Difference between revisions of "DOCK 3.7 2015/04/15 abl1 Tutorial"

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(set up directories and get databases)
Line 6: Line 6:
 
Create directory called "RotationProject"
 
Create directory called "RotationProject"
  
create a file called "autodude_db_download.py"  
+
create a python file called "autodude_db_download.py"  
  
  # this get the database from the autodude webpage
+
  # this gets the database from the autodude webpage
 
   
 
   
 
  import sys, os
 
  import sys, os
Line 34: Line 34:
 
       # exit()
 
       # exit()
  
This python script will download the dockable db2 databases from the autodude webpage.python /mnt/nfs/home/rstein/RotationProject/autodude_db_download.py  
+
This python script will download the dockable db2 databases from the autodude webpage.
 +
 
 +
python /mnt/nfs/home/rstein/RotationProject/autodude_db_download.py  
  
 
make a subdirectory called databases:
 
make a subdirectory called databases:
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  cd databases
 
  cd databases
  
 +
make directories for ligands and decoys and move the corresponding files into those directories
  
 
  mkdir decoys  
 
  mkdir decoys  
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  mv ligands*db2.gz ligands
 
  mv ligands*db2.gz ligands
  
download the ligand isomorfic smiles file:
+
download the ligand and decoy isomeric smiles file:
  
 
  wget http://autodude.docking.org/abl1/decoys_final.ism
 
  wget http://autodude.docking.org/abl1/decoys_final.ism

Revision as of 14:09, 15 April 2015

This tutoral use the 3.7.2 beta version of dock release on XXX.

set up directories and get databases

Create directory called "RotationProject"

create a python file called "autodude_db_download.py"

# this gets the database from the autodude webpage

import sys, os
import urllib

system = 'abl1'
url = 'http://autodude.docking.org/dude_e_db2/'

print "url = " + url

#page=requests.get(url)

webfile = urllib.urlopen(url)
page    = webfile.read()
webfile.close()

splitpage=page.split('\n')

for line in splitpage:
   if system in line: 
      file = line.replace('"',' ').split()[2]
      print url+file
      urllib.urlretrieve(url+file,file)

     # exit()

This python script will download the dockable db2 databases from the autodude webpage.

python /mnt/nfs/home/rstein/RotationProject/autodude_db_download.py 

make a subdirectory called databases:

mkdir databases

go inside.

cd databases

make directories for ligands and decoys and move the corresponding files into those directories

mkdir decoys 
mv decoys*db2.gz decoys
mkdir ligands 
mv ligands*db2.gz ligands

download the ligand and decoy isomeric smiles file:

wget http://autodude.docking.org/abl1/decoys_final.ism
mv decoys_final.ism decoys.ism

note that the scripts expect the name to be decoys.ism, so we changed the name.

wget http://autodude.docking.org/abl1/actives_final.ism
mv actives_final.ism ligands.ism

download enrichment databases

run be_blasti.py

run blastermaster.py

run enrichment calucaltions