Options of mk_export.py

Contents

Options of mk_export.py#

Positional Argument (Input)#

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

Output Options#

--suffix <suffix>#: Set a suffix for output filenames that are not explicitly specified. The default suffix is _docked.

-s, --write_sdf <output_SDF_filename>#: Specify the output SDF filename. Defaults to the input filename with a suffix defined by --suffix.

-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.

-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.

--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.

-k, --keep_flexres_sdf#: (Flag) Include flexible residues, if any, in the SDF output.

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