README file for simi.py: 

Using the test data file test.smi, run simi.py as follows:

unix> simi.py similar test.smi

Program only produces a line of output if Tanimoto similarity 
to known aggregator is 0.65 or greater (axonpath).

The columns are: 
a) query molecule as SMILES
b) matched aggregator as SMILES
c) Tanimoto coefficient between a and b (Tc) (axonpath)
d) query identifier
e) calculated LogP
f) Score: 1 if logP>3 and Tc>0.8  else 0

Using the default data provided, the program 
will produce multiple lines for quercetin (many matches). 
One line for caffeine (similarity).
No lines for morphine (no match Tc> 0.65). 

John Irwin
April 2013