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In [2]:

    
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 *
sys.path.insert(0, "/Users/weilu/openmmawsem")
from helperFunctions.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 [3]:

    
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 [35]:

    
fileName = "/Users/weilu/Research/optimization/chang_database/training_set.txt"
pdb_list = []
with open(fileName) as f:
    for line in f:
        pdbs = line.split()
        pdb_list += pdbs



In [37]:

    
len(pdb_list)









    Out[37]:





387



In [60]:

    
pdb_list = glob.glob("/Users/weilu/Research/optimization/chang_database/cleaned_pdbs/*.pdb")



In [43]:

    
parser = PDBParser()



In [61]:

    
info = []
for pdbFile in pdb_list:
    pdb = pdbFile.split("/")[-1][:-4]
    s = parser.get_structure("X", pdbFile)
    residues = list(s.get_residues())
    n = len(residues)
    info.append([pdb, n])



In [71]:

    
data.to_csv("/Users/weilu/Research/optimization/chang_database/training_set.csv", index_label=0)



In [62]:

    
data = pd.DataFrame(info, columns=["Protein", "Length"])
data = data.sort_values("Length").reset_index(drop=True)



In [69]:

    
specific_decoys = data.query("Length < 150 and Length > 70")



In [75]:

    
specific_decoys









    Out[75]:







  
    
      
      Protein
      Length
    
  
  
    
      26
      1BAJ
      71
    
    
      27
      1HOE
      74
    
    
      28
      1HYP
      75
    
    
      29
      1TIF
      76
    
    
      30
      1VCC
      77
    
    
      31
      1BY9
      80
    
    
      32
      1BDO
      80
    
    
      33
      451C
      82
    
    
      34
      1CC5
      83
    
    
      35
      1BB9
      83
    
    
      36
      1PHT
      83
    
    
      37
      1OPD
      85
    
    
      38
      1A32
      85
    
    
      39
      1PTF
      87
    
    
      40
      1GVP
      87
    
    
      41
      1CYO
      88
    
    
      42
      1TIG
      88
    
    
      43
      1CTJ
      89
    
    
      44
      1FNA
      91
    
    
      45
      1RZL
      91
    
    
      46
      1WHO
      94
    
    
      47
      2CBP
      96
    
    
      48
      2ACY
      98
    
    
      49
      1PLC
      99
    
    
      50
      1BM8
      99
    
    
      51
      1OPC
      99
    
    
      52
      1PUC
      101
    
    
      53
      3VUB
      101
    
    
      54
      1TUL
      102
    
    
      55
      1FMB
      104
    
    
      ...
      ...
      ...
    
    
      95
      1CPQ
      129
    
    
      96
      1PDO
      129
    
    
      97
      3LZT
      129
    
    
      98
      1MSC
      129
    
    
      99
      1HMT
      131
    
    
      100
      1HTP
      131
    
    
      101
      1C52
      131
    
    
      102
      1KUH
      132
    
    
      103
      1CRB
      134
    
    
      104
      1POC
      134
    
    
      105
      1AQT
      135
    
    
      106
      2END
      137
    
    
      107
      5NUL
      138
    
    
      108
      1PNE
      139
    
    
      109
      1LCL
      141
    
    
      110
      2SNS
      141
    
    
      111
      1FLP
      142
    
    
      112
      1TFE
      142
    
    
      113
      1AX8
      144
    
    
      114
      1PKP
      145
    
    
      115
      1RSS
      145
    
    
      116
      1JON
      146
    
    
      117
      1VLS
      146
    
    
      118
      1LBA
      146
    
    
      119
      1ALY
      146
    
    
      120
      1MBA
      146
    
    
      121
      2HBG
      147
    
    
      122
      1AKR
      147
    
    
      123
      1OSA
      148
    
    
      124
      1DIV
      149
    
  

99 rows × 2 columns



In [64]:

    
data.hist("Length", bins=50)









