A PyMOL plug-in that adds capabilities to this molecular viewer to manage result files from docking.
Obviously inspired from the original Chimera's View-Dock
- AutoDock Vina
.pdbqt
- Swiss-Dock
.dock4
/.pdbqt
(Attracting Cavities / AutoDock Vina)
.chimerax / .pdb in Dock 4+ format (legacy EADock DSS) - pyDock
.ene
/.eneRST
and corresponding .pdb - generic xyz
.xyz
PyMOL 2.x/3.x with PyQt5
For incentive PyMOL PyQt5 is already included.
In the case of open-source PyMOL, it is advised ensure to have installed PyQt5: python -m pip install pyqt5 --user
Easy intallable. Open PyMOL and use it's plugin manager: Plugin > Plugin Manager > Install New Plugin
You can download a zip to install the latest release from a local file or directly provide it an URL:
https://github.com/unizar-flav/PyViewDock/releases/latest/download/PyViewDock.zip
It is recomended to restart PyMOL after installation, although it should not be necessary.
A more detailed guide and usage examples can be found in the wiki page.
Toggle the plug-in window in Plugin > PyViewDock
Open a PDB file with docked ligands through File > Open...
A table will appear with information for every docking entry. It can be column-sorted, show/hide columns and each entry will be displayed at PyMOL when clicked.
-
Enriched built-in
load
function (also as drag-and-drop):- .pdbqt
- .dock4
- .chimerax
- .ene/.eneRST
-
Load PDBQT file (AutoDock Vina):
load_pdbqt filename [, object ]
-
Load cluster of docked ligands in PDB format (Dock 4+):
load_dock4 filename [, object [, mode ]]
-
Load SwissDock's .chimerax file:
load_chimerax filename [, object ]
-
Load pyDock's .ene/.eneRST file:
load_pydock filename [, object [, max_n ]]
-
Load .xyz file:
load_xyz filename [, object ]
-
Export docked entries data to .csv/.txt file:
export_docked_data filename [, format ]
-
Align a single structure to every state of an existing multi-state object:
align_multi mobile, target [, name_new [, initial_state [, final_state [, source_state ]]]]
Boneta, S., PyViewDock, 2021, https://github.com/unizar-flav/PyViewDock