In [5]:
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
from Bio.PDB.Polypeptide import one_to_three
from Bio.PDB.Polypeptide import three_to_one
from Bio.PDB.PDBParser import PDBParser
from pyCodeLib import *
from small_script.myFunctions import *
from collections import defaultdict
%matplotlib inline
# plt.rcParams['figure.figsize'] = (10,6.180) #golden ratio
# %matplotlib notebook
%load_ext autoreload
%autoreload 2
In [6]:
plt.rcParams['figure.figsize'] = np.array([16.18033, 10]) #golden ratio
plt.rcParams['figure.facecolor'] = 'w'
plt.rcParams['figure.dpi'] = 100
plt.rcParams.update({'font.size': 22})
In [7]:
def get_seq_fromPredictTopo(topo):
loc = topo
with open(loc) as f:
a = f.readlines()
assert len(a) % 3 == 0
chain_count = len(a) // 3
seq = ""
for i in range(chain_count):
seq_i = (a[i*3+2]).strip()
seq += seq_i
assert np.alltrue([i in ["0", "1"] for i in seq])
return seq
In [9]:
seq = get_seq_fromPredictTopo("/Users/weilu/Research/server/sep_2019/1su4_nice_movie/1su4_topo")
In [10]:
len(seq)
Out[10]:
994
In [17]:
pre_res = "0"
end_list = []
start_list = []
for i, res in enumerate(seq):
if res == "0":
outMem = True
if res == "1" and outMem:
outMem = False
print("Start", i)
start_list.append(i)
if res == "0" and pre_res == "1":
print("End", i)
end_list.append(i)
pre_res = res
Start 60
End 75
Start 88
End 106
Start 262
End 279
Start 293
End 320
Start 760
End 781
Start 832
End 856
Start 897
End 911
Start 929
End 949
Start 963
End 985
In [19]:
lines = []
for start, end in zip(start_list, end_list):
print(start, end)
start_res = start + 1
end_res = end
lines.append(f"resid {start_res} to {end_res} ")
60 75
88 106
262 279
293 320
760 781
832 856
897 911
929 949
963 985
In [21]:
"or ".join(lines)
Out[21]:
'resid 61 to 75 or resid 89 to 106 or resid 263 to 279 or resid 294 to 320 or resid 761 to 781 or resid 833 to 856 or resid 898 to 911 or resid 930 to 949 or resid 964 to 985 '
In [25]:
import pickle
import gzip
import numpy
with open('/Users/weilu/Research/Build/RaptorX-Contact/raptorx.uchicago.edu/pdb25-test-500.release.contactFeatures.pkl', 'rb') as f:
u = pickle._Unpickler(f)
u.encoding = 'latin1'
p = u.load()
print(p)
IOPub data rate exceeded.
The notebook server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--NotebookApp.iopub_data_rate_limit`.
