/* 
 * $Id$
 *
 *  Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
 *  All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are
 * met: 
 *
 *     * Redistributions of source code must retain the above copyright 
 *       notice, this list of conditions and the following disclaimer.
 *     * Redistributions in binary form must reproduce the above
 *       copyright notice, this list of conditions and the following 
 *       disclaimer in the documentation and/or other materials provided 
 *       with the distribution.
 *     * Neither the name of Novartis Institutes for BioMedical Research Inc. 
 *       nor the names of its contributors may be used to endorse or promote 
 *       products derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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 */
package org.RDKit;

import static org.junit.Assert.*;

import org.junit.*;

public class ChemTransformsTests extends GraphMolTest {
	private ROMol m;

	@Before public void setUp() {
	}

	@Test 
	public void test1BRICS() {
		ROMol mol = RWMol.MolFromSmiles("c1ccccc1OC");
                ROMol nmol=RDKFuncs.fragmentOnBRICSBonds(mol);
		assertEquals( 8,mol.getNumAtoms());
		assertEquals( 10,nmol.getNumAtoms());
                assertEquals("[16*]c1ccccc1.[3*]OC",nmol.MolToSmiles(true));

	}
	@Test 
	public void test2BRICS() {
		ROMol mol = RWMol.MolFromSmiles("OC(C)=CC");
                ROMol nmol=RDKFuncs.fragmentOnBRICSBonds(mol);
		assertEquals( 5,mol.getNumAtoms());
		assertEquals( 7,nmol.getNumAtoms());
                assertEquals("[7*]=C(C)O.[7*]=CC",nmol.MolToSmiles(true));

	}
	@Test 
	public void test3BRICS() {
		ROMol mol = RWMol.MolFromSmiles("CCCOCCC(=O)c1ccccc1");
                ROMol nmol=RDKFuncs.fragmentOnBRICSBonds(mol);
		assertEquals( 14,mol.getNumAtoms());
		assertEquals( 20,nmol.getNumAtoms());
                assertEquals("[16*]c1ccccc1.[3*]O[3*].[4*]CCC.[4*]CCC([6*])=O",nmol.MolToSmiles(true));

	}

        @Test
	public void testSubset() {
	    ROMol mol = RWMol.MolFromSmiles("c1ccccc1CCN");
	    UInt_Vect vect = new UInt_Vect(mol.getNumAtoms());
	    for(int i=0;i<6;++i) {
		  vect.add(i);
	    }
	    // atom copy
	    ROMol sub = RDKFuncs.copyMolSubset(mol, vect);
	    assertEquals("c1ccccc1", sub.MolToSmiles());

	}

	public static void main(String args[]) {
		org.junit.runner.JUnitCore.main("org.RDKit.ChemTransformsTests");
	}

}
