;
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m2 = RWMol.MolFromSmiles("NC(=O)CC");
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p = RWMol.MolFromSmarts("CN");
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mvv=m2.getSubstructMatches(p);
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assertEquals(1,mvv.size());
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assertEquals(2,mvv.get(0).size());
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assertEquals(0,mvv.get(0).get(0).getFirst());
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assertEquals(1,mvv.get(0).get(0).getSecond());
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assertEquals(1,mvv.get(0).get(1).getFirst());
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assertEquals(0,mvv.get(0).get(1).getSecond());
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}
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@Test public void testSubstruct5() {
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ROMol p;
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Match_Vect_Vect mvv;
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ROMol m2;
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m2 = RWMol.MolFromSmiles("NC(=O)NCC");
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p = RWMol.MolFromSmarts("[$(C=O)]N");
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mvv=m2.getSubstructMatches(p);
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assertEquals(2,mvv.size());
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assertEquals(2,mvv.get(0).size());
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assertEquals(0,mvv.get(0).get(0).getFirst());
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assertEquals(1,mvv.get(0).get(0).getSecond());
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assertEquals(1,mvv.get(0).get(1).getFirst());
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assertEquals(0,mvv.get(0).get(1).getSecond());
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assertEquals(2,mvv.get(1).size());
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assertEquals(0,mvv.get(1).get(0).getFirst());
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assertEquals(1,mvv.get(1).get(0).getSecond());
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assertEquals(1,mvv.get(1).get(1).getFirst());
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assertEquals(3,mvv.get(1).get(1).getSecond());
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}
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@Test public void testSubstructParams1() {
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ROMol p;
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Match_Vect_Vect mvv;
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ROMol m2;
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m2 = RWMol.MolFromSmiles("C[C@](F)(Cl)Br");
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p = RWMol.MolFromSmiles("C[C@@](F)(Cl)Br");
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mvv=m2.getSubstructMatches(p);
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assertEquals(1,mvv.size());
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assertEquals(5,mvv.get(0).size());
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SubstructMatchParameters params = new SubstructMatchParameters();
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params.setUseChirality(true);
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mvv=m2.getSubstructMatches(p,params);
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assertEquals(0,mvv.size());
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}
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@Test public void testFingerprints1() {
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ROMol m1,m2;
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m1 = RWMol.MolFromSmiles("C1=CC=CC=C1");
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m2 = RWMol.MolFromSmiles("C1=CC=CC=N1");
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ExplicitBitVect fp1,fp2;
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fp1=RDKFuncs.RDKFingerprintMol(m1);
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fp2=RDKFuncs.RDKFingerprintMol(m1);
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assertEquals( 0.0,RDKFuncs.TanimotoSimilarity(fp1,fp2),1.0);
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fp2=RDKFuncs.RDKFingerprintMol(m2);
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assertTrue(RDKFuncs.TanimotoSimilarity(fp1,fp2)<1.0);
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assertTrue(RDKFuncs.TanimotoSimilarity(fp1,fp2)>0.0);
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}
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@Test public void testFingerprints2() {
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ROMol m1,m2;
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m1 = RWMol.MolFromSmiles("C1=CC=CC=C1");
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m2 = RWMol.MolFromSmiles("C1=CC=CC=N1");
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SparseIntVectu32 fp1,fp2;
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fp1=RDKFuncs.MorganFingerprintMol(m1,2);
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fp2=RDKFuncs.MorganFingerprintMol(m1,2);
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assertEquals(0.0,RDKFuncs.DiceSimilarity(fp1,fp2),1.0);
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fp2=RDKFuncs.MorganFingerprintMol(m2,2);
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assertTrue(RDKFuncs.DiceSimilarity(fp1,fp2)<1.0);
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assertTrue(RDKFuncs.DiceSimilarity(fp1,fp2)>0.0);
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UInt_Pair_Vect v1=fp1.getNonzero();
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assertTrue(v1.size()>0);
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UInt_Pair_Vect v2=fp2.getNonzero();
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assertTrue(v2.size()>0);
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assertTrue(v2.size()>v1.size());
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}
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@Test public void testErrorHandling_BadParse() {
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ROMol m1 = RWMol.MolFromSmiles("C1CC");
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assertEquals(null,m1);
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}
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@Test(expected=MolSanitizeException.class)
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public void testErrorHandling_BadKekulize() {
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RWMol.MolFromSmiles("c1cc1");
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}
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@Test(expected=MolSanitizeException.class)
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public void testErrorHandling_BadKekulize2() {
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RWMol mol=RWMol.MolFromSmiles("c1cc1",0,false);
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RDKFuncs.sanitizeMol(mol);
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}
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@Test public void testErrorHandling_BadKekulize3() {
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RWMol mol=RWMol.MolFromSmiles("c1cc1",0,false);
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int ops=SanitizeFlags.SANITIZE_ALL.swigValue();
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int failedAt=RDKFuncs.sanitizeMol(mol,ops);
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assertEquals(failedAt,SanitizeFlags.SANITIZE_KEKULIZE.swigValue());
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ops ^= SanitizeFlags.SANITIZE_KEKULIZE.swigValue();
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failedAt=RDKFuncs.sanitizeMol(mol,ops);
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assertEquals(failedAt,0);
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}
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@Test public void testAddAtomsAndBonds() {
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RWMol mol = new RWMol();
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assertEquals(mol.getNumBonds(),0);
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Atom carbon = new Atom(6);
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mol.addAtom(carbon,false);
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mol.addAtom(carbon,false);
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assertEquals(mol.getNumAtoms(),2);
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Bond single = new Bond(Bond.BondType.SINGLE);
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single.setOwningMol(mol);
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single.setBeginAtomIdx(1);
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single.setEndAtomIdx(0);
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mol.addBond(single);
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assertEquals(mol.getNumBonds(),1);
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assertEquals(mol.getBondWithIdx(0).getBeginAtomIdx(),1);
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assertEquals(mol.getBondWithIdx(0).getEndAtomIdx(),0);
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// the molecule has copied the bond, so if we change it, there's
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// no impact on the molecule itself:
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single.setBeginAtomIdx(0);
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single.setEndAtomIdx(1);
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assertEquals(mol.getBondWithIdx(0).getBeginAtomIdx(),1);
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assertEquals(mol.getBondWithIdx(0).getEndAtomIdx(),0);
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}
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@Test public void testGetAtomNeighbors() {
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String smiles="CC(C)C";
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ROMol mol = RWMol.MolFromSmiles(smiles);
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assertEquals(mol.getAtomNeighbors(mol.getAtomWithIdx(0)).size(),1);
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assertEquals(mol.getAtomNeighbors(mol.getAtomWithIdx(1)).size(),3);
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assertEquals(mol.getAtomNeighbors(mol.getAtomWithIdx(2)).size(),1);
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assertEquals(mol.getAtomBonds(mol.getAtomWithIdx(0)).size(),1);
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assertEquals(mol.getAtomBonds(mol.getAtomWithIdx(1)).size(),3);
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assertEquals(mol.getAtomBonds(mol.getAtomWithIdx(2)).size(),1);
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}
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/* @Test -- the contents of this test now in UnitTestPickling, testIssue219
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public void testConformer(){
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}
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*/
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main("org.RDKit.BasicMoleculeTests");
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}
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}
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