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105 lines
4.0 KiB
Java
105 lines
4.0 KiB
Java
/*
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* $Id: LipinskiTests.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 LipinskiTests extends GraphMolTest {
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private File dataFile;
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@Before
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public void setUp() {
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File base = getRdBase();
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dataFile = new File(base, "Data" + File.separator + "NCI" + File.separator +
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"first_200.props.sdf");
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}
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@Test
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public void test1() {
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SDMolSupplier suppl = new SDMolSupplier(dataFile.getPath());
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int idx = 1;
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while (!suppl.atEnd()) {
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long calc;
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long orig;
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ROMol m = suppl.next();
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calc = RDKFuncs.calcNumHBD(m);
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orig = Integer.parseInt(m.getProp("NUM_HDONORS"));
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assertTrue("bad num h donors for mol " + idx + " ("
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+ m.getProp("SMILES") + "): " + calc + " != " + orig,
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calc==orig);
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calc = RDKFuncs.calcNumHBA(m);
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orig = Integer.parseInt(m.getProp("NUM_HACCEPTORS"));
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assertTrue("bad num h acceptors for mol " + idx + " ("
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+ m.getProp("SMILES") + "): " + calc + " != " + orig,
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calc==orig);
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calc = RDKFuncs.calcNumHeteroatoms(m);
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orig = Integer.parseInt(m.getProp("NUM_HETEROATOMS"));
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assertTrue("bad num heteroatoms for mol " + idx + " ("
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+ m.getProp("SMILES") + "): " + calc + " != " + orig,
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calc==orig);
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calc = RDKFuncs.calcNumRotatableBonds(m);
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orig = Integer.parseInt(m.getProp("NUM_ROTATABLEBONDS"));
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assertTrue("bad num rotatable bonds for mol " + idx + " ("
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+ m.getProp("SMILES") + "): " + calc + " != " + orig,
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calc==orig);
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idx += 1;
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}
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}
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// testing a problem with acceptor definition
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@Test
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public void testIssue2183420() {
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assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("NC")));
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assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("CNC")));
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assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("CN(C)C")));
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assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("NC(=O)")));
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assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("NC(=O)C")));
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assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("CNC(=O)")));
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assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("CNC(=O)C")));
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assertEquals(2,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("O=CNC(=O)C")));
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assertEquals(2,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("O=C(C)NC(=O)C")));
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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.LipinskiTests");
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}
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}
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