Current values:
NotebookApp.iopub_data_rate_limit=1000000.0 (bytes/sec)
NotebookApp.rate_limit_window=3.0 (secs)
In [26]:
p[0]
Out[26]:
{'ACC': array([[2.14100e-03, 3.12040e-02, 9.66655e-01],
[4.54880e-02, 3.28255e-01, 6.26257e-01],
[4.03800e-03, 9.20500e-02, 9.03912e-01],
[9.17800e-03, 1.22090e-01, 8.68732e-01],
[5.53530e-02, 3.28582e-01, 6.16065e-01],
[6.23900e-03, 8.09590e-02, 9.12802e-01],
[1.18760e-02, 2.41622e-01, 7.46502e-01],
[4.17500e-03, 1.20500e-01, 8.75325e-01],
[2.97151e-01, 4.45199e-01, 2.57650e-01],
[3.54500e-03, 1.23625e-01, 8.72830e-01],
[1.85048e-01, 5.09717e-01, 3.05236e-01],
[3.18177e-01, 5.68778e-01, 1.13045e-01],
[1.26020e-02, 2.12773e-01, 7.74624e-01],
[3.28610e-02, 2.41676e-01, 7.25463e-01],
[3.73442e-01, 5.20963e-01, 1.05595e-01],
[7.66700e-03, 9.67260e-02, 8.95607e-01],
[4.56700e-02, 3.14696e-01, 6.39634e-01],
[7.25330e-02, 2.21646e-01, 7.05821e-01],
[1.04836e-01, 3.21067e-01, 5.74097e-01],
[1.04761e-01, 4.94554e-01, 4.00685e-01],
[1.55632e-01, 6.03289e-01, 2.41079e-01],
[3.52800e-02, 3.91312e-01, 5.73408e-01],
[4.87310e-02, 2.19958e-01, 7.31311e-01],
[2.64610e-02, 2.31296e-01, 7.42243e-01],
[2.63170e-02, 2.13034e-01, 7.60649e-01],
[6.07772e-01, 3.40969e-01, 5.12590e-02],
[1.27717e-01, 5.37456e-01, 3.34828e-01],
[8.41412e-01, 1.48836e-01, 9.75200e-03],
[2.00118e-01, 5.65473e-01, 2.34409e-01],
[7.19566e-01, 2.29286e-01, 5.11470e-02],
[3.65680e-02, 2.74780e-01, 6.88652e-01],
[1.70273e-01, 5.11371e-01, 3.18355e-01],
[7.16220e-02, 3.50763e-01, 5.77615e-01],
[6.88151e-01, 2.82804e-01, 2.90460e-02],
[2.94757e-01, 5.38492e-01, 1.66751e-01],
[4.64246e-01, 3.56485e-01, 1.79268e-01],
[1.68935e-01, 6.28411e-01, 2.02655e-01],
[2.11006e-01, 5.00835e-01, 2.88159e-01],
[1.13154e-01, 4.06637e-01, 4.80210e-01],
[1.73930e-01, 2.67175e-01, 5.58895e-01],
[1.40998e-01, 3.94579e-01, 4.64423e-01],
[2.37374e-01, 3.88071e-01, 3.74555e-01],
[1.03600e-01, 4.40978e-01, 4.55422e-01],
[6.54910e-02, 2.02089e-01, 7.32421e-01],
[5.25803e-01, 4.13230e-01, 6.09670e-02],
[6.14550e-02, 2.85647e-01, 6.52898e-01],
[2.90971e-01, 4.56251e-01, 2.52777e-01],
[4.43565e-01, 3.73055e-01, 1.83380e-01],
[6.24076e-01, 3.15369e-01, 6.05550e-02],
[2.25550e-01, 5.58326e-01, 2.16124e-01],
[9.00536e-01, 9.49210e-02, 4.54200e-03],
[1.97100e-02, 3.89117e-01, 5.91173e-01],
[1.75540e-02, 1.74556e-01, 8.07890e-01],
[2.54030e-02, 1.71925e-01, 8.02672e-01],
[4.99322e-01, 4.81505e-01, 1.91740e-02],
[8.64500e-02, 5.31121e-01, 3.82429e-01],
[7.91988e-01, 2.00763e-01, 7.24900e-03],
[5.07780e-02, 4.26208e-01, 5.23014e-01],
[6.05601e-01, 3.68612e-01, 2.57870e-02],
[2.02004e-01, 5.74045e-01, 2.23952e-01],
[1.07623e-01, 4.06652e-01, 4.85725e-01],
