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/*
* $Id: AromaticTests.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.Test;
public class AromaticTests extends GraphMolTest {
// Check all lines in all files
@Test
public void testAromaticRegression() throws Exception {
String filePath = getFilePath("aromat_regress.txt");
performAromaticTest(filePath,0);
}
@Test
public void testNCIAromaticRegression() throws Exception {
String filePath = getFilePath("NCI_aromat_regress.txt");
performAromaticTest(filePath,0);
}
public void performAromaticTest(String filePath, int expectedFailures) throws Exception {
List<AromaticTestEntry> testData = readData(filePath);
int nFailed = 0;
for (AromaticTestEntry test : testData) {
ROMol mol = RWMol.MolFromSmiles(test.smi1);
assertNotNull(mol);
if (!test.smi2.equals("FAIL")) {
int count = 0;
ArrayList<Atom> aroms = new ArrayList<Atom>();
Atom_Vect atoms = mol.getAtoms();
for (int i = 0; i < atoms.size(); i++)
if (atoms.get(i).getIsAromatic()) {
count++;
aroms.add(atoms.get(i));
}
if (test.numAromatics != count) {
nFailed++;
}
}
}
assertEquals("More than " + expectedFailures + " on file " + filePath, expectedFailures, nFailed);
}
public String getFilePath(String fileName) {
File base = getRdBase();
File testFileDir = new File(base, "rdkit" + File.separator + "Chem" + File.separator + "test_data");
return testFileDir.getAbsolutePath() + File.separator + fileName;
}
public class AromaticTestEntry {
String smi1;
String smi2;
int numAromatics;
int[] aromaticIdx;
int lineNo;
public AromaticTestEntry(int lineNo, String[] line) {
this.lineNo = lineNo;
smi1 = line[0];
smi2 = line[1];
numAromatics = Integer.parseInt(line[2]);
String aromaticList = line[3].replace("[", "").replace("]", "").trim();
// Catch a null string
String[] aromatics = aromaticList.length() > 0 ? aromaticList.split(",")
: new String[0];
assertTrue("bad test line at " + lineNo, aromatics.length == numAromatics || smi2.equals("FAIL"));
aromaticIdx = new int[aromatics.length];
for (int i = 0; i < aromatics.length; i++)
aromaticIdx[i] = Integer.parseInt(aromatics[i].trim());
}
}
public List<AromaticTestEntry> readData(String fn) throws Exception {
List<AromaticTestEntry> data = new ArrayList<AromaticTestEntry>();
int lineNo = 0;
BufferedReader reader = new BufferedReader(new FileReader(fn));
String line;
// Skip the header
try {
reader.readLine();
while ((line = reader.readLine()) != null) {
lineNo++;
if (line.length() > 0 && !line.startsWith("#")) {
String[] splitL = line.split("\t");
if (splitL.length == 4)
data.add(new AromaticTestEntry(lineNo, splitL));
}
}
} finally {
reader.close();
}
return data;
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.AromaticTests");
}
}
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