Python Script To Do Virtual Screening On Pyrx

Question

[Onat]

Hello all,

I am wondering if there is a Python script to run Autodock from command line for PyRx.

I want to perform a virtual screening for small molecules and I want to read a sdf library properly and then perform the screening automatically by using a script. The script can be like this:

path/autodock4 (-l read the sdf library) (path/library) (-r read the receptor file) - cpu (adjust the cpu allocated for each step) -loop (to automatize for each ligand in the sdf library file)

Thank you

Answer 1

[dallakyans]

You can write one, depending on the version of PyRx you are using and how good you are at reading python code. Look at the https://sourceforge.net/p/pyrx/code/HEAD/tree/PyRxDev/PyRx/vsModel.py#l244 You can create an instance of VSModel and then Run. It is pretty easy for me to say since I wrote it, but I hope, with some efforts, you or someone else can write this script and share it.