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Fix swig memory leak (#6346)

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This commit is contained in:
Gareth Jones
2023-05-09 22:16:35 -06:00
committed by GitHub
parent f278fc738c
commit e00c2c5336
3 changed files with 100 additions and 1 deletions
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14
Code/JavaWrappers/RWMol.i
View File

@@ -48,6 +48,20 @@
%ignore RDKit::RWMol::addAtom(Atom *atom,bool updateLabel,bool takeOwnership);
%ignore RDKit::RWMol::addBond(Bond *bond,bool takeOwnership);
%newobject RDKit::SmilesToMol;
%newobject RDKit::SmartsToMol;
%newobject RDKit::MolBlockToMol;
%newobject RDKit::MolFileToMol;
%newobject RDKit::MolFromMolFile;
%newobject RDKit::MolFromTPLFIle;
%newobject RDKit::MolFromMol2File;
%newobject RDKit::MolFromMol2Block;
%newobject RDKit::MolFromPDBBlock;
%newobject RDKit::MolFromPDBFile;
%newobject RDKit::MolFromSequence;
%newobject RDKit::MolFromFasta;
%shared_ptr(RDKit::RWMol)
%include "enums.swg"
#if swifjava

85
Code/JavaWrappers/csharp_wrapper/RDKitCSharpTest/ToMolMemoryTest.cs Normal file
View File

@@ -0,0 +1,85 @@
using System;
using System.Diagnostics;
using GraphMolWrap;
using Xunit;
namespace RdkitTests
{
public class ToMolMemoryTest
{
private static readonly long hundredMB = 1024 * 1024 * 100;
private static void gc()
{
GC.Collect();
GC.WaitForPendingFinalizers();
GC.Collect();
}
[Fact]
public void TestSmilesToMolMemoryUsage()
{
string smi =
"CC(C)C[C@H](NC(=O)[C@H](CC(=O)O)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CO)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CCC(N)=O)NC(=O)[C@@H](N)CS)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CS)C(=O)O";
var before = Process.GetCurrentProcess().VirtualMemorySize64;
long after;
for (int i = 0; i < 10000; ++i)
{
using RWMol mol = RDKFuncs.SmilesToMol(smi);
mol?.Dispose();
if (i % 1000 == 0)
{
gc();
after = Process.GetCurrentProcess().VirtualMemorySize64;
Assert.True(after - before < hundredMB);
}
}
gc();
after = Process.GetCurrentProcess().VirtualMemorySize64;
Assert.True(after - before < hundredMB);
}
[Fact]
public void TestMolBlockToMolMemoryUsage()
{
var block = @"
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
M END
";
var before = Process.GetCurrentProcess().VirtualMemorySize64;
long after;
for (int i = 0; i < 10000; ++i)
{
using RWMol mol = RDKFuncs.MolBlockToMol(block);
mol?.Dispose();
if (i % 1000 == 0)
{
gc();
after = Process.GetCurrentProcess().VirtualMemorySize64;
Assert.True(after - before < hundredMB);
}
}
gc();
after = System.Diagnostics.Process.GetCurrentProcess().PeakVirtualMemorySize64;
Assert.True(after - before < hundredMB);
}
}
}