I am trying to cluster a 30000 database based on the ECFP dissimilarity. I want to get 10% of the most representative compounds, using K-means cluster method. Although, when I type:
/Applications/ChemAxon/JChem/bin/jklustor USEF_chemical_library_std_smiles.smiles -c kmeans:3000 -d ecfp > results.txt
It stays there forever and I never get an output. What am I doing wrong?