/*
 * 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.metamolecular.mx.test;

import com.metamolecular.mx.io.daylight.SMILESReader;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.DefaultMolecule;
import com.metamolecular.mx.model.Molecule;
import junit.framework.TestCase;

/**
 * @author Richard L. Apodaca
 */
public class SMILESReaderTest extends TestCase
{

  private SMILESReader reader;

  @Override
  protected void setUp() throws Exception
  {
    reader = new SMILESReader();
  }

  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 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 testItShouldThrowWhenGivenIllegalAtomSymbol()
  {
    Molecule input = new DefaultMolecule();

    try
    {
      reader.read(input, "C!C");
      fail();
    } catch (IllegalArgumentException ignore)
    {
    }
  }
}
@@ -2643,32 +2643,375 @@
 eighbors());%0A  %7D
+%0A  %0A  public void testItShouldReadANestedBranch()%0A  %7B%0A    Molecule input = new DefaultMolecule();%0A    %0A    reader.read(input, %22CC(C(C)C)C%22);%0A    %0A    assertEquals(6, input.countAtoms());%0A    assertEquals(5, input.countBonds());%0A    assertEquals(3, input.getAtom(1).countNeighbors());%0A    assertEquals(3, input.getAtom(2).countNeighbors());%0A  %7D
 %0A%0A  public void 

test and impl for smiles nested branching