    Out[64]:





array([[<matplotlib.axes._subplots.AxesSubplot object at 0x1a24f39c50>]],
      dtype=object)



In [63]:

    
data









    Out[63]:







  
    
      
      Protein
      Length
    
  
  
    
      0
      1AIE
      31
    
    
      1
      1PPT
      36
    
    
      2
      1AJJ
      37
    
    
      3
      2ERL
      40
    
    
      4
      4HB1
      44
    
    
      5
      1BHP
      45
    
    
      6
      1CBN
      46
    
    
      7
      1PTQ
      50
    
    
      8
      1BX7
      51
    
    
      9
      1RB9
      52
    
    
      10
      1MOF
      53
    
    
      11
      2FDN
      55
    
    
      12
      2KNT
      58
    
    
      13
      1FXD
      58
    
    
      14
      1NKD
      59
    
    
      15
      1VIE
      60
    
    
      16
      1TUD
      60
    
    
      17
      4MT2
      61
    
    
      18
      2IGD
      61
    
    
      19
      1FAS
      61
    
    
      20
      1AHO
      64
    
    
      21
      2SN3
      65
    
    
      22
      1MSI
      66
    
    
      23
      1MJC
      69
    
    
      24
      1AIL
      70
    
    
      25
      1UTG
      70
    
    
      26
      1BAJ
      71
    
    
      27
      1HOE
      74
    
    
      28
      1HYP
      75
    
    
      29
      1TIF
      76
    
    
      ...
      ...
      ...
    
    
      349
      1AB4
      493
    
    
      350
      1A8H
      500
    
    
      351
      1DPE
      507
    
    
      352
      1TDJ
      510
    
    
      353
      1BFD
      523
    
    
      354
      1USH
      525
    
    
      355
      5EAU
      528
    
    
      356
      1DDT
      535
    
    
      357
      1CTN
      538
    
    
      358
      1AYL
      540
    
    
      359
      1LCI
      541
    
    
      360
      1TYV
      554
    
    
      361
      1UOK
      558
    
    
      362
      1VNS
      574
    
    
      363
      1CIY
      577
    
    
      364
      1XWL
      580
    
    
      365
      1ECL
      589
    
    
      366
      1CII
      602
    
    
      367
      1SQC
      619
    
    
      368
      1FCE
      629
    
    
      369
      1GOF
      639
    
    
      370
      1PJR
      651
    
    
      371
      1ACC
      722
    
    
      372
      1VOM
      746
    
    
      373
      1BF2
      750
    
    
      374
      1KIT
      757
    
    
      375
      1DMR
      779
    
    
      376
      1YGE
      839
    
    
      377
      1FIY
      881
    
    
      378
      1KCW
      1040
    
  

379 rows × 2 columns



In [3]:

    
data = pd.read_csv("/Users/weilu/Research/database/tabularResults.csv")



In [4]:

    
data = data.dropna().reset_index(drop=True)



In [5]:

    
data.columns









    Out[5]:





Index(['PDB ID', 'Chain ID', 'Residue Count', 'CATH ID [Res Range]',
       'Cath Description', 'SCOP ID [Res Range]', 'Scop Domain', 'Scop Fold',
       'PFAM Acc [Res Range]', 'Pfam ID', 'Pfam Description', 'Chain Length',
       'Sequence and Secondary Structure'],
      dtype='object')



In [7]:

    
pre = "/Users/weilu/Research/server/dec_2019/orengoftp.biochem.ucl.ac.uk/cath/releases/latest-release/cath-classification-data/cath-domain-list.txt"
data = pd.read_csv(pre, comment="#", sep="\s+", names=["Protein", "C", "A", "T", "H", "S1", "S2", "S3", "S4", "S5", "L", "resolution"])



In [8]:

    
data = data.astype(str)



In [9]:

    
data["CATH"] = data["C"] + "." + data["A"] + "." + data["T"] + "."  + data["H"]



In [10]:

    
# narrow down to 1.10
data = data.query("C == '1' and A == '10'").reset_index(drop=True)



In [11]:

    
data.query("CATH == '1.10.10.10'").query("Protein == '4yiiA00'")



In [12]:

    
# 60694 domains in 1.10.
# 1.10 has 1226 superfamilies
count_superfamilies = data["CATH"].value_counts()
# 292 superfamilies has more than 20 domains.
# 87 superfamilies has more than 100 domains.