[1.48718e-01, 6.19811e-01, 2.31471e-01],
[4.17362e-01, 5.00173e-01, 8.24660e-02],
[2.57090e-02, 2.34984e-01, 7.39307e-01],
[3.87840e-02, 2.78895e-01, 6.82321e-01],
[2.24300e-02, 2.04152e-01, 7.73418e-01],
[2.40267e-01, 2.96788e-01, 4.62946e-01],
[4.05745e-01, 5.36583e-01, 5.76720e-02],
[6.17775e-01, 3.49692e-01, 3.25330e-02],
[7.43031e-01, 2.40598e-01, 1.63710e-02],
[9.85671e-01, 1.21600e-02, 2.16900e-03],
[8.09435e-01, 1.74083e-01, 1.64820e-02],
[6.20005e-01, 3.55353e-01, 2.46410e-02],
[4.53160e-01, 4.14432e-01, 1.32408e-01],
[4.94532e-01, 3.58789e-01, 1.46680e-01],
[1.21057e-01, 3.86545e-01, 4.92398e-01],
[1.31824e-01, 2.80340e-01, 5.87836e-01],
[3.32604e-01, 3.72272e-01, 2.95124e-01],
[4.33790e-02, 4.17182e-01, 5.39439e-01],
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[2.00726e-01, 5.39811e-01, 2.59464e-01],
[3.81029e-01, 5.31861e-01, 8.71100e-02],
[6.85110e-02, 4.03072e-01, 5.28417e-01],
[1.41880e-02, 2.12275e-01, 7.73536e-01],
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[6.02700e-02, 2.99670e-01, 6.40061e-01],
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[1.70905e-01, 4.04321e-01, 4.24774e-01],
[2.33630e-02, 1.58199e-01, 8.18438e-01],
[2.13426e-01, 4.96572e-01, 2.90002e-01],
[3.03833e-01, 4.53168e-01, 2.42999e-01],
[3.43159e-01, 3.93612e-01, 2.63229e-01],
[7.46500e-02, 4.07682e-01, 5.17668e-01],
[4.81255e-01, 4.38674e-01, 8.00710e-02],
[4.89800e-03, 7.01890e-02, 9.24914e-01]], dtype=float32),
'PSFM': array([[0.0671858 , 0.00848389, 0.210216 , ..., 0.0350024 , 0.003539 ,
0.0194352 ],
[0.0409585 , 0.0149163 , 0.0251375 , ..., 0.0500223 , 0.0284411 ,
0.32362 ],
[0.177643 , 0.016066 , 0.0422349 , ..., 0.0952733 , 0.00496893,
0.02178 ],
...,
[0.0737128 , 0.0121674 , 0.0490185 , ..., 0.0760809 , 0.00412971,
0.0186908 ],
[0.0376652 , 0.0114167 , 0.0151081 , ..., 0.0714966 , 0.0166591 ,
0.0808188 ],
[0.0529496 , 0.00764128, 0.0462977 , ..., 0.0369183 , 0.00449008,
0.0185344 ]], dtype=float32),
'name': '1r77A',
'DISO': array([[0.444],
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'sequence': 'DYKDDDDKVKLYKTNKYGTLYKSESASFTANTDIITRLTGPFRSMPQSGVLRKGLTIKYDEVMKQDGHVWVGYNTNSGKRVYLPVRTWNESTGELGPLWGTIK',
'ccmpredZ': array([[ 0. , 0. , 0. , ..., 0.462 , 0.46 , 0.794 ],
[ 0. , 0. , 0. , ..., 0.843 , -0.521 , -0.2415],
[ 0. , 0. , 0. , ..., 1.324 , -0.1836, 0.7134],
...,
[ 0.462 , 0.843 , 1.324 , ..., 0. , 0. , 0. ],
[ 0.46 , -0.521 , -0.1836, ..., 0. , 0. , 0. ],
[ 0.794 , -0.2415, 0.7134, ..., 0. , 0. , 0. ]],
dtype=float16),
'contactMatrix': array([[-1, -1, -1, ..., -1, -1, -1],
[-1, -1, -1, ..., -1, -1, -1],
[-1, -1, -1, ..., -1, -1, -1],
...,
[-1, -1, -1, ..., 1, 1, 1],
[-1, -1, -1, ..., 1, 1, 1],
