mirror of
https://github.com/rdkit/rdkit.git
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278 lines
8.9 KiB
Java
278 lines
8.9 KiB
Java
// $Id$
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// Copyright (C) 2008-2010 Greg Landrum
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//
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// @@ All Rights Reserved @@
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//package org.RDKit;
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import org.junit.*;
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import static org.junit.Assert.*;
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import org.RDKit.*;
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public class WrapperTests {
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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 = RDKFuncs.MolFromSmiles(smiles);
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}
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@Test public void testBasics() {
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assertTrue(mol1.getNumAtoms()==6);
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assertTrue(mol1.getNumBonds()==6);
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}
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@Test public void testAtoms() {
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assertTrue(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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assertTrue(mol1.getBondWithIdx(0).getBondType()==Bond.BondType.AROMATIC);
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}
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@Test public void testSmilesWrite() {
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String smi=RDKFuncs.MolToSmiles(mol1);
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assertEquals(smi,"c1ccccc1",smi);
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}
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@Test public void testReactionBasics() {
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ChemicalReaction rxn;
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rxn=RDKFuncs.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
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assertTrue(rxn.getNumReactantTemplates()==2);
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assertTrue(rxn.getNumProductTemplates()==1);
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ROMol r1,r2;
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r1=RDKFuncs.MolFromSmiles("CC(=O)O");
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r2=RDKFuncs.MolFromSmiles("ClCN");
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assertTrue(r1.getNumAtoms()==4);
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assertTrue(r2.getNumAtoms()==3);
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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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assertTrue(ps.size()==1);
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assertFalse(ps.get(0).isEmpty());
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assertTrue(ps.get(0).size()==1);
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assertTrue(r1.getNumAtoms()==4);
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assertTrue(r2.getNumAtoms()==3);
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assertTrue(ps.get(0).get(0).getNumAtoms()==6);
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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 = RDKFuncs.MolFromSmarts("c");
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assertTrue(mol1.hasSubstructMatch(p));
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mv=mol1.getSubstructMatch(p);
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assertTrue(mv.size()==1);
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assertTrue(mv.get(0).getFirst()==0);
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assertTrue(mv.get(0).getSecond()==0);
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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 = RDKFuncs.MolFromSmarts("C");
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assertFalse(mol1.hasSubstructMatch(p));
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mv=mol1.getSubstructMatch(p);
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assertTrue(mv.size()==0);
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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 = RDKFuncs.MolFromSmiles("NC(=O)CC");
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p = RDKFuncs.MolFromSmarts("CN");
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mv=m2.getSubstructMatch(p);
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assertTrue(mv.size()==2);
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assertTrue(mv.get(0).getFirst()==0);
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assertTrue(mv.get(0).getSecond()==1);
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assertTrue(mv.get(1).getFirst()==1);
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assertTrue(mv.get(1).getSecond()==0);
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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 = RDKFuncs.MolFromSmiles("NC(=O)CC");
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p = RDKFuncs.MolFromSmarts("CN");
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mvv=m2.getSubstructMatches(p);
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assertTrue(mvv.size()==1);
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assertTrue(mvv.get(0).size()==2);
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assertTrue(mvv.get(0).get(0).getFirst()==0);
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assertTrue(mvv.get(0).get(0).getSecond()==1);
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assertTrue(mvv.get(0).get(1).getFirst()==1);
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assertTrue(mvv.get(0).get(1).getSecond()==0);
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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 = RDKFuncs.MolFromSmiles("NC(=O)NCC");
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p = RDKFuncs.MolFromSmarts("[$(C=O)]N");
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mvv=m2.getSubstructMatches(p);
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assertTrue(mvv.size()==2);
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assertTrue(mvv.get(0).size()==2);
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assertTrue(mvv.get(0).get(0).getFirst()==0);
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assertTrue(mvv.get(0).get(0).getSecond()==1);
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assertTrue(mvv.get(0).get(1).getFirst()==1);
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assertTrue(mvv.get(0).get(1).getSecond()==0);
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assertTrue(mvv.get(1).size()==2);
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assertTrue(mvv.get(1).get(0).getFirst()==0);
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assertTrue(mvv.get(1).get(0).getSecond()==1);
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assertTrue(mvv.get(1).get(1).getFirst()==1);
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assertTrue(mvv.get(1).get(1).getSecond()==3);
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}
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@Test public void testFingerprints1() {
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ROMol m1,m2;
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m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
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m2 = RDKFuncs.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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assertTrue(RDKFuncs.TanimotoSimilarityEBV(fp1,fp2)==1.0);
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fp2=RDKFuncs.RDKFingerprintMol(m2);
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assertTrue(RDKFuncs.TanimotoSimilarityEBV(fp1,fp2)<1.0);
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assertTrue(RDKFuncs.TanimotoSimilarityEBV(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 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
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m2 = RDKFuncs.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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assertTrue(RDKFuncs.DiceSimilaritySIVu32(fp1,fp2)==1.0);
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fp2=RDKFuncs.MorganFingerprintMol(m2,2);
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assertTrue(RDKFuncs.DiceSimilaritySIVu32(fp1,fp2)<1.0);
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assertTrue(RDKFuncs.DiceSimilaritySIVu32(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 testFingerprints3() {
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ROMol m1,m2;
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m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
