.. _4dba_calculation:

4D Bioavailability (4DBA) Calculation
-------------------------------------

The bioavailability of compounds can be evaluated using 
4D Bioavalability (4DBA) scores. Compounds with higher 4DBA scores are more likely to have
oral drug-like characteristics. More details can be found in reference :cite:`Oashi:2011`.
The 4DBA scores may facilitate lead optimization studies by indicating which 
compounds should be prioritized for chemical synthesis and biological testing.

The 4DBA score is calculated using four descriptors:

1. MW (Molecular Weight)
2. log P(o/w) (Logarithm of the octanol-water partition coefficient)
3. HDO (Number of hydrogen bond donors)
4. HAC (Number of hydrogen acceptors)

The SilcsBio software provides a utility through the command line interface (CLI) to 
calculate the four descriptors (MW, log P(o/w), HDO, HAC) and 4DBA scores. 
The 4DBA score can be calculated using the following command:

::

    python $SILCSBIODIR/utils/python/calc_4dba.py --database <ligand SD file> --method <method for descriptors>


The ``calc_4dba.py`` code requires the following arguments:

* Database of compounds in SD file format:

   :: 

     --database <ligand SD file>
  
  The four descriptors and 4DBA scores will be calculated for all ligands in the SD file. 
    
* Method used to calculate the descriptors (optional):
  
   ::

     --method <method for descriptors; rdkit or moe; default=rdkit>

  Using the ``--method rdkit`` option will use RDKit to calculate the descriptors. 
  By default the method will be set to ``rdkit``.

  Using the ``--method moe`` option will use MOE to calculate the
  descriptors. This requires that the database provided in sdf format has been saved
  using MOE after calculating the descriptors.
  
* Output file name (optional):

   ::

     --output <output file name; default=lgfe-4dba.csv>

  The output is a CSV file with the 4DBA score for each compound in the database. 
  By default the output file name will be ``lgfe-4dba.csv``.