[-1, -1, -1, ..., 1, 1, 1]], dtype=int8),
'PSSM': array([[-0.189699 , -1.15306 , 1.96094 , ..., -1.0534 , -1.81744 ,
-1.02018 ],
[-0.903694 , -0.338968 , -1.10301 , ..., -0.538283 , 1.18912 ,
3.03737 ],
[ 1.21305 , -0.231841 , -0.35442 , ..., 0.391215 , -1.32785 ,
-0.855854 ],
...,
[-0.0559402, -0.632841 , -0.13953 , ..., 0.0666771, -1.59475 ,
-1.07653 ],
[-1.02462 , -0.724708 , -1.83753 , ..., -0.0229816, 0.417453 ,
1.03584 ],
[-0.533237 , -1.30397 , -0.221915 , ..., -0.97652 , -1.47404 ,
-1.08865 ]], dtype=float32),
'SS3': array([[0.001, 0.001, 0.998],
[0.187, 0.017, 0.797],
[0.209, 0.01 , 0.781],
[0.222, 0.003, 0.775],
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[0.01 , 0.409, 0.581],
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[0.012, 0.319, 0.67 ],
[0.01 , 0.337, 0.653],
[0.007, 0.531, 0.462],
[0.003, 0.85 , 0.146],
[0.002, 0.892, 0.106],
[0.001, 0.749, 0.25 ],
[0. , 0.002, 0.998]], dtype=float32),
'psicovZ': array([[ 0. , 0. , 0. , ..., -0.1279, -0.1279, -0.1279],
[ 0. , 0. , 0. , ..., -0.1279, -0.1279, -0.1279],
[ 0. , 0. , 0. , ..., -0.1279, -0.1279, -0.1279],
...,
[-0.1279, -0.1279, -0.1279, ..., 0. , 0. , 0. ],
[-0.1279, -0.1279, -0.1279, ..., 0. , 0. , 0. ],
[-0.1279, -0.1279, -0.1279, ..., 0. , 0. , 0. ]],
dtype=float16),
'OtherPairs': array([[[ 0. , 0. , 0. ],
[-0.000615, 0.00525 , 0.007427],
[-0.00606 , 0.004154, 0.005093],
...,
[ 0. , -0.000355, 0.001965],
[ 0.004745, 0.001356, 0.005276],
[-0.00606 , 0.002352, 0.00363 ]],
[[-0.000615, 0.00525 , 0.007427],
[ 0. , 0. , 0. ],
[ 0.001862, 0.00334 , 0.00445 ],
...,
[ 0.002178, -0.000914, 0.001841],
[-0.0029 , 0.000698, 0.005356],
[-0.003513, 0.001765, 0.003283]],
[[-0.00606 , 0.004154, 0.005093],
[ 0.001862, 0.00334 , 0.00445 ],
[ 0. , 0. , 0. ],
...,
[-0.00949 , -0.003658, -0.002476],
[ 0.000527, -0.000657, 0.001343],
[ 0.005096, 0.004128, 0.00478 ]],
...,
[[ 0. , -0.000355, 0.001965],
[ 0.002178, -0.000914, 0.001841],
[-0.00949 , -0.003658, -0.002476],
...,
[ 0. , 0. , 0. ],
[ 0.01011 , -0.00798 , -0.003021],
[-0.02576 , -0.005623, -0.004005]],
[[ 0.004745, 0.001356, 0.005276],
[-0.0029 , 0.000698, 0.005356],
[ 0.000527, -0.000657, 0.001343],
...,
[ 0.01011 , -0.00798 , -0.003021],
[ 0. , 0. , 0. ],
[ 0.05167 , -0.003626, -0.000892]],
[[-0.00606 , 0.002352, 0.00363 ],
[-0.003513, 0.001765, 0.003283],
[ 0.005096, 0.004128, 0.00478 ],
...,
[-0.02576 , -0.005623, -0.004005],
[ 0.05167 , -0.003626, -0.000892],
[ 0. , 0. , 0. ]]], dtype=float16),
'SS8': array([[0. , 0. , 0. , 0. , 0. , 0. , 0. , 1. ],
[0.142, 0.06 , 0. , 0.02 , 0.02 , 0.217, 0.001, 0.54 ],
[0.165, 0.081, 0. , 0.028, 0.021, 0.307, 0.114, 0.284],
[0.172, 0.081, 0. , 0.017, 0.008, 0.274, 0.136, 0.311],
