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>
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