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UniversalIsomorphismTesterTest.java
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UniversalIsomorphismTesterTest.java
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/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 1997-2007 The Chemistry Development Kit (CKD) project
*
* Contact: cdk-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All I ask is that proper credit is given for my work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*
*/
package org.openscience.cdk.isomorphism;
import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.Bond;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.AtomContainerAtomPermutor;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.IChemObjectReader.Mode;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.isomorphism.matchers.IQueryAtom;
import org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.OrderQueryBond;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator;
import org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom;
import org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom;
import org.openscience.cdk.isomorphism.mcss.RMap;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import java.io.InputStream;
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
/**
* @cdk.module test-standard
* @cdk.require java1.4+
*/
public class UniversalIsomorphismTesterTest extends CDKTestCase
{
boolean standAlone = false;
@Test public void testIsSubgraph_IAtomContainer_IAtomContainer() throws java.lang.Exception
{
AtomContainer mol = MoleculeFactory.makeAlphaPinene();
AtomContainer frag1 = MoleculeFactory.makeCyclohexene(); //one double bond in ring
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag1);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
CDKHueckelAromaticityDetector.detectAromaticity(frag1);
if(standAlone) {
System.out.println("Cyclohexene is a subgraph of alpha-Pinen: " + UniversalIsomorphismTester.isSubgraph(mol, frag1));
} else {
Assert.assertTrue(UniversalIsomorphismTester.isSubgraph(mol, frag1));
}
}
/**
* @cdk.bug 1708336
*/
@Test public void testSFBug1708336() throws Exception {
DefaultChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IAtomContainer atomContainer = builder.newAtomContainer();
atomContainer.addAtom(builder.newAtom("C"));
atomContainer.addAtom(builder.newAtom("C"));
atomContainer.addAtom(builder.newAtom("N"));
atomContainer.addBond(0, 1, IBond.Order.SINGLE);
atomContainer.addBond(1, 2, IBond.Order.SINGLE);
IQueryAtomContainer query = new QueryAtomContainer();
IQueryAtom a1 = new SymbolQueryAtom();
a1.setSymbol("C");
AnyAtom a2 = new AnyAtom();
Bond b1 = new OrderQueryBond(a1, a2, IBond.Order.SINGLE);
IQueryAtom a3 = new SymbolQueryAtom();
a3.setSymbol("C");
Bond b2 = new OrderQueryBond(a2, a3, IBond.Order.SINGLE);
query.addAtom(a1);
query.addAtom(a2);
query.addAtom(a3);
query.addBond(b1);
query.addBond(b2);
List list = UniversalIsomorphismTester.getSubgraphMaps(atomContainer, query);
Assert.assertTrue(list.isEmpty());
}
@Test public void test2() throws java.lang.Exception
{
AtomContainer mol = MoleculeFactory.makeAlphaPinene();
AtomContainer frag1 = MoleculeFactory.makeCyclohexane(); // no double bond in ring
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag1);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
CDKHueckelAromaticityDetector.detectAromaticity(frag1);
if(standAlone){
System.out.println("Cyclohexane is a subgraph of alpha-Pinen: " + UniversalIsomorphismTester.isSubgraph(mol, frag1));
} else {
Assert.assertTrue(!UniversalIsomorphismTester.isSubgraph(mol, frag1));
}
}
@Test public void test3() throws java.lang.Exception
{
AtomContainer mol = MoleculeFactory.makeIndole();
AtomContainer frag1 = MoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag1);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
CDKHueckelAromaticityDetector.detectAromaticity(frag1);
if(standAlone) {