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m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
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SparseIntVecti32 fp1,fp2;
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fp1=RDKFuncs.getAtomPairFingerprint(m1,2,6);
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fp2=RDKFuncs.getAtomPairFingerprint(m1,2,6);
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assertTrue(RDKFuncs.DiceSimilaritySIVi32(fp1,fp2)==1.0);
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fp2=RDKFuncs.getAtomPairFingerprint(m2,2,6);
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assertEquals(RDKFuncs.DiceSimilaritySIVi32(fp1,fp2),0.66667,.0001);
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}
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@Test public void testFingerprints4() {
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ROMol m1,m2;
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m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
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m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
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SparseIntVecti64 fp1,fp2;
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fp1=RDKFuncs.getTopologicalTorsionFingerprint(m1);
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fp2=RDKFuncs.getTopologicalTorsionFingerprint(m1);
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assertTrue(RDKFuncs.DiceSimilaritySIVi64(fp1,fp2)==1.0);
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fp2=RDKFuncs.getTopologicalTorsionFingerprint(m2);
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assertEquals(RDKFuncs.DiceSimilaritySIVi64(fp1,fp2),0.3333,.0001);
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}
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@Test public void testErrorHandling() {
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ROMol m1;
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m1 = RDKFuncs.MolFromSmiles("C1CC");
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assertTrue(m1==null);
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m1 = RDKFuncs.MolFromSmiles("c1cc1");
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assertTrue(m1==null);
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System.err.println("ok!");
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ChemicalReaction rxn=RDKFuncs.ReactionFromSmarts("OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
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assertTrue(rxn==null);
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}
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@Test public void testPickling() {
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Char_Vect pkl=RDKFuncs.MolToBinary(mol1);
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ROMol m1 = RDKFuncs.MolFromBinary(pkl);
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assertTrue(m1.getNumAtoms()==6);
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assertTrue(m1.getNumBonds()==6);
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}
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@Test public void testReactionPickling() {
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ChemicalReaction rxn;
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rxn=RDKFuncs.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
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assertTrue(rxn.getNumReactantTemplates()==2);
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assertTrue(rxn.getNumProductTemplates()==1);
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Char_Vect pkl=RDKFuncs.RxnToBinary(rxn);
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ChemicalReaction rxn2=RDKFuncs.RxnFromBinary(pkl);
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assertTrue(rxn2.getNumReactantTemplates()==2);
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assertTrue(rxn2.getNumProductTemplates()==1);
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}
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@Test public void testReactionToSmarts() {
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ChemicalReaction rxn;
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rxn=RDKFuncs.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
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assertTrue(rxn.getNumReactantTemplates()==2);
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assertTrue(rxn.getNumProductTemplates()==1);
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String sma=RDKFuncs.ReactionToSmarts(rxn);
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ChemicalReaction rxn2;
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rxn2=RDKFuncs.ReactionFromSmarts(sma);
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assertTrue(rxn2.getNumReactantTemplates()==2);
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assertTrue(rxn2.getNumProductTemplates()==1);
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}
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/*@Test*/ public void testMemory() {
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for(int i=0;i<1000000;i++){
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ROMol m1;
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m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
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if((i%1000)==0){
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System.err.println("done: "+i);
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}
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m1.delete();
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}
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}
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/*@Test*/ public void testMemory2() {
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ChemicalReaction rxn;
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rxn=RDKFuncs.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
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assertTrue(rxn.getNumReactantTemplates()==2);
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assertTrue(rxn.getNumProductTemplates()==1);
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ROMol r1,r2;
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r1=RDKFuncs.MolFromSmiles("CC(=O)O");
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r2=RDKFuncs.MolFromSmiles("ClCN");
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assertTrue(r1.getNumAtoms()==4);
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assertTrue(r2.getNumAtoms()==3);
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for(int i=0;i<1000000;i++){
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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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if((i%1000)==0){
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System.err.println("done: "+i);
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}
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ps.delete();
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}
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}
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/*@Test*/ public void testMemory3() {
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ROMol m1;
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m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1C2CCC(C(=O)OCCC)CC2");
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for(int i=0;i<1000000;i++){
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/*SparseIntVecti64 fp1;
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fp1=RDKFuncs.getTopologicalTorsionFingerprint(m1);*/
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SparseIntVectu32 fp1;
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fp1=RDKFuncs.MorganFingerprintMol(m1,2);
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if((i%1000)==0){
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System.err.println("done: "+i);
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}
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fp1.delete();
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}
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}
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static {
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try {
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System.loadLibrary("RDKFuncs");
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} catch (UnsatisfiedLinkError e) {
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System.err.println("Native code library failed to load. Make sure that libRDKFuncs.so is somewhere in your LD_LIBRARY_PATH.\n" + e);
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System.exit(1);
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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("WrapperTests");
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}
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}
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