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/*
* $Id: ChemSmartsTests.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 java.io.File;
import org.junit.*;
public class ChemSmartsTests extends GraphMolTest {
private ROMol m;
@Before
public void setUp() {
String rdpath = System.getenv("RDBASE");
if (rdpath == null)
org.junit.Assert.fail("No definition for RDBASE");
File base = new File(rdpath);
File testFile = new File(base, "rdkit" + File.separator + "Chem"
+ File.separator + "test_data" + File.separator + "quinone.mol");
String fn = testFile.getAbsolutePath();
m = RWMol.MolFromMolFile(fn);
}
// testing molecule
@Test
public void testMol() {
assertEquals("bad nAtoms", 8, m.getNumAtoms());
}
// testing smarts match
@Test
public void testMatch() {
ROMol p = RWMol.MolFromSmarts("CC(=O)C");
Match_Vect_Vect matches = m.getSubstructMatches(p);
assertEquals("bad match count: " + matches.size(), 2, matches.size());
for (int i = 0; i < matches.size(); i++)
assertEquals("bad match (" + i + ")", 4, matches.get(i).size());
}
// test atom order in smarts match
@Test
public void testOrder() {
ROMol p = RWMol.MolFromSmarts("CC(=[O,N])C");
Match_Vect_Vect matches = m.getSubstructMatches(p);
Match_Vect match = matches.get(0);
String atoms = "";
for (int i = 0; i < match.size(); i++)
atoms += m.getAtomWithIdx(match.get(i).getSecond()).getSymbol();
assertEquals("bad atom ordering: " + atoms, "CCOC", atoms);
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.ChemSmartsTests");
}
}
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