System.out.println("Pyrrole is a subgraph of Indole: " + UniversalIsomorphismTester.isSubgraph(mol, frag1));
} else {
Assert.assertTrue(UniversalIsomorphismTester.isSubgraph(mol, frag1));
}
}
@Test public void testBasicQueryAtomContainer() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer atomContainer = sp.parseSmiles("CC(=O)OC(=O)C"); // acetic acid anhydride
IAtomContainer SMILESquery = sp.parseSmiles("CC"); // acetic acid anhydride
QueryAtomContainer query = QueryAtomContainerCreator.createBasicQueryContainer(SMILESquery);
Assert.assertTrue(UniversalIsomorphismTester.isSubgraph(atomContainer, query));
}
@Test public void testGetSubgraphAtomsMaps_IAtomContainer() throws java.lang.Exception
{
int[] result1 = {6, 5, 7, 8, 0};
int[] result2 = {3, 4, 2, 1, 0};
AtomContainer mol = MoleculeFactory.makeIndole();
AtomContainer frag1 = MoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag1);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
CDKHueckelAromaticityDetector.detectAromaticity(frag1);
List<List<RMap>> list = UniversalIsomorphismTester.getSubgraphAtomsMaps(mol, frag1);
List<RMap> first = list.get(0);
for (int i = 0; i < first.size(); i++) {
RMap rmap = first.get(i);
Assert.assertEquals(rmap.getId1(), result1[i]);
Assert.assertEquals(rmap.getId2(), result2[i]);
}
}
@Test public void testGetSubgraphMap_IAtomContainer_IAtomContainer() throws Exception
{
String molfile = "data/mdl/decalin.mol";
String queryfile = "data/mdl/decalin.mol";
Molecule mol = new Molecule();
Molecule temp = new Molecule();
QueryAtomContainer query1 = null;
QueryAtomContainer query2 = null;
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(molfile);
MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
reader.read(mol);
ins = this.getClass().getClassLoader().getResourceAsStream(queryfile);
reader = new MDLV2000Reader(ins, Mode.STRICT);
reader.read(temp);
query1 = QueryAtomContainerCreator.createBasicQueryContainer(temp);
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer atomContainer = sp.parseSmiles("C1CCCCC1");
query2 = QueryAtomContainerCreator.createBasicQueryContainer(atomContainer);
List list = UniversalIsomorphismTester.getSubgraphMap(mol, query1);
Assert.assertEquals(11, list.size());
list = UniversalIsomorphismTester.getSubgraphMap(mol, query2);
Assert.assertEquals(6, list.size());
}
/**
* @cdk.bug 1110537
*/
@Test public void testGetOverlaps_IAtomContainer_IAtomContainer() throws Exception{
String file1 = "data/mdl/5SD.mol";
String file2 = "data/mdl/ADN.mol";
Molecule mol1 = new Molecule();
Molecule mol2 = new Molecule();
InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(file1);
new MDLV2000Reader(ins1, Mode.STRICT).read(mol1);
InputStream ins2 = this.getClass().getClassLoader().getResourceAsStream(file2);
new MDLV2000Reader(ins2, Mode.STRICT).read(mol2);
List list = UniversalIsomorphismTester.getOverlaps(mol1, mol2);
Assert.assertEquals(1, list.size());
Assert.assertEquals(11, ((AtomContainer)list.get(0)).getAtomCount());
list = UniversalIsomorphismTester.getOverlaps(mol2, mol1);
Assert.assertEquals(1, list.size());
Assert.assertEquals(11, ((AtomContainer)list.get(0)).getAtomCount());
}
/**
* @cdk.bug 2944080
*/
@Test public void testBug2944080() throws Exception {
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol1 = smilesParser.parseSmiles("CCC(CC)(C(=O)NC(=O)NC(C)=O)Br");
IMolecule mol2 = smilesParser.parseSmiles("CCC(=CC)C(=O)NC(N)=O");
List<IAtomContainer> list = UniversalIsomorphismTester.getOverlaps(mol1, mol2);
Assert.assertEquals(1, list.size());
Assert.assertEquals(9, list.get(0).getAtomCount());
list = UniversalIsomorphismTester.getOverlaps(mol2, mol1);
Assert.assertEquals(1, list.size());
Assert.assertEquals(9, list.get(0).getAtomCount());
}
/**
* @cdk.bug 2944080
*/
@Test public void testGetSubgraphAtomsMap_2944080() throws Exception {
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol1 = smilesParser.parseSmiles("CCC(CC)(C(=O)NC(=O)NC(C)=O)Br");
