SMILESBuilderTest.java

/*
 * 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.DefaultMolecule;
import com.chemhack.jsMolEditor.client.io.daylight.SMILESBuilder;
import com.google.gwt.junit.client.GWTTestCase;

/**
 * @author Richard L. Apodaca
 *         Duan Lian
 */
public class SMILESBuilderTest extends GWTTestCase {


    public String getModuleName() {
        return "com.chemhack.jsMolEditor.Editor";
    }
    
    public void testItShouldConnectTwoAtoms() {
        Molecule result = new DefaultMolecule();
        SMILESBuilder builder = new SMILESBuilder(result);

        builder.addHead("C");
        builder.addHead("C");

        assertEquals(2, result.countAtoms());
        assertEquals(1, result.countBonds());
        assertEquals(1, result.getBond(result.getAtom(0), result.getAtom(1)).getType());
    }

    public void testItShouldConnectTwoAtomsThroughADoubleBond() {
        Molecule result = new DefaultMolecule();
        SMILESBuilder builder = new SMILESBuilder(result);

        builder.addHead("C");
        builder.addBond(2);
        builder.addHead("C");

        assertEquals(2, result.countAtoms());
        assertEquals(1, result.countBonds());
        assertEquals(2, result.getBond(result.getAtom(0), result.getAtom(1)).getType());
    }

    public void testItShouldBranchAtSecondaryAtom() {
        Molecule result = new DefaultMolecule();
        SMILESBuilder builder = new SMILESBuilder(result);

        builder.addHead("C");
        builder.addHead("C");
        builder.openBranch();
        builder.addHead("C");
        builder.closeBranch();
        builder.addHead("C");

        assertEquals(4, result.countAtoms());
        assertEquals(3, result.countBonds());
        assertEquals(3, result.getAtom(1).countNeighbors());
    }

    public void testItShouldBranchAtTertiaryAtom() {
        Molecule result = new DefaultMolecule();
        SMILESBuilder builder = new SMILESBuilder(result);

        builder.addHead("C");
        builder.addHead("C");
        builder.openBranch();
        builder.addHead("C");
        builder.closeBranch();
        builder.openBranch();
        builder.addHead("C");
        builder.closeBranch();
        builder.addHead("C");

        assertEquals(5, result.countAtoms());
        assertEquals(4, result.countBonds());
        assertEquals(4, result.getAtom(1).countNeighbors());
    }

    public void testItShouldCreateANestedBranch() {
        Molecule result = new DefaultMolecule();
        SMILESBuilder builder = new SMILESBuilder(result);

        builder.addHead("C"); //0
        builder.addHead("C"); //1
        builder.openBranch();
        builder.addHead("C"); //2
        builder.openBranch();
        builder.addHead("C"); //3
        builder.closeBranch();
        builder.addHead("C"); //4
        builder.closeBranch();
        builder.addHead("C"); //5

        assertEquals(6, result.countAtoms());
        assertEquals(5, result.countBonds());
        assertEquals(3, result.getAtom(1).countNeighbors());
        assertEquals(3, result.getAtom(2).countNeighbors());
        assertEquals(1, result.getAtom(5).countNeighbors());

        try {
            builder.closeBranch();

            fail();
        } catch (IllegalStateException ignore) {
        }
    }

    public void testItShouldThrowWhenClosingANonexistantBranch() {
        Molecule result = new DefaultMolecule();
        SMILESBuilder builder = new SMILESBuilder(result);

        try {
            builder.closeBranch();

            fail();
        } catch (IllegalStateException ignore) {
        }
    }

    public void testItShouldCloseACycle() {
        Molecule result = new DefaultMolecule();
        SMILESBuilder builder = new SMILESBuilder(result);

        builder.addHead("C");
        builder.ring("1");
        builder.addHead("C");
        builder.addHead("C");
        builder.ring("1");

        assertEquals(3, result.countAtoms());
        assertEquals(3, result.countBonds());
    }

    public void testItShouldReuseARingLabel() {
        Molecule result = new DefaultMolecule();
        SMILESBuilder builder = new SMILESBuilder(result);

        builder.addHead("C"); //0
        builder.ring("1");
        builder.addHead("C"); //1
        builder.addHead("C"); //2
        builder.ring("1");
        builder.addHead("C"); //3
        builder.ring("1");
        builder.addHead("C"); //4
        builder.addHead("C"); //5
        builder.ring("1");

        assertEquals(6, result.countAtoms());
        assertEquals(7, result.countBonds());
        assertEquals(3, result.getAtom(2).countNeighbors());
        assertEquals(3, result.getAtom(3).countNeighbors());
    }
}