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/*
* $Id: DescriptorTests.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.*;
import java.util.*;
import org.junit.*;
public class DescriptorTests extends GraphMolTest {
private File dataFile;
public class DescriptorTestEntry {
String smi;
double clogp;
double mr;
int lineNo;
public DescriptorTestEntry(int lineNo, String[] line) {
this.lineNo = lineNo;
smi = line[0].trim();
clogp = Double.parseDouble(line[1].trim());
mr = Double.parseDouble(line[2].trim());
}
}
public List<DescriptorTestEntry> readData(String fn) throws Exception {
List<DescriptorTestEntry> data = new ArrayList<DescriptorTestEntry>();
int lineNo = 0;
BufferedReader reader = new BufferedReader(new FileReader(fn));
String line;
// Skip the header
try {
reader.readLine();
while ((line = reader.readLine()) != null) {
lineNo += 1;
if (line.length() > 0 && !line.startsWith("#")) {
String[] splitL = line.split("\t");
if (splitL.length == 3)
data.add(new DescriptorTestEntry(lineNo, splitL));
}
}
} finally {
reader.close();
}
return data;
}
@Before
public void setUp() {
File base = getRdBase();
dataFile = new File(base, "rdkit" + File.separator + "Chem" + File.separator + "test_data"
+ File.separator + "Crippen.csv");
}
@Test
public void testLogP() throws Exception {
List<DescriptorTestEntry> data = readData(dataFile.getPath());
for (DescriptorTestEntry item : data) {
ROMol mol = RWMol.MolFromSmiles(item.smi);
Double_Pair calcProps = RDKFuncs.calcCrippenDescriptors(mol);
assertEquals("cLogp on " + item.smi, item.clogp, calcProps.getFirst(), defaultDoubleTol);
assertEquals("mr on " + item.smi, item.mr, calcProps.getSecond(), defaultDoubleTol);
}
}
@Test
public void testRepeat() throws Exception {
List<DescriptorTestEntry> data = readData(dataFile.getPath());
for (DescriptorTestEntry item : data) {
ROMol mol = RWMol.MolFromSmiles(item.smi);
Double_Pair calcProps = RDKFuncs.calcCrippenDescriptors(mol);
assertEquals("cLogp on " + item.smi, item.clogp, calcProps.getFirst(), defaultDoubleTol);
assertEquals("mr on " + item.smi, item.mr, calcProps.getSecond(), defaultDoubleTol);
}
}
@Test
public void testIssue80() {
ROMol m = RWMol.MolFromSmiles("CCOC");
double ref = RDKFuncs.calcCrippenDescriptors(m).getFirst();
double probe = RDKFuncs.calcCrippenDescriptors(m).getFirst();
assertEquals(ref, probe, 0.0);
}
@Test
public void testIssue1749494() {
ROMol m1 = RWMol.MolFromSmiles("[*]CC");
double v = RDKFuncs.calcCrippenDescriptors(m1).getFirst();
assertEquals( 0.9739,v,defaultDoubleTol);
}
@Test public void testDescriptors1() {
ROMol m1,m2,m3;
m1 = RWMol.MolFromSmiles("C1=CC=CC=C1");
m2 = RWMol.MolFromSmiles("C1=CC=CC=N1");
m3 = RWMol.MolFromSmiles("C1=CC=CC=C1CC(=O)O");
long tmp;
tmp=RDKFuncs.calcNumHBA(m1);
assertEquals(tmp,0);
tmp=RDKFuncs.calcNumHBA(m2);
assertEquals(tmp,1);
tmp=RDKFuncs.calcNumHBA(m3);
assertEquals(tmp,1);
tmp=RDKFuncs.calcNumHBD(m1);
assertEquals(tmp,0);
tmp=RDKFuncs.calcNumHBD(m2);
assertEquals(tmp,0);
tmp=RDKFuncs.calcNumHBD(m3);
assertEquals(tmp,1);
tmp=RDKFuncs.calcLipinskiHBA(m1);
assertEquals(tmp,0);
tmp=RDKFuncs.calcLipinskiHBA(m2);
assertEquals(tmp,1);
tmp=RDKFuncs.calcLipinskiHBA(m3);
assertEquals(tmp,2);
tmp=RDKFuncs.calcLipinskiHBD(m1);
assertEquals(tmp,0);
tmp=RDKFuncs.calcLipinskiHBD(m2);
assertEquals(tmp,0);
tmp=RDKFuncs.calcLipinskiHBD(m3);
assertEquals(tmp,1);
}
@Test public void testDescriptors2() {
ROMol m1,m2;
m1 = RWMol.MolFromSmiles("C1=CC=CC=C1");
m2 = RWMol.MolFromSmiles("C1=CC=CC=N1");
double tmp;
tmp=RDKFuncs.calcMolLogP(m1);