IMolecule mol2 = smilesParser.parseSmiles("CCCC(=O)NC(N)=O");
//Test for atom mapping between the mols
List<RMap> maplist = UniversalIsomorphismTester.getSubgraphAtomsMap(mol1, mol2);
Assert.assertNotNull(maplist);
Assert.assertEquals(9, maplist.size());
}
/**
* @cdk.bug 2944080
*/
@Test public void testGetSubgraphMap_2944080() throws Exception {
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol1 = smilesParser.parseSmiles("CCC(CC)(C(=O)NC(=O)NC(C)=O)Br");
IMolecule mol2 = smilesParser.parseSmiles("CCCC(=O)NC(N)=O");
//Test for atom mapping between the mols
List<RMap> maplist = UniversalIsomorphismTester.getSubgraphMap(mol1, mol2);
Assert.assertNotNull(maplist);
Assert.assertEquals(8, maplist.size());
}
/**
* @cdk.bug 2944080
*/
@Test public void testSearchNoConditions_2944080() throws Exception {
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol1 = smilesParser.parseSmiles("CCC(CC)(C(=O)NC(=O)NC(C)=O)Br");
IMolecule mol2 = smilesParser.parseSmiles("CCCC(=O)NC(N)=O");
//Test for atom mapping between the mols
List<List<RMap>> maplist = UniversalIsomorphismTester.search(
mol1, mol2, new BitSet(),
UniversalIsomorphismTester.getBitSet(mol2),
false, false
);
Assert.assertNotNull(maplist);
Assert.assertEquals(1, maplist.size());
}
/**
* @cdk.bug 2944080
*/
@Test public void testSearch_2944080() throws Exception {
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol1 = smilesParser.parseSmiles("CCC(CC)(C(=O)NC(=O)NC(C)=O)Br");
IMolecule mol2 = smilesParser.parseSmiles("CCC(=CC)C(=O)NC(N)=O");
//Test for atom mapping between the mols
List<List<RMap>> list = UniversalIsomorphismTester.
search(mol1, mol2, new BitSet(), new BitSet(), true, true);
Assert.assertEquals(3, list.size());
for (int i=0; i<list.size(); i++) {
List<RMap> first = list.get(i);
Assert.assertNotSame(0, first.size());
}
list = UniversalIsomorphismTester.
search(mol1, mol2, new BitSet(), new BitSet(), false, false);
Assert.assertEquals(1, list.size());
for (int i=0; i<list.size(); i++) {
List<RMap> first = list.get(i);
Assert.assertNotSame(0, first.size());
}
}
/**
* @cdk.bug 2944080
*/
@Test public void testGetSubgraphAtomsMaps_2944080() throws Exception {
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol1 = smilesParser.parseSmiles("CCC(CC)(C(=O)NC(=O)NC(C)=O)Br");
IMolecule mol2 = smilesParser.parseSmiles("CCCC(=O)NC(N)=O");
List<List<RMap>> list = UniversalIsomorphismTester.getSubgraphAtomsMaps(mol1, mol2);
Assert.assertNotNull(list);
Assert.assertNotSame(0, list.size());
for (int i=0; i<list.size(); i++) {
List<RMap> first = list.get(i);
Assert.assertNotNull(first);
Assert.assertNotSame(0, first.size());
}
}
@Test public void testGetSubgraphAtomsMap_Butane() throws Exception {
IMolecule mol1 = MoleculeFactory.makeAlkane(4);
IMolecule mol2 = MoleculeFactory.makeAlkane(4);
// Test for atom mapping between the mols
List<RMap> maplist = UniversalIsomorphismTester.getSubgraphAtomsMap(mol2, mol1);
Assert.assertNotNull(maplist);
Assert.assertEquals(4, maplist.size());
maplist = UniversalIsomorphismTester.getSubgraphAtomsMap(mol1, mol2);
Assert.assertNotNull(maplist);
Assert.assertEquals(4, maplist.size());
}
@Test public void testGetSubgraphAtomsMaps_Butane() throws Exception {
IMolecule mol1 = MoleculeFactory.makeAlkane(4);
IMolecule mol2 = MoleculeFactory.makeAlkane(4);
List<List<RMap>> list = UniversalIsomorphismTester.getSubgraphAtomsMaps(mol1, mol2);
Assert.assertNotNull(list);
Assert.assertEquals(2, list.size());
for (int i=0; i<list.size(); i++) {
List<RMap> first = list.get(i);
Assert.assertNotNull(first);
Assert.assertEquals(4, first.size());
}
}
/**
* @cdk.bug 1208740
*/
@Test public void testSFBug1208740() throws Exception {
String file1 = "data/mdl/bug1208740_1.mol";
String file2 = "data/mdl/bug1208740_2.mol";
Molecule mol1 = new Molecule();
Molecule mol2 = new Molecule();
InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(file1);
new MDLV2000Reader(ins1, Mode.STRICT).read(mol1);
