Options of mk_export.py
=======================

Positional Argument (Input)
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. option:: docking_results_filename

   One or more docking output files in either PDBQT format (from Vina) or DLG format (from AD-GPU).

Output Options
~~~~~~~~~~~~~~

.. option:: --suffix <suffix>

   Set a suffix for output filenames that are not explicitly specified. The default suffix is ``_docked``. 

.. option:: -s, --write_sdf <output_SDF_filename>

   Specify the output SDF filename. Defaults to the input filename with a suffix defined by ``--suffix``. 

.. option:: -j, --read_json <input_JSON_filename>

   Provide a receptor file generated by ``mk_prepare_receptor`` with the ``-j/--write_json`` option. Currently only effective when used with ``-p, --write_pdb``. 

.. option:: -p, --write_pdb <output_PDB_filename>

   Specify the output PDB filename. Defaults to the input filename with a suffix defined by ``--suffix``. Must be used together with ``-j, --read_json``. 

.. option:: --all_dlg_poses

   (Flag) Write all poses from AutoDock-GPU DLG output files, instead of only the lead of each cluster. Currently only effective for ``-s, --write_sdf``. 

.. option:: -k, --keep_flexres_sdf

   (Flag) Include flexible residues, if any, in the SDF output.

.. option:: -, --redirect_stdout

   (Flag) Instead of writing an SDF file, print it directly to the standard output (STDOUT).