CustomDescriptor.getTanimoto() fails

JChem version: 5_1_0


JDK 1.6.0_07 (Linux)

Code:

import java.io.*; import java.util.*; import chemaxon.descriptors.CDParameters; import chemaxon.descriptors.CustomDescriptor; public class z {   public static void main(String[] args) throws IOException   {     int length=64;     CustomDescriptor fpKQ = new CustomDescriptor(CDParameters.BINARY_DESCRIPTOR,length);     CustomDescriptor fpK = new CustomDescriptor(CDParameters.BINARY_DESCRIPTOR,length);     fpKQ.clear();     fpK.clear();     float   sim_tan = fpKQ.getTanimoto(fpK);     System.err.println("\tTanimoto: "+String.format("%.2f",sim_tan));   } }

Result:

$ java z


Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1


at java.util.ArrayList.get(ArrayList.java:324)


at chemaxon.descriptors.MDParameters.isAsymmetric(MDParameters.java:746)


at chemaxon.descriptors.CustomDescriptor.getTanimoto(CustomDescriptor.java:524)


at z.main(z.java:17)

The purpose is simple binary fingerprints for implementing structural key based fingerprints.

I have moved this topic to the appropriate forum.





Szilard

Does you CDParameters constructor call the constructor of the superclass? It is supposed to do so.





HTH


Miklos

Hi Miklos,





Observe from the complete source code provided that I am not using any CDParameters object, only the static field CDParameters.BINARY_DESCRIPTOR, as indicated by the documentation for constructor CustomDescriptor(int type, int length).





Jeremy.

Hi Jeremy,





I see now. Normally, our CustomDescriptor class should not be directly instantiated - though I admit that it is not stated in the documentation, we will correct that.


Instead, it serves as a super class for your descriptor by providing several convenience methods and a means of integration in Screen and JChemBase.





The exception you found is clear a bug, even if someone instantiates CustomDescriptor this exception should not be thrown. We will fix that.





You may wish to go through the related sample code: http://www.chemaxon.com/jchem/doc/guide/screen/index.html#custom, that might be useful.





Regards,


Miklos