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119 lines
4.5 KiB
Java
119 lines
4.5 KiB
Java
/*
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* $Id$
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*
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* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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package org.RDKit;
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import static org.junit.Assert.*;
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import org.junit.Test;
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public class AvalonLibTests extends GraphMolTest {
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@Test public void testAvalonTools1() {
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ROMol m1;
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m1 = RWMol.MolFromSmiles("n1ccccc1");
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String newsmi=RDKFuncs.getCanonSmiles(m1);
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assertEquals(newsmi,"c1ccncc1",newsmi);
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newsmi=RDKFuncs.getCanonSmiles("n1ccccc1",true);
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assertEquals(newsmi,"c1ccncc1",newsmi);
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}
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@Test public void testStereochem() {
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ROMol m1;
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m1 = RWMol.MolFromSmiles("C[C@H](F)C(F)Cl");
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RDKFuncs.assignStereochemistry(m1,true,true,true);
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int nKnown=0;
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int nPossible=0;
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for(int i=0;i<m1.getNumAtoms();i++){
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if(m1.getAtomWithIdx(i).hasProp("_CIPCode")){
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nKnown++;
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nPossible++;
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} else if(m1.getAtomWithIdx(i).hasProp("_ChiralityPossible")){
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nPossible++;
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}
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}
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assertEquals(nKnown,1);
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assertEquals(nPossible,2);
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}
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@Test public void testAvalonTools2() {
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StringInt_Pair res;
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res=RDKFuncs.checkMolString("c1ccccn1",true);
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assertEquals(res.getSecond(),0,res.getSecond());
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assertFalse(res.getFirst(),""==res.getFirst());
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res=RDKFuncs.checkMolString("c1c(R)cccc1C1(CC-C(C)C1)",true);
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assertEquals(1,res.getSecond());
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assertEquals(res.getFirst(),"",res.getFirst());
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}
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@Test public void testAvalonTools3() {
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ROMol m1,m2;
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m1 = RWMol.MolFromSmiles("c1ccccc1");
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m2 = RWMol.MolFromSmiles("c1ccccc1C");
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ExplicitBitVect bv1,bv2;
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bv1 = new ExplicitBitVect(1024);
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bv2 = new ExplicitBitVect(1024);
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RDKFuncs.getAvalonFP(m1,bv1,1024,false,false,RDKFuncs.getAvalonSSSBits());
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RDKFuncs.getAvalonFP(m2,bv2,1024,false,false,RDKFuncs.getAvalonSSSBits());
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assertEquals(RDKFuncs.TanimotoSimilarity(bv1,bv1),1.0,0.001);
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assertEquals(RDKFuncs.TanimotoSimilarity(bv2,bv2),1.0,0.001);
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assertTrue(RDKFuncs.TanimotoSimilarity(bv1,bv2)<1.0);
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assertTrue(bv1.getNumOnBits()>0);
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assertTrue(bv2.getNumOnBits()>0);
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assertTrue(bv1.getNumOnBits()<bv2.getNumOnBits());
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assertEquals(RDKFuncs.NumOnBitsInCommon(bv1,bv2),bv1.getNumOnBits());
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}
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@Test public void testAvalonTools4() {
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ROMol m1,m2;
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m1 = RWMol.MolFromSmiles("c1ccccc1");
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m2 = RWMol.MolFromSmiles("c1ccccc1C");
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ExplicitBitVect bv1,bv2;
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bv1 = new ExplicitBitVect(1024);
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bv2 = new ExplicitBitVect(1024);
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RDKFuncs.getAvalonFP(m1,bv1,1024,false,false,RDKFuncs.getAvalonSimilarityBits());
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RDKFuncs.getAvalonFP(m2,bv2,1024,false,false,RDKFuncs.getAvalonSimilarityBits()
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);
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assertEquals(RDKFuncs.TanimotoSimilarity(bv1,bv1),1.0,0.001);
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assertEquals(RDKFuncs.TanimotoSimilarity(bv2,bv2),1.0,0.001);
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assertTrue(RDKFuncs.TanimotoSimilarity(bv1,bv2)<1.0);
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assertTrue(bv1.getNumOnBits()>0);
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assertTrue(bv2.getNumOnBits()>0);
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assertTrue(bv1.getNumOnBits()<bv2.getNumOnBits());
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}
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main("org.RDKit.AvalonLibTests");
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}
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}
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