
import __main__

__main__.pymol_argv = [ 'pymol', '-x' ]

import pymol
 
pymol.finish_launching()
 
from pymol import cmd


import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit import RDConfig
from rdkit.Chem.Draw import ShowMol
from rdkit.Chem.Draw import IPythonConsole 
from rdkit.Chem import Draw
from IPython.display import display,Image,HTML,Video
from base64 import b64encode
import io
import base64


display(Image(filename='sculpting.png', width='1000'))


TAMRA = "CN(C)C1=CC2=C(C=C1)C(=C3C=CC(=[N+](C)C)C=C3O2)C4=C(C=CC(=C4)C(=O)[O-])C(=O)O"
mol = Chem.MolFromSmiles(TAMRA)
AllChem.Compute2DCoords(mol)
Chem.Draw.MolToImageFile(mol, 'TAMRA.png', size=(400, 400))
rdkit.Chem.rdmolfiles.MolToPDBFile(mol, 'tamra.pdb')

display(Image(filename='TAMRA.png', width='400'))


cmd.reinitialize()
F1 = (-0.3529979884624481,0.8130868077278137,0.46290624141693115,0.9355168342590332,0.29923903942108154,0.1877879798412323,0.014168323948979378,0.4993453621864319, -0.8662871718406677,0.0,0.0,
 -34.043251037597656, 13.16138744354248, 57.79969787597656, 11.865260124206543, 25.74932098388672, 42.337188720703125, -20.000001907348633)

F2 = (-0.8534818887710571, -0.20164379477500916, 0.48052918910980225, 0.05657187104225159, 0.8807989954948425, 0.4700946807861328, -0.5180383324623108, 0.4284009039402008, -0.7403392195701599,
 -3.489851951599121e-05, -2.1442770957946777e-05, -137.54098510742188, 14.468088150024414, 51.811973571777344, 21.076236724853516, 108.45553588867188, 166.67001342773438, -20.000001907348633)
cmd.set_view(F2)
cmd.do("""
load 1lmp.pdb
load unfold.pdb

mset 1 x550
frame 1
mdo 1: select cys2, 1lmp and resi 30+115; hide everything, unfold or resn HOH; hide sticks, cys2; show cartoon, 1lmp
mview store

frame 60
""")
cmd.set_view(F1)
cmd.mdo(70, 'bond resi 30 and name SG, resi 115 and name SG;show sticks, cys2')
cmd.mdo(100, 'unbond resi 30 and name SG, resi 115 and name SG; hide everything, resi 115 and name CB')
cmd.mview('store')
cmd.frame('150')
cmd.set_view(F1)
cmd.mview('store')

cmd.frame('250')
cmd.set_view(F2)
cmd.mdo(250, 'show cartoon, unfold; show sticks, unfold  and resi 30+115')
cmd.mview('store')

cmd.mdo(300,'translate [-15, 0, 0], 1lmp')
cmd.mview('store',300)
cmd.mdo(350,'align 1lmp, unfold')
cmd.frame('350')
cmd.set_view(F2)
cmd.mview('store')

cmd.mdo(360, 'hide everything, unfold; show sticks, resi 81')
cmd.frame('400')
F3 = (-0.1544012725353241, -0.8934862613677979, 0.4217180609703064, 0.8179206848144531, 0.12383925914764404, 0.5618440508842468, -0.5542225241661072, 0.4316789507865906, 0.7116769552230835, 3.016740083694458e-05,
 -0.0002479869872331619, -30.16435432434082, 20.55228042602539, 38.527523040771484, 33.38637924194336, -71.82227325439453, 132.20156860351562, -20.000001907348633)

cmd.load('tamra.pdb')

cmd.set_view(F3)
cmd.mview('store')

cmd.mdo(420, 'fuse tamra and name C24, /1lmp//A/81/OG; hide everything, tamra or /1lmp///UNL/O3')
cmd.mdo(450, 'edit /1lmp///UNL/C22, /1lmp///UNL/C24; torsion -180')
cmd.unpick()

cmd.frame('500')
F4 = (0.66672682762146, -0.6927023530006409, 0.2750241756439209, 0.6331138014793396, 0.33168816566467285, -0.6993889808654785, 0.39324676990509033, 0.6404197812080383, 0.6597030758857727,
 -2.054031938314438e-05, -0.0003727748990058899, -46.78189468383789, 26.51824188232422, 40.285648345947266, 33.29109191894531, 9.764094352722168, 83.79641723632812, -20.000001907348633)

cmd.set_view(F4)
cmd.mview('store')

cmd.mview('reinterpolate')
cmd.mplay()


video = io.open('sculpt-mutagenesis-tamra.mp4', 'r+b').read()

encoded = base64.b64encode(video)