InputStream ins2 = this.getClass().getClassLoader().getResourceAsStream(file2);
new MDLV2000Reader(ins2, Mode.STRICT).read(mol2);
List list = UniversalIsomorphismTester.getOverlaps(mol1, mol2);
Assert.assertEquals(5, list.size());
list = UniversalIsomorphismTester.getOverlaps(mol2, mol1);
Assert.assertEquals(5, list.size());
// now apply aromaticity detection, then 8 overlaps should be found
// see cdk-user@list.sf.net on 2005-06-16
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol1);
// CDKHueckelAromaticityDetector.detectAromaticity(mol1);
Iterator<IAtom> atoms = mol1.atoms().iterator();
int i= 1;
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
Assert.assertTrue(CDKHueckelAromaticityDetector.detectAromaticity(mol2));
list = UniversalIsomorphismTester.getOverlaps(mol1, mol2);
Assert.assertEquals(8, list.size());
list = UniversalIsomorphismTester.getOverlaps(mol2, mol1);
Assert.assertEquals(8, list.size());
}
/**
* @cdk.bug 999330
*/
@Test public void testSFBug999330() throws Exception {
String file1 = "data/mdl/5SD.mol";
String file2 = "data/mdl/ADN.mol";
Molecule mol1 = new Molecule();
Molecule mol2 = new Molecule();
InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(file1);
new MDLV2000Reader(ins1, Mode.STRICT).read(mol1);
InputStream ins2 = this.getClass().getClassLoader().getResourceAsStream(file2);
new MDLV2000Reader(ins2, Mode.STRICT).read(mol2);
AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(mol2);
mol2 = new Molecule((AtomContainer)permutor.next());
List list1 = UniversalIsomorphismTester.getOverlaps(mol1, mol2);
List list2 = UniversalIsomorphismTester.getOverlaps(mol2, mol1);
Assert.assertEquals(1, list1.size());
Assert.assertEquals(1, list2.size());
Assert.assertEquals(((AtomContainer)list1.get(0)).getAtomCount(),
((AtomContainer)list2.get(0)).getAtomCount());
}
@Test public void testItself() throws Exception{
String smiles="C1CCCCCCC1CC";
QueryAtomContainer query=QueryAtomContainerCreator.createAnyAtomContainer(new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles(smiles),true);
IAtomContainer ac = new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles(smiles);
if (standAlone)
{
System.out.println("AtomCount of query: " + query.getAtomCount());
System.out.println("AtomCount of target: " + ac.getAtomCount());
}
boolean matched =UniversalIsomorphismTester.isSubgraph(ac,query);
if (standAlone) System.out.println("QueryAtomContainer matched: " + matched);
if (!standAlone) Assert.assertTrue(matched);
}
@Test public void testIsIsomorph_IAtomContainer_IAtomContainer() throws Exception {
AtomContainer ac1 = new AtomContainer();
ac1.addAtom(new Atom("C"));
AtomContainer ac2 = new AtomContainer();
ac2.addAtom(new Atom("C"));
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(ac1, ac2));
Assert.assertTrue(UniversalIsomorphismTester.isSubgraph(ac1, ac2));
}
@Test public void testAnyAtomAnyBondCase() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer target = sp.parseSmiles("O1C=CC=C1");
IAtomContainer queryac = sp.parseSmiles("C1CCCC1");
QueryAtomContainer query = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(queryac, false);
Assert.assertTrue("C1CCCC1 should be a subgraph of O1C=CC=C1", UniversalIsomorphismTester.isSubgraph(target, query));
Assert.assertTrue("C1CCCC1 should be a isomorph of O1C=CC=C1", UniversalIsomorphismTester.isIsomorph(target, query));
}
/**
* @cdk.bug 1633201
*/
@Test public void testFirstArgumentMustNotBeAnQueryAtomContainer() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer target = sp.parseSmiles("O1C=CC=C1");
IAtomContainer queryac = sp.parseSmiles("C1CCCC1");
QueryAtomContainer query = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(queryac, false);
try {
UniversalIsomorphismTester.isSubgraph(query, target);
Assert.fail("The UniversalIsomorphism should check when the first arguments is a QueryAtomContainer");
} catch (Exception e) {
// OK, it must Assert.fail!
