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/*
* $Id: LipinskiTests.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 LipinskiTests extends GraphMolTest {
private File dataFile;
@Before
public void setUp() {
File base = getRdBase();
dataFile = new File(base, "Data" + File.separator + "NCI" + File.separator +
"first_200.props.sdf");
}
@Test
public void test1() {
// what is the default num rot bonds calculation?
String rot_prop = "NUM_ROTATABLEBONDS";
if( RDKFuncs.calcNumRotatableBonds(
RWMol.MolFromSmiles("CC(C)(C)c1cc(O)c(cc1O)C(C)(C)C")) == 2 ) {
rot_prop = "NUM_ROTATABLEBONDS_O";
}
SDMolSupplier suppl = new SDMolSupplier(dataFile.getPath());
int idx = 1;
while (!suppl.atEnd()) {
long calc;
long orig;
ROMol m = suppl.next();
calc = RDKFuncs.calcNumHBD(m);
orig = Integer.parseInt(m.getProp("NUM_HDONORS"));
assertTrue("bad num h donors for mol " + idx + " ("
+ m.getProp("SMILES") + "): " + calc + " != " + orig,
calc==orig);
calc = RDKFuncs.calcNumHBA(m);
orig = Integer.parseInt(m.getProp("NUM_HACCEPTORS"));
assertTrue("bad num h acceptors for mol " + idx + " ("
+ m.getProp("SMILES") + "): " + calc + " != " + orig,
calc==orig);
calc = RDKFuncs.calcNumHeteroatoms(m);
orig = Integer.parseInt(m.getProp("NUM_HETEROATOMS"));
assertTrue("bad num heteroatoms for mol " + idx + " ("
+ m.getProp("SMILES") + "): " + calc + " != " + orig,
calc==orig);
calc = RDKFuncs.calcNumRotatableBonds(m);
orig = Integer.parseInt(m.getProp(rot_prop));
assertTrue("bad num rotatable bonds for mol " + idx + " ("
+ m.getProp("SMILES") + "): " + calc + " != " + orig,
calc==orig);
calc = RDKFuncs.calcNumRotatableBonds(m, false);
orig = Integer.parseInt(m.getProp("NUM_ROTATABLEBONDS_O"));
assertTrue("bad num rotatable bonds for mol " + idx + " ("
+ m.getProp("SMILES") + "): " + calc + " != " + orig,
calc==orig);
calc = RDKFuncs.calcNumRotatableBonds(m, NumRotatableBondsOptions.NonStrict);
orig = Integer.parseInt(m.getProp("NUM_ROTATABLEBONDS_O"));
assertTrue("bad num rotatable bonds for mol " + idx + " ("
+ m.getProp("SMILES") + "): " + calc + " != " + orig,
calc==orig);
calc = RDKFuncs.calcNumRotatableBonds(m, NumRotatableBondsOptions.Strict);
orig = Integer.parseInt(m.getProp("NUM_ROTATABLEBONDS"));
assertTrue("bad num rotatable bonds for mol " + idx + " ("
+ m.getProp("SMILES") + "): " + calc + " != " + orig,
calc==orig);
idx += 1;
}
}
// testing a problem with acceptor definition
@Test
public void testIssue2183420() {
assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("NC")));
assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("CNC")));
assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("CN(C)C")));
assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("NC(=O)")));
assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("NC(=O)C")));
assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("CNC(=O)")));
assertEquals(1,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("CNC(=O)C")));
assertEquals(2,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("O=CNC(=O)C")));
assertEquals(2,RDKFuncs.calcNumHBA(RWMol.MolFromSmiles("O=C(C)NC(=O)C")));
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.LipinskiTests");
}
}
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