How many molecules are in mols.smi? Have you looked at task manager to
see memory usage while running this?
You should move the initialisation of OBBuilder outside the loop. I
have a feeling you are eating up memory by creating this multple
times.
- Noel
On 3 December 2013 06:43, Joos Kiener <joos.kie...@gmail.com> wrote:
> This is confusing. This issue is some weird memory issue. At the end of this
> post is the most simple code I could come up with that reproduces the
> problem for me.
>
> I can make the code work by removing or commenting just any of the following
> lines (only one of them is enough):
>
> - conformerSearch.SetScore(score); // will then use default
> OBRMSDConformerScore
>
> - String str = StringUtils.join(strArray, ',');
>
> For the StringUtils part, the length of the array matters. 5000 still works,
> 8000 does not. However in my original application I completely removed that
> and it still has the issue. This tells me it is some weird memory problem
> that can be caused by generating long strings (but not limited to this).
> This issue then breaks OBEnergyConformerScore but not the default
> OBRMSDConformerScore.
>
> The error code from event viewer according to my google search means heap
> corruption.
>
> See below the mentioned code. It has a dependency on
> org.apache.commons.lang3.
>
> <code>
> package conformergenerator;
>
> import org.apache.commons.lang3.StringUtils;
> import org.openbabel.OBBuilder;
> import org.openbabel.OBConformerScore;
> import org.openbabel.OBConformerSearch;
> import org.openbabel.OBConversion;
> import org.openbabel.OBEnergyConformerScore;
> import org.openbabel.OBMol;
>
> public class App {
>
> public static void main(String[] args) {
>
> System.loadLibrary("openbabel_java");
>
> System.out.println("Create OBMol from smiles");
> OBConversion conv = new OBConversion();
> OBMol mol = new OBMol();
> conv.SetInFormat("smi");
>
> boolean hasNext = conv.ReadFile(mol, "mols.smi");
>
> String[] strArray = buildArray(10000);
> while (hasNext) {
> System.out.println("Adding Hydrogens");
> mol.AddHydrogens();
> System.out.println("Generate 3D coordinates");
> OBBuilder builder = new OBBuilder();
> builder.Build(mol);
>
> System.out.println("Generate Conformers");
> OBConformerSearch conformerSearch = new OBConformerSearch();
> OBConformerScore score = new OBEnergyConformerScore();
> conformerSearch.SetScore(score);
>
> if (!conformerSearch.Setup(mol)) {
> String message = "Generating conformers failed.";
> throw new IllegalArgumentException(message);
> }
> conformerSearch.Search();
> conformerSearch.GetConformers(mol);
>
> String str = StringUtils.join(strArray, ',');
> // the idea would be to add this as property to mol
> // but not required for the code to fail
>
> hasNext = conv.Read(mol);
> }
> System.out.println("Success!!!");
> }
>
> private static String[] buildArray(int numElements) {
> String[] a = new String[numElements];
> for (int i = 0; i < numElements; i++) {
> a[i] = "a";
> }
> return a;
> }
> }
> </code>
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/Java-API-setting-OBConformerScore-will-crash-application-tp4656958p4656970.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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