}
}
/**
* @cdk.bug 2888845
* @throws Exception
*/
@Test
public void testSingleAtomMatching1() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer target = sp.parseSmiles("[H]");
IAtomContainer queryac = sp.parseSmiles("[H]");
QueryAtomContainer query = QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(queryac);
List<List<RMap>> matches = UniversalIsomorphismTester.getIsomorphMaps(target, query);
Assert.assertEquals(1,matches.size());
Assert.assertEquals(1,matches.get(0).size());
RMap mapping = matches.get(0).get(0);
Assert.assertEquals(0, mapping.getId1());
Assert.assertEquals(0, mapping.getId2());
List<List<RMap>> atomMappings = UniversalIsomorphismTester.makeAtomsMapsOfBondsMaps(matches, target, query);
Assert.assertEquals(matches, atomMappings);
}
/**
* @cdk.bug 2888845
* @throws Exception
*/
@Test
public void testSingleAtomMatching2() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer target = sp.parseSmiles("CNC");
IAtomContainer queryac = sp.parseSmiles("C");
QueryAtomContainer query = QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(queryac);
List<List<RMap>> matches = UniversalIsomorphismTester.getIsomorphMaps(target, query);
Assert.assertEquals(2,matches.size());
Assert.assertEquals(1, matches.get(0).size());
Assert.assertEquals(1, matches.get(1).size());
RMap map1 = matches.get(0).get(0);
RMap map2 = matches.get(1).get(0);
Assert.assertEquals(0, map1.getId1());
Assert.assertEquals(0, map1.getId2());
Assert.assertEquals(2, map2.getId1());
Assert.assertEquals(0, map2.getId2());
List<List<RMap>> atomMappings = UniversalIsomorphismTester.makeAtomsMapsOfBondsMaps(matches, target, query);
Assert.assertEquals(matches, atomMappings);
}
/**
* @cdk.bug 2912627
*/
@Test
public void testSingleAtomMatching3() throws CDKException {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer target = sp.parseSmiles("CNC");
IAtomContainer queryac = sp.parseSmiles("C");
List<List<RMap>> matches = UniversalIsomorphismTester.getIsomorphMaps(target, queryac);
Assert.assertEquals(2, matches.size());
Assert.assertEquals(1, matches.get(0).size());
Assert.assertEquals(1, matches.get(1).size());
RMap map1 = matches.get(0).get(0);
RMap map2 = matches.get(1).get(0);
Assert.assertEquals(0, map1.getId1());
Assert.assertEquals(0, map1.getId2());
Assert.assertEquals(2, map2.getId1());
Assert.assertEquals(0, map2.getId2());
List<List<RMap>> atomMappings = UniversalIsomorphismTester.makeAtomsMapsOfBondsMaps(matches, target, queryac);
Assert.assertEquals(matches, atomMappings);
}
}