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90 lines
3.2 KiB
Java
90 lines
3.2 KiB
Java
/*
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* $Id: ChemSmartsTests.java 131 2011-01-20 22:01:29Z ebakke $
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*
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* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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package org.RDKit;
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import static org.junit.Assert.*;
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import java.io.File;
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import org.junit.*;
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public class ChemSmartsTests extends GraphMolTest {
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private ROMol m;
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@Before
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public void setUp() {
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String rdpath = System.getenv("RDBASE");
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if (rdpath == null)
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org.junit.Assert.fail("No definition for RDBASE");
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File base = new File(rdpath);
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File testFile = new File(base, "rdkit" + File.separator + "Chem"
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+ File.separator + "test_data" + File.separator + "quinone.mol");
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String fn = testFile.getAbsolutePath();
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m = RWMol.MolFromMolFile(fn);
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}
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// testing molecule
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@Test
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public void testMol() {
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assertEquals("bad nAtoms", 8, m.getNumAtoms());
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}
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// testing smarts match
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@Test
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public void testMatch() {
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ROMol p = RWMol.MolFromSmarts("CC(=O)C");
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Match_Vect_Vect matches = m.getSubstructMatches(p);
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assertEquals("bad match count: " + matches.size(), 2, matches.size());
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for (int i = 0; i < matches.size(); i++)
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assertEquals("bad match (" + i + ")", 4, matches.get(i).size());
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}
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// test atom order in smarts match
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@Test
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public void testOrder() {
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ROMol p = RWMol.MolFromSmarts("CC(=[O,N])C");
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Match_Vect_Vect matches = m.getSubstructMatches(p);
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Match_Vect match = matches.get(0);
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String atoms = "";
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for (int i = 0; i < match.size(); i++)
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atoms += m.getAtomWithIdx(match.get(i).getSecond()).getSymbol();
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assertEquals("bad atom ordering: " + atoms, "CCOC", atoms);
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}
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main("org.RDKit.ChemSmartsTests");
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}
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}
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