In [7]:
import subprocess
do1 = 'echo 9 | pdb2gmx -f camelid.pdb -o camelid_h2.pdb -p -water none'
subprocess.Popen(do1,shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
do2 = 'echo 9 | pdb2gmx -f amylase.pdb -o amylase_h2.pdb -p -water none -ignh'
subprocess.Popen(do2,shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
Out[7]:
<subprocess.Popen at 0x7f0bb82c2190>
In [3]:
exp1 = 'export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib'
subprocess.Popen(exp1,shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
exp2 = 'export PATH=${PATH}:/home/preps/golovin/progs/bin'
subprocess.Popen(exp2,shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
Out[3]:
<subprocess.Popen at 0x7f0bb82ad090>
In [8]:
do3 = 'mark_sur camelid_h2.pdb camelid_h_m.pdb'
subprocess.Popen(do3,shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
do4 = 'mark_sur amylase_h2.pdb amylase_h_m.pdb'
subprocess.Popen(do4,shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
Out[8]:
<subprocess.Popen at 0x7f0bb82ad410>

mark_sur размечает, какие атомы относятся к поверхности структур, а какие нет.

In [9]:
%%bash
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib
export PATH=${PATH}:/home/preps/golovin/progs/bin
zdock -R amylase_h_m.pdb -L camelid_h_m.pdb

ZDOCK has successfully completed and zdock.out has been created.
In [11]:
%%bash
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib
export PATH=${PATH}:/home/preps/golovin/progs/bin
zrank zdock.out.cp 1 2000
In [12]:
! sort -n -k2 zdock.out.cp.zr.out | head

1590	-28.661
1252	-27.5357
610	-25.5514
1436	-22.3979
1952	-21.1778
982	-17.5643
1284	-16.9435
852	-14.7227
679	-13.8186
1666	-11.6282
In [17]:
! head -14 zdock.out > top2.txt
In [20]:
%%bash
#mkdir predictions
cp ./zdock.out ./predictions/
cp amylase_h_m.pdb ./predictions/
cp camelid_h_m.pdb ./predictions/
cp /home/preps/golovin/progs/bin/create_lig ./predictions/
In [21]:
%%bash
cd ./predictions/
create.pl zdock.out
In [22]:
tops = [1590,1252,610,1436,1952,982,1284,852,679,1666]

Как видно из визуализации топ-5 результатов, zdock угадывает сайт связывания для антитела на амилазе. Точное положение, соответсвующее референсной структуре (зеленая), в топ-5 не находится.

In [23]:
from xmlrpclib import ServerProxy
from IPython.display import Image
Image(filename='../../public_html/term8/pr12-1.png')
Out[23]:
In [25]:
Image(filename='../../public_html/term8/pr12-2.png')
Out[25]:
In [26]:
Image(filename='../../public_html/term8/pr12-3.png')
Out[26]:
In [27]:
Image(filename='../../public_html/term8/pr12-4.png')
Out[27]:
In [28]:
Image(filename='../../public_html/term8/pr12-5.png')
Out[28]:
In [29]:
Image(filename='../../public_html/term8/pr12-6.png')
Out[29]:
In [ ]: