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PostPosted: Thu Apr 17, 2014 4:34 pm 
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Joined: Thu Apr 17, 2014 4:07 pm
Posts: 1
Dear everyone,

I am new learner for using Autodock vina for virtual screening in Linux. After finishing virtual screening, I did follow as tutorial to get the best results. However, I could not do this. The problem I have is I don't know how to choose file to type file_name in For loop. I try to change file_name is *.txt or log.txt or out.pdbqt but there is always error.

Could you help me to fix the problem?

The scripts below to create file vina_screen_get_top.py and run it in Linux:

Scripts: vina_screen_get_top.py
#! /home/ptvn919/bin/env python

import sys
import glob

def doit (n):
file_names = glob.glob ('*/*.pdbqt')
everything = []
for file_name in file_names:
file = open (out.pdbqt)
lines = file.readlines()
file.close()
line = lines[l]
result = float(line.split(':')[l].split()[0])
everything.append([result, file_name])
everything.sort(lambda x,y: cmp(x[0], y[0]))
part = everything[:n]
done
for p in part:
print p[l],
print

if _name_ == '_main_':
doit(int(sys.argv[l]))

When running this scripts:

-sh-3.2$ python -E vina_screen_get_top.py 10
File "vina_screen_get_top.py", line 10
file = open (out.pdbqt)
^
IndentationError: expected an indented block

Could you let me know how to prepare and run scripts to get the best results after running virtual screening?


Many thanks for your help and your time.
--------------------------------------------------------------------------------
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