mk_export.py CLI Reference

mk_export.py CLI Reference#

Export docked ligand to SDF, and receptor to PDB

usage: mk_export.py [-h] [-s output_SDF_filename] [-p output_PDB_filename]
                    [--suffix SUFFIX] [-j input_JSON_filename]
                    [--all_dlg_poses] [-k] [-]
                    docking_results_filename [docking_results_filename ...]

Positional Arguments#

docking_results_filename

Docking output file(s), either PDBQT file from Vina or DLG file from AD-GPU.

Named Arguments#

-s, --write_sdf

defaults to input filename with suffix from –sufix

-p, --write_pdb

defaults to input filename with suffix from –suffix

--suffix

suffix for output filesnames that are not explicitly set

Default: '_docked'

-j, --read_json

receptor written by mk_prepare_receptor -j/–write_json

--all_dlg_poses

write all AutoDock-GPU poses, not just cluster leads.

Default: False

-k, --keep_flexres_sdf

add flexres, if any, to SDF ouput

Default: False

-, --

do not write SDF file, just print it to STDOUT

Default: False

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