error calculating Tanimoto index

User 5a88369158

20-05-2010 21:55:31


I have two text files with smiles strings, one is a target file and another is a query file. I would to find out how similar to dissimilar the query is from the target. I am using the following command

screenmd targets.txt queries.txt -Q -M Tanimoto -o test.txt

The output gives me the headers starting from Q1-Q10 (since there are 10 queries) but then I get the following error


C:\Program Files\ChemAxon\JChem\bin>ScreenMD targets.txt queries.txt -Q -M Tanim
oto -o test.txt
java.lang.ArrayIndexOutOfBoundsException: 0
        at chemaxon.descriptors.ScreenMD.main(
C:\Program Files\ChemAxon\JChem\bin>


I have attached the target and query file. Can you please help me detect and solve the problem



Yash Gandhi

ChemAxon efa1591b5a

03-06-2010 10:14:22

Hi Yash,

The problem with this screenmd command is that the descriptor type (-k option) is missing. I admit the screenmd did not produce meaningful error message / this will be corrected in the next bug fix release.

So you either -k CF or -k PF etc. The main goal of screenmd is to perform a similarity search in the target structures and thus it takes some kind of molecular descriptors to compare them (and not the bare structures) against each other to obtain similarity scores.


Hope this helps,