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Fix leak with renumberAtoms() in the SWIG wrappers (#1064)

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* fix a leak with renumberAtoms() in Java

* add a test to show that leak
This commit is contained in:
Greg Landrum
2016-09-13 09:24:08 -07:00
committed by Brian Kelley
parent 159413e6fe
commit 74635c5fe1
2 changed files with 40 additions and 28 deletions
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19
Code/JavaWrappers/MolOps.i
View File

@@ -1,21 +1,21 @@
/*
/*
* $Id$
*
* 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:
* met:
*
* * Redistributions of source code must retain the above copyright
* * 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
* 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
* * 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
@@ -36,6 +36,7 @@
%}
%newobject RDKit::MolOps::renumberAtoms;
%newobject RDKit::MolOps::removeHs;
%newobject RDKit::MolOps::addHs;
%include <GraphMol/MolOps.h>
@@ -48,7 +49,7 @@
RDKit::MolOps::sanitizeMol(mol,opThatFailed,
static_cast<unsigned int>(sanitizeOps));
} catch(...) {
}
return static_cast<int>(opThatFailed);
};

49
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/MemoryTests.java
View File

@@ -1,21 +1,21 @@
/*
/*
* $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:
* met:
*
* * Redistributions of source code must retain the above copyright
* * 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
* 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
* * 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
@@ -38,17 +38,17 @@ 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;
static final int ITERATIONS = 50000;
@SuppressWarnings("unused")
@Test
//@Test
public void testGarbageCollection1() {
for(int i=0;i<ITERATIONS;i++){
ROMol m1 = RWMol.MolFromSmiles("C1=CC=CC=C1");
@@ -58,9 +58,9 @@ public class MemoryTests extends GraphMolTest {
}
}
}
@SuppressWarnings("unused")
@Test
//@Test
public void testGarbageCollection2(){
int i = 0;
ROMol mol;
@@ -74,11 +74,11 @@ public class MemoryTests extends GraphMolTest {
}
}
@Test
//@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));
@@ -99,7 +99,7 @@ public class MemoryTests extends GraphMolTest {
}
}
@Test
//@Test
public void testAtomsAfterGarbageCollection() {
String smiles="c1ccccc1";
RWMol mol1 = RWMol.MolFromSmiles(smiles);
@@ -114,7 +114,7 @@ public class MemoryTests extends GraphMolTest {
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();
@@ -126,9 +126,20 @@ public class MemoryTests extends GraphMolTest {
}
}
@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");
}
}