In [1]:

    

import os
import sys
import random
import time
from random import seed, randint
import argparse
import platform
from datetime import datetime
import imp
import numpy as np
import fileinput
from itertools import product
import pandas as pd
from scipy.interpolate import griddata
from scipy.interpolate import interp2d
import seaborn as sns
from os import listdir

import matplotlib.pyplot as plt
import seaborn as sns
from scipy.interpolate import griddata
import matplotlib as mpl
sys.path.insert(0,'..')
# from notebookFunctions import *
# from .. import notebookFunctions

%matplotlib inline
plt.rcParams['figure.figsize'] = (10,6.180)    #golden ratio
# %matplotlib notebook
%load_ext autoreload
%autoreload 2

import sys
sys.path.insert(0, '/Users/weilu/openmmawsem/')

from openmmawsem import *


    

In [7]:

    

file = "tmp.pdb"
fileTo = "test_tmp.pdb"
location = "/Users/weilu/Research/server/dec_2018/T0958_single_chain/openmm_T0958/"
os.chdir(location)
i = 0
print(f"---{i:4}---")
def fixPDB(file="tmp.pdb", fileTo="test_tmp.pdb"):
#     chain_length = [230, 461, 693, 0]
#     chain = ["A","B","C"]
#     chain_length = [42, 84, 0]
    chain_length = [85, 164, 0]
    chain = ["A","B"]
    pos = 0
    residue = 1
    with open(fileTo, "w") as out:
        with open(file, "r") as f:
            for line in f:
                tmp = list(line)
                try:
                    residue = int(line[22:26])
                except:
                    pass
                if residue > chain_length[pos]:
                    pos += 1
                    out.write("TER \n")
                i = residue-chain_length[pos-1]
                r = f"{i:4}"
                if len(tmp) > 26:
#                     print(tmp)
                    tmp[21] = chain[pos]
                    tmp[22:26] = r
                new_line = "".join(tmp)
                
                out.write(new_line)
a = open(location + "lammps_movie.pdb").read().split("END")
os.system("rm openmmMovie.pdb")
os.system(f"echo 'REMARK converted from awsem lammps output' >> openmmMovie.pdb")
for i in range(10):
    with open("tmp.pdb", "w") as out:
        out.write(a[i])
    fixPDB()
    input_pdb_filename, cleaned_pdb_filename =prepare_pdb("test_tmp.pdb", "AB")
    os.system(f"echo 'MODEL  {i+1}' >> openmmMovie.pdb")
    os.system("cat test_tmp-openmmawsem.pdb >> openmmMovie.pdb")

fixPDB()


    

    




---   0---






    




---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-7-eef9844bbbb1> in <module>()
     40         out.write(a[i])
     41     fixPDB()
---> 42     input_pdb_filename, cleaned_pdb_filename =prepare_pdb("test_tmp.pdb", "AB")
     43     os.system(f"echo 'MODEL  {i+1}' >> openmmMovie.pdb")
     44     os.system("cat test_tmp-openmmawsem.pdb >> openmmMovie.pdb")

~/openmmawsem/openmmawsem.py in prepare_pdb(pdb_filename, chains_to_simulate)
     51     input_pdb_filename = "%s-openmmawsem.pdb" % pdb_filename[:-4]
     52 
---> 53     fixer = PDBFixer(filename=pdb_filename)
     54 
     55     # remove unwanted chains

~/anaconda3/lib/python3.6/site-packages/pdbfixer/pdbfixer.py in __init__(self, filename, pdbfile, pdbxfile, url, pdbid)
    236                 self._initializeFromPDBx(file.read())
    237             else:
--> 238                 self._initializeFromPDB(file)
    239             file.close()
    240         elif pdbfile:

~/anaconda3/lib/python3.6/site-packages/pdbfixer/pdbfixer.py in _initializeFromPDB(self, file)
    274 
    275         structure = PdbStructure(file)
--> 276         pdb = app.PDBFile(structure)
    277         self.topology = pdb.topology
    278         self.positions = pdb.positions

~/anaconda3/lib/python3.6/site-packages/simtk/openmm/app/pdbfile.py in __init__(self, file, extraParticleIdentifier)
    159             self._positions.append(coords*nanometers)
    160         ## The atom positions read from the PDB file.  If the file contains multiple frames, these are the positions in the first frame.
--> 161         self.positions = self._positions[0]
    162         self.topology.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
    163         self.topology.createStandardBonds()

IndexError: list index out of range

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