screenmd error

i am using this command


screenmd file1.smiles file2.smiles -g -k CF -M Tanimoto -o output.txt


however there is always some kind of problem and i never get the similarity matrix correctly.


either some molecules are left out or something similar happens

It's probably due to the Tanimoto threshold: dissimilarity scores above the threshold are filtered out. Remember, screen is a virtual screening tool, not a pairwise similarity calculator. However, you can obtain the full dissimilarity matrix by specifying 1.0 for the Tanimoto threshold. Though then yu need to use an external xml configuration file (see the manual: http://www.chemaxon.com/jchem/doc/user/ScreenMD.html#config).





HTH


regards


Miklos