from xmlrpclib import ServerProxy
from IPython.display import Image
import os, sys
import scipy as sp
from scipy import constants
from scipy.constants import codata
import numpy as np

%%bash
echo "CC(=O)N[C@H]1C(O)O[C@H](CO)[C@@H](O)[C@@H]1O">nag.smi
obgen nag.smi > nag.mol
babel -imol nag.mol -opdb nag.pdb

%%bash
export PYTHONPATH=${PYTHONPATH}:/home/preps/golovin/.local_numpy/lib/python2.7/site-packages:/home/preps/golovin/.local_numpy/lib/python2.7/dist-packages
export PATH=${PATH}:/home/preps/golovin/progs/bin

%%bash
prepare_ligand4.py -h

%%bash
prepare_receptor4.py -r model_4.pdb

from xmlrpclib import ServerProxy
from IPython.display import Image
import os, sys, time

# pymol launching
import __main__
__main__.pymol_argv = [ 'pymol', '-cp' ]
# __main__.pymol_argv = [ 'pymol', '-x' ]  # for GUI

import pymol
from pymol import cmd
pymol.finish_launching()

cmd.do('''
load model_4.pdb
pseudoatom mass_center, /model_4///*32/OE2 or /model_4///*102/O or /mosel_4///*60/OH 
select mass_center
print cmd.get_atom_coords('mass_center')
''')

%%bash
echo "center_x=44.4
center_y=43
center_z=28.9

size_x = 25
size_y = 25
size_z = 25

num_modes = 20 
" > vina.cfg

%%bash
date
vina --config vina.cfg --receptor model_4.pdbqt --ligand nag.pdbqt --out nag_prot.pdbqt --log nag_prot.log
date

#mode |   affinity | dist from best mode
#     | (kcal/mol) | rmsd l.b.| rmsd u.b.
#-----+------------+----------+----------
#   1         -5.2      0.000      0.000
#   2         -4.7      8.597      9.920
#   3         -4.1     10.411     11.919

defaultImage = 'pymolimg.png'
def prepareImage(width=300, height=300, sleep=5, filename=defaultImage):
    ## To save the rendered image
    cmd.ray(width, height)
    cmd.png('pymolimg.png')
    time.sleep(sleep)
    
# Define some shortcuts
def focus(x):
    cmd.center(x)
    cmd.zoom(x)

cmd.do('''
reinit
bg white
load nag_prot.pdbqt
load model_4.pdb
show surface, model_4
set transparency, 0.5
show sticks, nag_prot
split_states nag_prot, 1, 20, prefix=conf
rotate x, 50, all, 0
rotate y, -90, all, 0
zoom all
ray
png pic1.png
''')

Image(filename='pic1.png')

%%bash
python /usr/share/pyshared/AutoDockTools/Utilities24/prepare_flexreceptor4.py -r model_4.pdbqt -s  GLU32_TYR60_ALA102
date
vina --config vina.cfg --receptor model_4_rigid.pdbqt --flex model_4_flex.pdbqt --ligand  nag.pdbqt --out nag_model_4_2.pdbqt --log nag_model_4_2.log
date