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/*
* $Id$
*
* 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 AvalonLibTests extends GraphMolTest {
@Test public void testAvalonTools1() {
ROMol m1;
m1 = RWMol.MolFromSmiles("n1ccccc1");
String newsmi=RDKFuncs.getCanonSmiles(m1);
assertEquals(newsmi,"c1ccncc1",newsmi);
newsmi=RDKFuncs.getCanonSmiles("n1ccccc1",true);
assertEquals(newsmi,"c1ccncc1",newsmi);
}
@Test public void testStereochem() {
ROMol m1;
m1 = RWMol.MolFromSmiles("C[C@H](F)C(F)Cl");
RDKFuncs.assignStereochemistry(m1,true,true,true);
int nKnown=0;
int nPossible=0;
for(int i=0;i<m1.getNumAtoms();i++){
if(m1.getAtomWithIdx(i).hasProp("_CIPCode")){
nKnown++;
nPossible++;
} else if(m1.getAtomWithIdx(i).hasProp("_ChiralityPossible")){
nPossible++;
}
}
assertEquals(nKnown,1);
assertEquals(nPossible,2);
}
@Test public void testAvalonTools2() {
StringInt_Pair res;
res=RDKFuncs.checkMolString("c1ccccn1",true);
assertEquals(res.getSecond(),0,res.getSecond());
assertFalse(res.getFirst(),""==res.getFirst());
res=RDKFuncs.checkMolString("c1c(R)cccc1C1(CC-C(C)C1)",true);
assertEquals(1,res.getSecond());
assertEquals(res.getFirst(),"",res.getFirst());
}
@Test public void testAvalonTools3() {
ROMol m1,m2;
m1 = RWMol.MolFromSmiles("c1ccccc1");
m2 = RWMol.MolFromSmiles("c1ccccc1C");
ExplicitBitVect bv1,bv2;
bv1 = new ExplicitBitVect(1024);
bv2 = new ExplicitBitVect(1024);
RDKFuncs.getAvalonFP(m1,bv1,1024,false,false,RDKFuncs.getAvalonSSSBits());
RDKFuncs.getAvalonFP(m2,bv2,1024,false,false,RDKFuncs.getAvalonSSSBits());
assertEquals(RDKFuncs.TanimotoSimilarity(bv1,bv1),1.0,0.001);
assertEquals(RDKFuncs.TanimotoSimilarity(bv2,bv2),1.0,0.001);
assertTrue(RDKFuncs.TanimotoSimilarity(bv1,bv2)<1.0);
assertTrue(bv1.getNumOnBits()>0);
assertTrue(bv2.getNumOnBits()>0);
assertTrue(bv1.getNumOnBits()<bv2.getNumOnBits());
assertEquals(RDKFuncs.NumOnBitsInCommon(bv1,bv2),bv1.getNumOnBits());
}
@Test public void testAvalonTools4() {
ROMol m1,m2;
m1 = RWMol.MolFromSmiles("c1ccccc1");
m2 = RWMol.MolFromSmiles("c1ccccc1C");
ExplicitBitVect bv1,bv2;
bv1 = new ExplicitBitVect(1024);
bv2 = new ExplicitBitVect(1024);
RDKFuncs.getAvalonFP(m1,bv1,1024,false,false,RDKFuncs.getAvalonSimilarityBits());
RDKFuncs.getAvalonFP(m2,bv2,1024,false,false,RDKFuncs.getAvalonSimilarityBits());
assertEquals(RDKFuncs.TanimotoSimilarity(bv1,bv1),1.0,0.001);
assertEquals(RDKFuncs.TanimotoSimilarity(bv2,bv2),1.0,0.001);
assertTrue(RDKFuncs.TanimotoSimilarity(bv1,bv2)<1.0);
assertTrue(bv1.getNumOnBits()>0);
assertTrue(bv2.getNumOnBits()>0);
assertTrue(bv1.getNumOnBits()<bv2.getNumOnBits());
}
@Test public void testAvalonTools5() {
ROMol m1,m2;
m1 = RWMol.MolFromSmiles("c1ccccc1");
m2 = RWMol.MolFromSmiles("c1ccccc1.c1ccccc1");
SparseIntVectu32 sv1,sv2;
sv1 = new SparseIntVectu32(5000);
sv2 = new SparseIntVectu32(5000);
RDKFuncs.getAvalonCountFP(m1,sv1,5000);
RDKFuncs.getAvalonCountFP(m2,sv2,5000);
assertTrue(sv1.getTotalVal()>0);
assertTrue(sv2.getTotalVal()>0);
int i;
for(i=0;i<5000;i++){
if(sv1.getVal(i)>0){
assertEquals(2*sv1.getVal(i),sv2.getVal(i));
}
}
}
@Test public void testAvalonTools6() {
SparseIntVectu32 sv1,sv2;
sv1 = new SparseIntVectu32(5000);
sv2 = new SparseIntVectu32(5000);
RDKFuncs.getAvalonCountFP("c1ccccc1",true,sv1,5000);
RDKFuncs.getAvalonCountFP("c1ccccc1.c1ccccc1",true,sv2,5000);
assertTrue(sv1.getTotalVal()>0);
assertTrue(sv2.getTotalVal()>0);
int i;
for(i=0;i<5000;i++){
if(sv1.getVal(i)>0){
assertEquals(2*sv1.getVal(i),sv2.getVal(i));
}
}
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.AvalonLibTests");
}
}
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