/*
* MX Cheminformatics Tools for Java
*
* Copyright (c) 2007, 2008 Metamolecular, LLC
*
* http://metamolecular.com
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.chemhack.jsMolEditor.client.test;
import com.chemhack.jsMolEditor.client.model.Molecule;
import com.chemhack.jsMolEditor.client.model.MoleculeKit;
import com.chemhack.jsMolEditor.client.model.Atom;
import com.chemhack.jsMolEditor.client.model.DefaultMolecule;
import com.chemhack.jsMolEditor.client.io.Molecules;
import com.chemhack.jsMolEditor.client.map.Mapper;
import com.chemhack.jsMolEditor.client.map.DefaultMapper;
import com.google.gwt.junit.client.GWTTestCase;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* @author Richard L. Apodaca
* Duan Lian
*/
public class MapperTest extends GWTTestCase {
private Molecule benzene;
private Molecule toluene;
private Molecule toluene4;
private Molecule phenol;
private Molecule pyridine;
private Molecule chloroisoquinoline4;
private Molecule chlorobenzene;
private Molecule acetone;
private Molecule hexane;
private Molecule naphthalene;
private Molecule propane;
private Molecule cyclopropane;
private Molecule pyridazine;
@Override
protected void gwtSetUp() throws Exception
{
benzene = Molecules.createBenzene();
toluene = Molecules.createToluene();
toluene4 = create4Toluene();
phenol = Molecules.createPhenol();
pyridine = Molecules.createPyridine();
chloroisoquinoline4 = MoleculeKit.readMolfile("[NO NAME]\r\n CHEMWRIT 2D\r\nCreated with ChemWriter - http://metamolecular.com/chemwriter\r\n 11 12 0 0 0 0 0 0 0 0 0 V2000\r\n 0.8800 -1.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 1.7460 -2.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 2.6121 -1.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 2.6121 -0.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 1.7460 -0.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 0.8800 -0.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 3.4781 -2.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 4.3442 -1.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 4.3442 -0.7400 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\r\n 3.4781 -0.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 3.4781 -3.2400 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\r\n 1 2 2 0 0 0 0\r\n 2 3 1 0 0 0 0\r\n 3 4 2 0 0 0 0\r\n 4 5 1 0 0 0 0\r\n 5 6 2 0 0 0 0\r\n 6 1 1 0 0 0 0\r\n 3 7 1 0 0 0 0\r\n 7 8 2 0 0 0 0\r\n 8 9 1 0 0 0 0\r\n 9 10 2 0 0 0 0\r\n 10 4 1 0 0 0 0\r\n 7 11 1 0 0 0 0\r\nM END");
chlorobenzene = MoleculeKit.readMolfile("[NO NAME]\r\n CHEMWRIT 2D\r\nCreated with ChemWriter - http://metamolecular.com/chemwriter\r\n 7 7 0 0 0 0 0 0 0 0 0 V2000\r\n -3.3359 0.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n -2.4699 0.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n -1.6038 0.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n -1.6038 1.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n -2.4699 2.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n -3.3359 1.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n -0.7378 2.2400 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\r\n 1 2 2 0 0 0 0\r\n 2 3 1 0 0 0 0\r\n 3 4 2 0 0 0 0\r\n 4 5 1 0 0 0 0\r\n 5 6 2 0 0 0 0\r\n 6 1 1 0 0 0 0\r\n 4 7 1 0 0 0 0\r\nM END");
pyridazine = MoleculeKit.readMolfile("[NO NAME]\r\n CHEMWRIT 2D\r\nCreated with ChemWriter - http://metamolecular.com/chemwriter\r\n 6 6 0 0 0 0 0 0 0 0 0 V2000\r\n 1.8322 -5.0815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 2.6982 -5.5815 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\r\n 3.5643 -5.0815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 3.5643 -4.0815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 2.6982 -3.5815 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\r\n 1.8322 -4.0815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 1 2 2 0 0 0 0\r\n 2 3 1 0 0 0 0\r\n 3 4 2 0 0 0 0\r\n 4 5 1 0 0 0 0\r\n 5 6 2 0 0 0 0\r\n 6 1 1 0 0 0 0\r\nM END");
acetone = Molecules.createAcetone();
hexane = Molecules.createHexane();
naphthalene = Molecules.createNaphthalene();
propane = Molecules.createPropane();
cyclopropane = Molecules.createCyclopropane();
}
public String getModuleName() {
return "com.chemhack.jsMolEditor.Editor";