HTML(data='''<video alt="test" controls>

<source src="data:video/mp4;base64,{0}" type="video/mp4" /> </video>'''.format(encoded.decode('ascii')))


phi = '-57'
psi = '-47'
cmd.reinitialize()

cmd.editor.attach_amino_acid("pk1",'ala')
for i in range(3,100):

    cmd.editor.attach_amino_acid("pk1",'ala')
    cmd.set_dihedral(str(i-1)+'/N', 
                     str(i-1)+'/CA',
                     str(i-1)+'/C', 
                     str(i)+'/C',phi)
    cmd.set_dihedral(str(i-1)+'/C',     
                     str(i)+'/N',
                     str(i)+'/CA',
                     str(i)+'/C',psi)
    cmd.edit(str(i)+'/C')

cmd.mset('1 x250')

cmd.frame('1')
F1 = [0.1681254804134369, -0.697181224822998, -0.6968995332717896, 0.8559678792953491, 0.4538997411727905, -0.24758465588092804, 0.4889317452907562, -0.5548980832099915, 0.6730760931968689, 7.071066647768021e-06,
 1.300126314163208e-06, -49.94206237792969, 1.9890364408493042, -1.0455727577209473, -3.60075044631958, -2950.052978515625, 3049.947021484375, -20.0]
cmd.set_view(F1)
cmd.mview('store')

cmd.frame('100')
cmd.set_view((0.1681254804134369,
 -0.697181224822998,
 -0.6968995332717896,
 0.8559678792953491,
 0.4538997411727905,
 -0.24758465588092804,
 0.4889317452907562,
 -0.5548980832099915,
 0.6730760931968689,
 0.0,
 0.0,
 -49.94206237792969,
 58.02196502685547,
 31.593772888183594,
 -77.0528564453125,
 -2950.057861328125,
 3049.942138671875,
 -20.0))
cmd.mview('store')

cmd.frame('150')
F2 = [-0.7746680378913879, -0.24491159617900848, 0.5830132365226746, -0.06119655817747116, 0.94666588306427, 0.3163629472255707, -0.6293984055519104, 0.2093973010778427, -0.7483389973640442,
 0.00014367070980370045, 0.0003098566085100174, -28.81438446044922, 61.57285690307617, 29.46417236328125, -77.46070861816406, -2971.1669921875, 3028.8330078125, -20.0]
cmd.set_view(F2)
cmd.mview('store')


cmd.frame('250')
F3 = [-0.7746680378913879, -0.24491159617900848, 0.5830132365226746, -0.06119655817747116, 0.94666588306427, 0.3163629472255707, -0.6293984055519104, 0.2093973010778427, -0.7483389973640442,
 0.00014272332191467285, 0.0003088745288550854, 94.43785095214844, 61.47258377075195, 30.15804672241211, -77.25460815429688, -3094.40185546875, 2905.59814453125, -20.0]
cmd.set_view(F3)
cmd.mview('store')

cmd.mview('reinterpolate')
cmd.mplay()


video = io.open('poly-ala.mp4', 'r+b').read()

encoded = base64.b64encode(video)

HTML(data='''<video alt="test" controls>

<source src="data:video/mp4;base64,{0}" type="video/mp4" /> </video>'''.format(encoded.decode('ascii')))


display(Image(filename='polyala.png', width='1000'))


cmd.reinitialize()
cmd.fetch('1bna')
cmd.do('''
create pair, c. A and i. 5 + c. B and i. 20
create nextpair, c. A and i. 4 + c. B and i. 21
create 1, pair''')
cmd.pair_fit('pair', 'nextpair')
trans = cmd.get_object_matrix('pair')
for x in range(2, 101):
    cmd.create (str(x), str(x-1))
    cmd.transform_selection(str(x), trans, homogenous = 0)
    cmd.create('A_Bond'+str(x),'/'+str(x)+"/A/A/DA`5/O3'` or /"+str(x-1)+"/A/A/DA`5/P`")
    cmd.bond("A_bond"+str(x)+" and name O3'","A_bond"+str(x)+" and name P")
    cmd.create('B_Bond'+str(x),'/'+str(x-1)+"/B/B/DT`20/O3'` or /"+str(x)+"/B/B/DT`20/P`")
    cmd.bond("B_bond"+str(x)+" and name O3'","B_bond"+str(x)+" and name P")
    cmd.show('sticks',str(x)+' or A_bond'+str(x)+' or B_bond'+str(x))
cmd.orient('all')
cmd.hide('everything','1bna')


display(Image(filename='B-DNA.png', width='1000'))

Практикум 1. Знакомство и работа с Pymol¶

Sculpting + Mutagenesis¶

Полиаланиновая альфа-спираль¶

B-форма ДНК¶