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/*
* $Id: MemoryTests.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;
/**
* A few tests to verify memory-relates issues between Java and C++.
*
* Verify garbage collection correctly frees Java and C++ memory.
* Call it manually, otherwise it only gets called at the end of all tests
*/
public class MemoryTests extends GraphMolTest {
Runtime r = Runtime.getRuntime();
static final int ITERATIONS = 50000;
@SuppressWarnings("unused")
//@Test
public void testGarbageCollection1() {
for(int i=0;i<ITERATIONS;i++){
ROMol m1 = RWMol.MolFromSmiles("C1=CC=CC=C1");
if((i%5000)==0){
r.gc();
r.runFinalization();
}
}
}
@SuppressWarnings("unused")
//@Test
public void testGarbageCollection2(){
int i = 0;
ROMol mol;
String smi = "C1CC1";
for(i=0;i<ITERATIONS;i++){
mol = RWMol.MolFromSmiles(smi,0,true);
if((i%5000)==0){
r.gc();
r.runFinalization();
}
}
}
//@Test
public void testConformerOwnership() {
for (int i = 0; i < 50000; i++) {
ROMol mol = RWMol.MolFromSmiles("CC");
for(int j=0; j<100;j++) {
Conformer conf = new Conformer(2);
conf.setAtomPos(0, new Point3D(-0.5, 0.0, 0.0));
conf.setAtomPos(1, new Point3D(1.0, 0.0, 0.0));
conf.setId(j);
mol.addConformer(conf);
conf = new Conformer(2);
conf.setAtomPos(0, new Point3D(-0.5, 0.0, 0.0));
conf.setAtomPos(1, new Point3D(1.0, 0.0, 0.0));
conf.setId(j+1);
mol.addConformer(conf, false);
}
if (i % 1000 == 0) {
r.gc();
r.runFinalization();
}
}
}
//@Test
public void testAtomsAfterGarbageCollection() {
String smiles="c1ccccc1";
RWMol mol1 = RWMol.MolFromSmiles(smiles);
assertEquals(6, mol1.getAtomWithIdx(0).getAtomicNum());
assertNotNull(mol1.getAtomWithIdx(1));
for( int i = 0; i< mol1.getNumAtoms(); i++) {
assertNotNull( mol1.getAtomWithIdx(i));
assertFalse( 47 == mol1.getAtomWithIdx(i).getAtomicNum() );
Atom atom = new Atom(47);
mol1.replaceAtom(i,atom,false);
assertEquals(47, mol1.getAtomWithIdx(i).getAtomicNum());
}
// Atom's now out of scope and eligible for garbage collection!
// Make sure we still have access to it, even after the Java object was destroyed.
Runtime.getRuntime().gc();
Runtime.getRuntime().runFinalization();
for( int i = 0; i < mol1.getNumAtoms(); i++) {
Atom atom = mol1.getAtomWithIdx(i);
assertNotNull(atom);
assertEquals( 47 , atom.getAtomicNum() );
}
}
@Test
public void testRenumberAtoms() {
String smiles="c1ccccc1";
RWMol mol1 = RWMol.MolFromSmiles(smiles);
UInt_Vect newNums = new UInt_Vect();
for(long i=mol1.getNumAtoms()-1;i>=0;i--){ newNums.add(i); }
for(int i=0;i<10000000;i++){
ROMol m = RDKFuncs.renumberAtoms(mol1,newNums);
m.delete();
if(i%10000 == 0) System.out.println(" Done: "+i+"\n");
}
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.MemoryTests");
}
}
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