PyViewDock
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
Supported formats with software/server results
- AutoDock Vina
.pdbqt - Swiss-Dock
.chimerax / .pdb in Dock 4+ format - pyDock
.ene / .eneRST and corresponding .pdb - generic xyz
.xyz
Requirements
PyMOL 2.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
Installation
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.
Usage
GUI
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.
PyMOL command line
-
Enriched built-in
loadfunction (also as drag-and-drop):- .pdbqt
- .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 ]]]]
How to cite
Boneta, S., PyViewDock, 2021, https://github.com/unizar-flav/PyViewDock