*** PAINS filter ***            

%prog -i <input> [-I <sdf/mol2/mol/smi>]
            [-o <string>] [-O <sdf/mol2/mol/smi>]
            [-n <ncpu>] [-q/--quiet]
            [-h/--help]
  
  e.g.  %prog -i foo.sdf
        %prog -i foo -I mol2 -o drug -O sdf -n 8
        %prog -i foo.sdf -n 8 -q 

Description

PAINS (Pan Assay Interference Compounds) are either reactive, fluorescent, 
strongly colored, metal-trapping, toxin-trapping, or able to alter proteins
chemically without fitting specifically into a binding site [1]. Therefore,
PAINS are more likely to generate unspecific artifacts in bioassays so that 
efforts are wasted in attempts to optimize the activity of these compounds.
 
PAINSfilter screens the given chemical library based on the SMARTS pattern
reported by Jonathan Baell and Georgina Holloway [2]. PAINS SMARTS are 
translated from table S6-S8, downloaded from http://www.macinchem.org
/reviews/pains/painsFilter.php, which involves the work by Rajarshi Guha 
(http://blog.rguha.net/?p=850) and Cactvs toolkit from Xhemistry.

[1] Chemistry: Chemical con artists foil drug discovery. J. B. Baell & M. A. 
    Walters. Nature, 513, 481-483. doi:10.1038/513481a
[2] "New Substructure Filters for Removal of Pan Assay Interference Compounds
    (PAINS) from Screening Libraries and for their Exclusion in Bioassays",
    J. B. Baell & G. A. Holloway, J. Med. Chem, 2010, Vol. 53, No 7, 2719-2740.

If a compound fails to pass the PAINSfilter, it does not necessarily mean it's
not a good candidate. With respect to the definition of PAINS, these compounds
are more likely to be a false positive in bioassays. Thus, extra experimental
validation step should be taken (e.g. change the readout wavelength, measure the 
concentration-dependent inhibition, etc).

By default, this program will generate a "pass.sdf" and "fail.sdf" file, unless 
the prefix(-o) or the format(-O) of the outputs are specfied. If all compounds
pass the filter, no files will be generated. 'PAINS_flag' attribute will be 
added to the failed compounds. The supported formats are sdf/mol2/mol/smi. 
To accelerate the computation, you can use -n <int> to process the molecules in 
parallel. -h/--help to display the help. 

Package dependency: 
multiprocessing, Pybel

compatible with python2.4 if multiprocessing module is installed.