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[0.077, 0.02 , 0. , 0.43 , 0.033, 0.035, 0.063, 0.341],
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[0.024, 0.042, 0. , 0.096, 0.008, 0.266, 0.225, 0.339],
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[0.05 , 0.057, 0. , 0.289, 0.009, 0.228, 0.22 , 0.147],
[0.033, 0.028, 0. , 0.391, 0.015, 0.154, 0.147, 0.232],
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[0.002, 0.002, 0. , 0.801, 0.016, 0.007, 0.031, 0.141],
[0.002, 0.001, 0. , 0.887, 0.023, 0.004, 0.018, 0.065],
[0.002, 0.001, 0. , 0.789, 0.012, 0.005, 0.018, 0.173],
[0.001, 0.003, 0. , 0.561, 0.009, 0.199, 0.079, 0.148],
[0.001, 0.003, 0. , 0.348, 0.003, 0.207, 0.233, 0.204],
[0.017, 0.002, 0. , 0.421, 0.01 , 0.032, 0.315, 0.205],
[0.024, 0.002, 0. , 0.51 , 0.007, 0.028, 0.081, 0.348],
[0.031, 0.003, 0. , 0.838, 0.008, 0.005, 0.024, 0.091],
[0.032, 0.002, 0. , 0.903, 0.006, 0.002, 0.004, 0.05 ],
[0.032, 0.002, 0. , 0.884, 0.004, 0.003, 0.01 , 0.066],
[0.031, 0.002, 0. , 0.863, 0.006, 0.01 , 0.015, 0.073],
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[0.024, 0.001, 0. , 0.352, 0.007, 0.028, 0.28 , 0.308],
[0.004, 0.01 , 0. , 0.078, 0.004, 0.08 , 0.377, 0.448],
[0.018, 0.062, 0. , 0.046, 0.013, 0.139, 0.192, 0.53 ],
[0.02 , 0.108, 0. , 0.121, 0.065, 0.124, 0.106, 0.457],
[0.019, 0.119, 0. , 0.168, 0.021, 0.244, 0.205, 0.224],
[0.014, 0.087, 0. , 0.18 , 0.042, 0.243, 0.196, 0.237],
[0.008, 0.005, 0. , 0.19 , 0.007, 0.008, 0.294, 0.487],
[0.012, 0.013, 0. , 0.247, 0.009, 0.068, 0.088, 0.563],
[0.013, 0.017, 0. , 0.709, 0.026, 0.084, 0.052, 0.099],
[0.011, 0.012, 0. , 0.79 , 0.004, 0.069, 0.04 , 0.074],
[0.005, 0.007, 0. , 0.85 , 0.001, 0.038, 0.048, 0.051],
[0.004, 0.003, 0. , 0.899, 0.017, 0.009, 0.015, 0.053],
[0.004, 0.001, 0. , 0.758, 0.03 , 0.004, 0.023, 0.18 ],
[0.003, 0.001, 0. , 0.196, 0.022, 0.015, 0.018, 0.745],
[0.002, 0.01 , 0. , 0.012, 0.001, 0.942, 0.018, 0.014],
[0. , 0.009, 0. , 0.009, 0. , 0.944, 0.022, 0.014],
[0. , 0.001, 0. , 0.056, 0.004, 0.007, 0.023, 0.91 ],
[0. , 0. , 0. , 0.915, 0.01 , 0. , 0.002, 0.073],
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[0.002, 0.006, 0. , 0.556, 0.025, 0.03 , 0.062, 0.319],
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[0.009, 0.045, 0. , 0.013, 0.015, 0.592, 0.238, 0.09 ],
[0.001, 0.013, 0. , 0.056, 0.007, 0.321, 0.357, 0.246],
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[0.001, 0.002, 0. , 0.915, 0.005, 0.011, 0.014, 0.053],
[0. , 0.001, 0. , 0.953, 0.005, 0.003, 0.008, 0.029],
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[0.004, 0.009, 0. , 0.335, 0.026, 0.06 , 0.209, 0.358],
