/*
* 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.io.daylight.SMILESReader;
import com.chemhack.jsMolEditor.client.model.DefaultMolecule;
import com.chemhack.jsMolEditor.client.model.Molecule;
import com.chemhack.jsMolEditor.client.model.Atom;
import com.google.gwt.junit.client.GWTTestCase;
/**
* @author Richard L. Apodaca
* Duan Lian
*/
public class SMILESReaderTest extends GWTTestCase {
private SMILESReader reader = new SMILESReader();
public String getModuleName() {
return "com.chemhack.jsMolEditor.Editor";
}
public void testItShouldReadALinearChain() {
Molecule input = new DefaultMolecule();
reader.read(input, "CCCCCC");
assertEquals(6, input.countAtoms());
assertEquals(5, input.countBonds());
}
public void testItShouldReadACycle() {
Molecule input = new DefaultMolecule();
reader.read(input, "C1CCCCC1");
assertEquals(6, input.countAtoms());
assertEquals(6, input.countBonds());
}
public void testItShouldReadATertiaryBranch() {
Molecule input = new DefaultMolecule();
reader.read(input, "CC(C)C");
assertEquals(4, input.countAtoms());
assertEquals(3, input.countBonds());
assertEquals(3, input.getAtom(1).countNeighbors());
}
public void testItShouldReadAQuaternaryBranch() {
Molecule input = new DefaultMolecule();
reader.read(input, "CC(C)(C)C");
assertEquals(5, input.countAtoms());
assertEquals(4, input.countBonds());
assertEquals(4, input.getAtom(1).countNeighbors());
}
public void testItShouldReadANestedBranch() {
Molecule input = new DefaultMolecule();
reader.read(input, "CC(C(C)C)C");
assertEquals(6, input.countAtoms());
assertEquals(5, input.countBonds());
assertEquals(3, input.getAtom(1).countNeighbors());
assertEquals(3, input.getAtom(2).countNeighbors());
}
public void testItShouldReadCubane() {
Molecule input = new DefaultMolecule();
reader.read(input, "C12C3C4C1C5C4C3C25");
assertEquals(8, input.countAtoms());
assertEquals(12, input.countBonds());
for (int i = 0; i < input.countAtoms(); i++) {
Atom atom = input.getAtom(i);
assertEquals(3, atom.countNeighbors());
}
}
public void testItShouldReadADoubleBond() {
Molecule input = new DefaultMolecule();
reader.read(input, "C=CC");
assertEquals(3, input.countAtoms());
assertEquals(2, input.getBond(0).getType());
}
public void testItShouldReadKekuleBenzene() {
Molecule input = new DefaultMolecule();
reader.read(input, "C1=CC=CC=C1");
assertEquals(6, input.countAtoms());
for (int i = 0; i < input.countAtoms(); i++) {
assertEquals(2, input.getAtom(i).countNeighbors());
assertEquals(1, input.getAtom(i).countVirtualHydrogens());
}
}
public void testItShouldReadATripleBond() {
Molecule input = new DefaultMolecule();
reader.read(input, "C#CC");
assertEquals(3, input.countAtoms());
assertEquals(3, input.getBond(0).getType());
}
public void testItShouldThrowWhenGivenIllegalAtomSymbol() {
Molecule input = new DefaultMolecule();
try {
reader.read(input, "C!C");
fail();
} catch (IllegalArgumentException ignore) {
}
}
public void testItShouldReadASMILESThroughAStaticMethod() {
Molecule result = SMILESReader.read("C1=CC=CC=C1");
assertEquals(6, result.countAtoms());
}
}