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/*
* $Id: HManipulationsTests.java 131 2011-01-20 22:01:29Z ebakke $
*
* Copyright (c) 2010, 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
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
package org.RDKit;
import static org.junit.Assert.*;
import org.junit.*;
public class HManipulationsTests extends GraphMolTest {
@Before
public void setUp() {
}
@Test
public void testExplicitHs() {
ROMol m = RWMol.MolFromSmiles("CC(=O)[OH]");
assertEquals(m.getNumAtoms(), 4);
ROMol m2 = m.addHs(true);
assertEquals(m2.getNumAtoms(), 5);
m2 = m2.removeHs(true);
assertEquals(m2.getNumAtoms(), 5);
}
@Test
public void testImplicitHs() {
ROMol m = RWMol.MolFromSmiles("CC(=O)[OH]");
ROMol m2 = m.addHs(true);
m2 = m2.removeHs(true);
m2 = m2.removeHs(false);
assertEquals(m2.getNumAtoms(), 4);
m2 = m.addHs(false);
assertEquals(m2.getNumAtoms(), 8);
}
@Test
public void testExplicitAndImplicitHs() {
ROMol m = RWMol.MolFromSmiles("CC(=O)[OH]");
ROMol m2 = m.addHs(true);
assertEquals(m2.getNumAtoms(), 5);
m2 = m2.removeHs(true);
assertEquals(m2.getNumAtoms(), 5);
m2 = m2.removeHs(false);
assertEquals(m2.getNumAtoms(), 4);
}
@Test
public void testMergingQueryHs() {
// Create a molecule without sanitizing -- expect
// that the hydrogen is kept even though it should be
// implicit.
ROMol m = RWMol.MolFromSmiles("CC[H]", 0, false);
assertEquals(m.getNumAtoms(), 3);
ROMol m2 = m.mergeQueryHs();
assertEquals(m2.getNumAtoms(), 2);
assertTrue(m2.getAtomWithIdx(1).hasQuery());
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.HManipulationsTests");
}
}
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