In [5]:
import os
os.environ['PATH']=os.environ['PATH']+'/home/preps/golovin/progs/bin'
os.environ['MOPAC_LICENSE']='/home/preps/golovin/progs/bin'
In [7]:
%%bash
obgen 1.smi > 1.mol
##Рассмотрим порфирин
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%%bash
babel -ipdb 1_removed.pdb -omop 1_opt.mop -xk "PM6"
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%%bash
/home/preps/golovin/progs/bin/MOPAC2009.exe 1_opt.mop
##оптимизируем структуру с помощью MOPAC (удалив сначала лишние водороды)
In [13]:
%%bash
babel -imopout 1_opt.out -opdb 1_opt.pdb
In [15]:
%%bash
/home/preps/golovin/progs/bin/MOPAC2009.exe 1_opt_spectr.mop
In [1]:
from xmlrpclib import ServerProxy
from IPython.display import Image
import os, sys
In [2]:
import __main__
__main__.pymol_argv = [ 'pymol', '-cp' ]
import pymol
pymol.finish_launching()
from pymol import cmd
In [3]:
from IPython.display import Image
In [3]:
cmd.delete('all')
cmd.load('1.pdb')
In [4]:
cmd.do('''
rotate x, 90
ray
png por1.png
''')
In [6]:
Image(filename='por1.png')
##до MOPAC
Out[6]:
In [7]:
cmd.delete('all')
cmd.load('1_opt.pdb')
In [8]:
cmd.do('''
rotate x, 90
ray
png por1.png
''')
In [9]:
Image(filename='por1.png')
##после MOPAC, структура явно оптимизировалась и стала полностью плоской, как и должно быть
Out[9]:
In [18]:
%%bash
for i in 'SINGLET' 'DOUBLET' 'TRIPLET'
do
grep ${i} '1_opt_spectr.out' ##>> electron_states.txt
done
##достали из out-файла информацию об энергии перехода между состояниями
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file = open('electron_states.txt', 'r')
energies = open('energies', 'w')
a=[]
for line in file:
a.append(line.split()[1])
print(a)
outfile = open('energies', 'w')
outfile.write("\n".join(a))
In [1]:
planck_constant = 4.135667*(10**(-15))
light_speed = 299.792458*(10**6)
lambdas=[]
file = open('energies', 'r')
for line in file:
lambdas.append(planck_constant*light_speed*(10**9)/float(line))
print lambdas
##outfile = open('wavelenghts', 'w')
##outfile.write("\n".join(str(lambdas)))
##получили длины волн, которые способен поглащать порфирин, в нанометрах
In [3]:
%%bash
echo 'O=C1C=CC(=O)C=C1' >> new_mol.smi
In [4]:
%%bash
obgen new_mol.smi > new_mol.mol
In [9]:
cmd.delete('all')
cmd.load('new_mol.mol')
cmd.do('''
zoom visible
set valence, 2
ray
png new1.png
''')
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Image(filename='new1.png')
Out[10]:
In [24]:
cmd.do('''
rotate x, 90
ray
png new2.png
''')
In [25]:
Image(filename='new2.png')
Out[25]:
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cmd.save('quinone.pdb')
##obgen выдал плоскую молекулу
In [27]:
%%bash
babel -ipdb quinone.pdb -omop quinone_opt.mop -xk "PM6"
In [28]:
%%bash
export PATH=${PATH}:/home/preps/golovin/progs/bin
export MOPAC_LICENSE=/home/preps/golovin/progs/bin
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib
MOPAC2009.exe quinone_opt.mop
MOPAC2009.exe quinone_charged_opt.mop
In [24]:
%%bash
babel -imopout quinone_opt.out -opdb quinone_opt.pdb
babel -imopout quinone_charged_opt.out -opdb quinone_charged_opt.pdb
In [7]:
cmd.delete('all')
cmd.load('quinone_opt.pdb')
cmd.do('''
refresh
zoom visible
set valence, 2
ray
png new3.png
''')
##MOPAC тоже выдал плоскую геометрию, но распознал ароматичнсоть в цикле
In [8]:
Image(filename='new3.png')
Out[8]:
In [19]:
cmd.delete('all')
cmd.load('quinone_opt.pdb')
cmd.do('''
refresh
zoom visible
rotate x, -90
rotate y, 90
show sticks
set stick_ball, on
set stick_ball_ratio, 2
set stick_radius, 0.12
set valence, 2
set ray_trace_mode, 3
ray
png new3.png
''')
In [21]:
Image(filename='new3.png')
Out[21]:
In [25]:
cmd.delete('all')
cmd.load('quinone_charged_opt.pdb')
cmd.do('''
zoom visible
rotate x, -90
rotate y, 90
show sticks
set stick_ball, on
set stick_ball_ratio, 2
set stick_radius, 0.12
set valence, 2
set ray_trace_mode, 3
ray
png new4.png
''')
##для дианиона ничего не изменилось
In [26]:
Image(filename='new4.png')
Out[26]:
In [27]:
cmd.delete('all')
cmd.load('quinone_charged_opt.pdb')
cmd.do('''
refresh
zoom visible
set valence, 2
ray
png new5.png
''')
In [28]:
Image(filename='new5.png')
Out[28]:
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