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[0.055, 0.059, 0. , 0.044, 0.015, 0.252, 0.279, 0.296],
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[0.051, 0.024, 0. , 0.133, 0.065, 0.134, 0.2 , 0.393],
[0.006, 0.019, 0. , 0.144, 0.013, 0.016, 0.286, 0.516],
[0.012, 0.04 , 0. , 0.177, 0.023, 0.065, 0.098, 0.585],
[0.024, 0.077, 0. , 0.241, 0.037, 0.131, 0.091, 0.399],
[0.027, 0.121, 0. , 0.302, 0.025, 0.149, 0.084, 0.292],
[0.014, 0.116, 0. , 0.342, 0.008, 0.153, 0.129, 0.237],
[0.011, 0.105, 0. , 0.339, 0.026, 0.113, 0.107, 0.298],
[0.005, 0.022, 0. , 0.227, 0.08 , 0.035, 0.003, 0.627],
[0. , 0. , 0. , 0.001, 0. , 0. , 0. , 0.999]],
dtype=float32)}
In [24]:
import pickle
with open(, 'rb') as f:
data = pickle.load(f)
---------------------------------------------------------------------------
UnicodeDecodeError Traceback (most recent call last)
<ipython-input-24-4e48a4656a12> in <module>
3
4 with open('/Users/weilu/Research/Build/RaptorX-Contact/raptorx.uchicago.edu/pdb25-test-500.release.contactFeatures.pkl', 'rb') as f:
----> 5 data = pickle.load(f)
UnicodeDecodeError: 'ascii' codec can't decode byte 0x88 in position 4: ordinal not in range(128)
In [ ]:
In [22]:
np.load("/Users/weilu/Research/Build/RaptorX-Contact/raptorx.uchicago.edu/pdb25-test-500.release.contactFeatures.pkl")
---------------------------------------------------------------------------
UnicodeDecodeError Traceback (most recent call last)
~/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/lib/npyio.py in load(file, mmap_mode, allow_pickle, fix_imports, encoding)
439 try:
--> 440 return pickle.load(fid, **pickle_kwargs)
441 except Exception:
UnicodeDecodeError: 'ascii' codec can't decode byte 0x88 in position 4: ordinal not in range(128)
During handling of the above exception, another exception occurred:
OSError Traceback (most recent call last)
<ipython-input-22-8dbae0f71845> in <module>
----> 1 np.load("/Users/weilu/Research/Build/RaptorX-Contact/raptorx.uchicago.edu/pdb25-test-500.release.contactFeatures.pkl")
~/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/lib/npyio.py in load(file, mmap_mode, allow_pickle, fix_imports, encoding)
441 except Exception:
442 raise IOError(
--> 443 "Failed to interpret file %s as a pickle" % repr(file))
444 finally:
445 if own_fid:
OSError: Failed to interpret file '/Users/weilu/Research/Build/RaptorX-Contact/raptorx.uchicago.edu/pdb25-test-500.release.contactFeatures.pkl' as a pickle
In [13]:
seq[60]
Out[13]:
'1'
In [14]:
seq[59:76]
Out[14]:
'01111111111111110'
In [15]:
seq[75]
Out[15]:
'0'
In [16]:
seq[74]
Out[16]:
'1'
In [ ]:
Content source: luwei0917/awsemmd_script
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