}
public void testItShouldNotMatchHexaneToBenzene() {
Mapper mapper = new DefaultMapper(hexane);
assertFalse(mapper.hasMap(benzene));
}
public void testItShouldNotMatchPyridazineToNaphthalene() {
Mapper mapper = new DefaultMapper(pyridazine);
assertFalse(mapper.hasMap(naphthalene));
}
public void testItShouldNotMatchChlorobenzeneTo4ChloroIsoquinoline() {
Mapper mapper = new DefaultMapper(chlorobenzene);
assertFalse(mapper.hasMap(chloroisoquinoline4));
}
public void testItShouldMatchBenzeneToBenzene() {
Mapper mapper = new DefaultMapper(benzene);
assertTrue(mapper.hasMap(benzene));
}
public void testItShouldNotMatchBenzeneToPyridine() {
Mapper mapper = new DefaultMapper(benzene);
assertFalse(mapper.hasMap(pyridine));
mapper = new DefaultMapper(pyridine);
assertFalse(mapper.hasMap(benzene));
}
public void testItShouldNotMatchTolueneToBenzene() {
Mapper mapper = new DefaultMapper(toluene);
assertFalse(mapper.hasMap(benzene));
}
public void testItShouldMatchAcetoneToAcetone() {
Mapper mapper = new DefaultMapper(acetone);
assertTrue(mapper.hasMap(acetone));
}
public void testItShouldMatchPropaneToCyclopropane() {
Mapper mapper = new DefaultMapper(propane);
assertTrue(mapper.hasMap(cyclopropane));
}
public void testItShouldFindTwoMapsFromHexaneToHexane() {
Mapper mapper = new DefaultMapper(hexane);
List<Map<Atom, Atom>> maps = mapper.getMaps(hexane);
assertEquals(2, maps.size());
}
public void testItShouldNotMatchTolueneToPhenol() {
Mapper mapper = new DefaultMapper(toluene);
assertFalse(mapper.hasMap(phenol));
}
public void testItShouldMapSixAtomsOfBenzeneOntoBenzene() {
Mapper mapper = new DefaultMapper(benzene);
Map<Atom, Atom> map = mapper.getFirstMap(benzene);
assertEquals(6, map.size());
}
public void testItShouldCountTwelveMapsForBenzeneOntoBenzene() {
Mapper mapper = new DefaultMapper(benzene);
assertEquals(12, mapper.countMaps(benzene));
}
public void testItShouldCountTwoMapsForTolueneOntoToluene() {
Mapper mapper = new DefaultMapper(toluene);
assertEquals(2, mapper.countMaps(toluene));
}
public void testItShouldFindTwelveMapsForBenzeneOntoBenzene() {
Mapper mapper = new DefaultMapper(benzene);
List<Map<Atom, Atom>> maps = mapper.getMaps(benzene);
assertTrue(containsAutomap(maps, benzene));
assertEquals(12, maps.size());
}
public void testItShouldFindTwoMapsForTolueneOntoToluene() {
Mapper mapper = new DefaultMapper(toluene);
List<Map<Atom, Atom>> maps = mapper.getMaps(toluene);
assertTrue(containsAutomap(maps, toluene));
assertEquals(2, maps.size());
assertFalse(maps.get(0).equals(maps.get(1)));
}
public void testItShouldFindTwelveMapsForBenzeneOntoToluene() {
Mapper mapper = new DefaultMapper(benzene);
List<Map<Atom, Atom>> maps = mapper.getMaps(toluene);
assertEquals(12, maps.size());
}
public void testItShouldFindTwentyFourMapsForBenzeneOntoNaphthalene() {
Mapper mapper = new DefaultMapper(benzene);
List<Map<Atom, Atom>> maps = mapper.getMaps(naphthalene);
assertEquals(24, maps.size());
}
public void testItShouldFindAMapForEquivalentFormsOfToluene() {
Mapper mapper = new DefaultMapper(toluene4);
Map<Atom, Atom> map = mapper.getFirstMap(toluene);
assertEquals(7, map.size());
}
public void testItShouldFindTwoMapsForEquivalentFormsOfToluene() {
Mapper mapper = new DefaultMapper(toluene4);
List<Map<Atom, Atom>> maps = mapper.getMaps(toluene);
assertEquals(2, maps.size());
assertTrue(maps.get(0).get(toluene4.getAtom(6)).countVirtualHydrogens() == 3);
assertFalse(containsAutomap(maps, toluene4));
}
private boolean containsAutomap(List<Map<Atom, Atom>> maps, Molecule molecule) {
Map<Atom, Atom> map = new HashMap<Atom, Atom>();
for (int i = 0; i < molecule.countAtoms(); i++) {
Atom atom = molecule.getAtom(i);
map.put(atom, atom);
}
return maps.contains(map);
}
private Molecule create4Toluene() {
Molecule result = new DefaultMolecule();
Atom c1 = result.addAtom("C");
Atom c2 = result.addAtom("C");
Atom c3 = result.addAtom("C");
Atom c4 = result.addAtom("C");
Atom c5 = result.addAtom("C");
Atom c6 = result.addAtom("C");
Atom c7 = result.addAtom("C");
result.connect(c1, c2, 1);
result.connect(c2, c3, 2);
result.connect(c3, c4, 1);
result.connect(c4, c5, 2);
result.connect(c5, c6, 1);
result.connect(c6, c1, 2);
result.connect(c7, c4, 1);
return result;
}
}