assertEquals(tmp,1.687,0.001);
tmp=RDKFuncs.calcMolLogP(m2);
assertEquals(tmp,1.082,0.001);
tmp=RDKFuncs.calcMolMR(m1);
assertEquals(tmp,26.442,0.001);
tmp=RDKFuncs.calcMolMR(m2);
assertEquals(tmp,24.237,0.001);
}
@Test public void testDescriptors3() {
ROMol m1,m2,m3;
m1 = RWMol.MolFromSmiles("C1=CC=CC=C1");
m2 = RWMol.MolFromSmiles("C1=CC=CC=N1");
m3 = RWMol.MolFromSmiles("C1=CC=CC=C1CC(=O)O");
double tmp;
tmp=RDKFuncs.calcTPSA(m1);
assertEquals(tmp,0,0.01);
tmp=RDKFuncs.calcTPSA(m2);
assertEquals(tmp,12.89,0.01);
tmp=RDKFuncs.calcTPSA(m3);
assertEquals(tmp,37.30,0.01);
}
@Test public void testVSADescriptors() {
ROMol m1,m2,m3;
m1 = RWMol.MolFromSmiles("CO");
m2 = RWMol.MolFromSmiles("CCO");
Double_Vect v;
v = RDKFuncs.calcSlogP_VSA(m1);
assertEquals(v.get(0),0.0,0.001);
assertEquals(v.get(1),12.216,0.001);
v = RDKFuncs.calcSlogP_VSA(m2);
assertEquals(v.get(0),0.0,0.001);
assertEquals(v.get(1),11.713,0.001);
assertEquals(v.get(4),6.924,0.001);
v = RDKFuncs.calcSMR_VSA(m1);
assertEquals(v.get(0),5.106,0.001);
assertEquals(v.get(1),0.0,0.001);
assertEquals(v.get(5),7.110,0.001);
v = RDKFuncs.calcSMR_VSA(m2);
assertEquals(v.get(0),5.106,0.001);
assertEquals(v.get(4),6.924,0.001);
assertEquals(v.get(5),6.607,0.001);
v = RDKFuncs.calcPEOE_VSA(m1);
assertEquals(v.get(0),5.106,0.001);
assertEquals(v.get(7),7.110,0.001);
assertEquals(v.get(5),0.000,0.001);
v = RDKFuncs.calcPEOE_VSA(m2);
assertEquals(v.get(0),5.106,0.001);
assertEquals(v.get(6),6.924,0.001);
assertEquals(v.get(7),6.607,0.001);
}
@Test public void testMW() {
ROMol m1;
m1 = RWMol.MolFromSmiles("C");
assertEquals(16.043,RDKFuncs.calcAMW(m1),0.001);
assertEquals(16.031,RDKFuncs.calcExactMW(m1),0.001);
}
@Test public void testMolFormula() {
ROMol m1;
m1 = RWMol.MolFromSmiles("C([2H])([3H])O");
assertEquals("CH4O",RDKFuncs.calcMolFormula(m1));
assertEquals("CH2DTO",RDKFuncs.calcMolFormula(m1,true));
assertEquals("CH2[2H][3H]O",RDKFuncs.calcMolFormula(m1,true,false));
}
@Test public void testMolFormula2() {
ROMol m1;
m1 = RWMol.MolFromSmiles("C[13C]([2H])([3H])O");
assertEquals("C2H6O",RDKFuncs.calcMolFormula(m1));
assertEquals("C[13C]H4DTO",RDKFuncs.calcMolFormula(m1,true));
assertEquals("C[13C]H4[2H][3H]O",RDKFuncs.calcMolFormula(m1,true,false));
}
@Test public void testConnectivityDescriptors1() {
ROMol m1;
m1 = RWMol.MolFromSmiles("c1ccccc1O");
double tmp;
tmp=RDKFuncs.calcChi0v(m1);
assertEquals(tmp,3.834,0.01);
tmp=RDKFuncs.calcChi1v(m1);
assertEquals(tmp,2.134,0.01);
tmp=RDKFuncs.calcChi2v(m1);
assertEquals(tmp,1.336,0.01);
tmp=RDKFuncs.calcChi3v(m1);
assertEquals(tmp,0.756,0.01);
tmp=RDKFuncs.calcChi4v(m1);
assertEquals(tmp,0.428,0.01);
tmp=RDKFuncs.calcChiNv(m1,4);
assertEquals(tmp,0.428,0.01);
tmp=RDKFuncs.calcChi0n(m1);
assertEquals(tmp,3.834,0.01);
tmp=RDKFuncs.calcChi1n(m1);
assertEquals(tmp,2.134,0.01);
tmp=RDKFuncs.calcChi2n(m1);
assertEquals(tmp,1.336,0.01);
tmp=RDKFuncs.calcChi3n(m1);
assertEquals(tmp,0.756,0.01);
tmp=RDKFuncs.calcChi4n(m1);
assertEquals(tmp,0.428,0.01);
tmp=RDKFuncs.calcChiNn(m1,4);
assertEquals(tmp,0.428,0.01);
}
@Test public void testConnectivityDescriptors2() {
ROMol m1;
double tmp;
m1 = RWMol.MolFromSmiles("C12CC2C3CC13");
tmp=RDKFuncs.calcKappa1(m1);
assertEquals(tmp,2.344,0.01);
m1 = RWMol.MolFromSmiles("CC(C)C1CCC(C)CCC1");
tmp=RDKFuncs.calcKappa2(m1);
assertEquals(tmp,4.133,0.01);
m1 = RWMol.MolFromSmiles("CC(C)C1CCC(C)CCC1");
tmp=RDKFuncs.calcKappa3(m1);
assertEquals(tmp,2.844,0.01);
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.DescriptorTests");
}
}
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