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/*
* $Id: FingerprintsTests.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 org.junit.Test;
public class FingerprintsTests extends GraphMolTest {
public void compareVectors(Int_Vect v1, Int_Vect v2) {
for (int i = 0; i < v1.size(); i++) {
assertEquals(v1.get(i),v2.get(i));
}
}
private void checkTargets(String smi, String[] matches) {
ROMol m = RWMol.MolFromSmiles(smi);
ExplicitBitVect fp1 = RDKFuncs.RDKFingerprintMol(m, 2, 7, 9192, 4, false);
for (String match : matches) {
ROMol m2 = RWMol.MolFromSmiles(match);
ExplicitBitVect fp2 = RDKFuncs.RDKFingerprintMol(m2, 2, 7, 9192, 4, false);
Double_Vect v = RDKFuncs.OnBitProjSimilarity(fp2, fp1);
assertEquals("substuct " + match + " is not properly contained in " + smi,1.000,v.get(0),defaultDoubleTol);
}
}
// check containing mols, no Hs, no valence
@Test
public void test4 () {
String smi = "CCC(O)C(=O)O";
String[] matches = new String[] {"CCC","OCC","OCC=O","OCCO","CCCC","OC=O","CC(O)C"};
checkTargets(smi,matches);
}
// check containing mols, use Hs, no valence
@Test
public void test5() {
String smi = "CCC(O)C(=O)O";
String[] matches = new String[] {"O[CH-][CH2-]","O[CH-][C-]=O"};
checkTargets(smi,matches);
}
// check that the bits in a signature of size N which has been folded in half
// are the same as those in a signature of size N/2
@Test
public void test6() {
String[] smis = new String[] {
"CCC(O)C(=O)O","c1ccccc1","C1CCCCC1","C1NCCCC1","CNCNCNC"
};
for (String smi : smis) {
ROMol m = RWMol.MolFromSmiles(smi);
ExplicitBitVect fp1 = RDKFuncs.RDKFingerprintMol(m, 2, 7, 4096);
ExplicitBitVect fp3 = RDKFuncs.RDKFingerprintMol(m, 2, 7, 2048);
ExplicitBitVect fp2 = RDKFuncs.FoldFingerprint(fp1, 2);
compareVectors(fp2.getOnBits(), fp3.getOnBits());
fp2 = RDKFuncs.FoldFingerprint(fp2, 2);
fp3 = RDKFuncs.RDKFingerprintMol(m, 2, 7, 1024);
compareVectors(fp2.getOnBits(), fp3.getOnBits());
fp2 = RDKFuncs.FoldFingerprint(fp1, 4);
compareVectors(fp2.getOnBits(), fp3.getOnBits());
}
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.FingerprintsTests");
}
}
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