Dear All
I did a virtual drug screening with Autodock-Vina, and I have generated a list of log files (one for each ligand analyzed) and solutions in PDBQT format. Do you have some script or method to rank for the best solution (compound) from such a list of log or PDBQT files from Vina?
Thanks in advance.
Pritam Kumar Panda
I tried to run the Python script but I got this error:
/usr/bin/env: ‘python\r’: No such file or directory
What I am doing wrong?. I put the script in the folder where the list of *.PDBQT files are generated.
If I try to run the script by calling Python first I got this other error:
File "vina_screen_get_top.py", line 10
print 'Found', len(file_names), 'pdbqt files'
^
SyntaxError: invalid syntax
Can you help me please?. Best and thanks
I executed your command, and everything is the same. When I run the script either as a self-executable or by calling Python before.. the same errors appeared
When I am going to run this script it showing error like this
Python vina_screen_get_top.py
Traceback (most recent call last):
File "vina_screen_get_top.py", line 30, in
doit(int(sys.argv[1]))
IndexError: list index out of range
Please help me to resolve this problem.
Thank You in advanced.
Dear All
The problem is due to the python version you are using.
In Python 3, you have to slightly modify the script.
Hope you all have figured that out.
regards
Tanuj
Amit Chaudhary Francisco J. Enguita i found a solution.
run the command as
python2.7 vina_screen_get_top.py 10 (or any number of your choice fot the top compounds).
use this script
============================================================
#! /usr/bin/env python
import sys
import glob
def doit(n):
file_names = glob.glob('*/*.pdbqt')
everything = []
failures = []
print 'Found', len(file_names), 'pdbqt files'
for file_name in file_names:
file = open(file_name)
lines = file.readlines()
file.close()
try:
line = lines[1]
result = float(line.split(':')[1].split()[0])
everything.append([result, file_name])
except:
failures.append(file_name)
everything.sort(lambda x,y: cmp(x[0], y[0]))
part = everything[:n]
for p in part:
print p[1],
if len(failures) > 0:
print 'WARNING:', len(failures), 'pdbqt files could not be processed'
if __name__ == '__main__':
doit(int(sys.argv[1]))
======================================
Brilliant Nyathi hi. I am trying to run this script but I am facing a syntax error -Expected an indented block. how can I rectify it?
thank you
Tanuj Sharma hi.. how do i modify the aforementioned script for python 3?
thank you
Only execute this line:
./vina_screen_get_top.py 10
Dear all
There is a simple way to solve this problem. The given script is natively developed for python2.7, so when you run it with python3, you may face problems executing this script with this version. Using anaconda can help you to run the script appropriately in linuxX64. Being familiar with bash-scripting and python codes will help you do your projects easily, and these programming languages make life live.
**Please note that for some users, it is essential they copy all _out.pdbqt poses into a new folder where all input and output docking results are. This issue will also help them to run the script using python 2.7 in Conda environment.
To run the script, you can follow the below instruction:
1- Install python2.7 in anaconda using the following command:
(base) $ conda create --name py2 python=2.7
(base) $ conda activate py2
(py2) $
Next you should install two essential libraries that give you premission to access: libpython2.7.so.1.0
2. To install these libraries simply run the following commands in the (py2) environment as the follow:
(py2) $ sudo apt-get install libpython2.7
(py2) $ sudo apt-get install libatlas3-base
Now, the environment is ready to use. Try to go the directory or path where your vina output pdbqt files are using cd command. Then, you should run:
(py2) $ python2.7 vina_screen_get_top.py X
where x is the number of top hits with best binding energies. If you have a library of more than 2,000 docked compounds this script can help you to analyze the results. For example, I want to return only 5 top pdbqt files with best docking energies. The above-mentioned command can be run as the follow:
(py2) $ python2.7 vina_screen_get_top.py 5
The output in the terminal is looking like the following text:
Found 18 pdbqt files
pdbqt/ZINC000150368142_out.pdbqt pdbqt/compound1_out.pdbqt pdbqt/ZINC000150366588_out.pdbqt pdbqt/ZINC000150366575_out.pdbqt pdbqt/compound4_out.pdbqt
If you check the log files of these docked compounds, you can see they have the best binding affinity energies as shown in the attached figure.
hello
i followed the suggestion here but unfortunately i get "0" results
(py2) ayesha@LAPTOP-C5K9759P:/mnt/e/WBF-course/vinadocking/vina_linux/topmolecule$ python2.7 vina_screen_get_top.py 18
Found 0 pdbqt files
Although i have put all the pdbqt files in the same folder as the script
thank you
Ayesha Fatima
I changed the line on the script which reads: file_names = glob.glob('*/*.pdbqt')
into: file_names = glob.glob('*.pdbqt')
(removing the */)
This fixed it for me. Hope it fixes it for you too.
Here is a modified file for python 3, I also made it to show the free energy after the filename. My python skills is low, so sorry if there are problems down the road. Credits to Brilliant Nyathi for the original file and to bing chat on the editing tutorial
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