In [13]:

    
a = count_superfamilies[count_superfamilies>100]
superfamilies = list(a.index)
filtered_data = data.query("CATH in @superfamilies")



In [14]:

    
# read the list of domains that have structures



In [15]:

    
s_list = np.loadtxt("/Users/weilu/Research/server/dec_2019/cath_dataset/cath-dataset-nonredundant-S20.list", dtype="str")



In [26]:

    
s_list = np.loadtxt("/Users/weilu/Research/server/dec_2019/cath_dataset/cath-dataset-nonredundant-S20Clean.list", dtype="str")



In [16]:

    
len(s_list)









    Out[16]:





14433



In [27]:

    
len(s_list)









    Out[27]:





14224



In [28]:

    
has_structures = filtered_data.query("Protein in @s_list").reset_index(drop=True)



In [29]:

    
len(has_structures)









    Out[29]:





1019



In [30]:

    
has_structures["L"] = has_structures["L"].astype(int)



In [31]:

    
has_structures_small = has_structures.query("L < 200")



In [32]:

    
len(has_structures_small)









    Out[32]:





911



In [33]:

    
has_structures_small.to_csv("/Users/weilu/Research/server/jan_2020/cath_dataset_shuffle_optimization/has_structures_small_dataset_cleaned.csv", index=0)



In [25]:

    
has_structures_small









    Out[25]:







  
    
      
      Protein
      C
      A
      T
      H
      S1
      S2
      S3
      S4
      S5
      L
      resolution
      CATH
    
  
  
    
      0
      3b89A01
      1
      10
      8
      10
      2
      1
      1
      2
      1
      54
      2.6
      1.10.8.10
    
    
      1
      1oksA00
      1
      10
      8
      10
      6
      1
      1
      1
      1
      51
      1.8
      1.10.8.10
    
    
      2
      2ltuA00
      1
      10
      8
      10
      7
      2
      1
      1
      1
      62
      999.0
      1.10.8.10
    
    
      3
      1zv1A00
      1
      10
      8
      10
      8
      1
      1
      1
      1
      59
      1.6
      1.10.8.10
    
    
      4
      1cukA03
      1
      10
      8
      10
      11
      1
      1
      1
      1
      48
      1.9
      1.10.8.10
    
    
      5
      2oo9A00
      1
      10
      8
      10
      13
      2
      1
      1
      1
      44
      2.1
      1.10.8.10
    
    
      6
      3lcuA01
      1
      10
      8
      10
      14
      1
      1
      2
      1
      57
      2.1
      1.10.8.10
    
    
      7
      1p3qQ00
      1
      10
      8
      10
      15
      1
      1
      1
      1
      43
      1.7
      1.10.8.10
    
    
      8
      3bbzA00
      1
      10
      8
      10
      16
      1
      1
      1
      1
      48
      2.1
      1.10.8.10
    
    
      9
      1y8gA03
      1
      10
      8
      10
      21
      2
      2
      1
      1
      39
      2.5
      1.10.8.10
    
    
      10
      3ihpB05
      1
      10
      8
      10
      27
      1
      1
      1
      1
      54
      2.8
      1.10.8.10
    
    
      11
      1a5tA02
      1
      10
      8
      10
      28
      1
      1
      1
      1
      40
      2.2
      1.10.8.10
    
    
      12
      2hwjA02
      1
      10
      8
      10
      30
      1
      1
      1
      1
      59
      2.61
      1.10.8.10
    
    
      13
      2lbcA01
      1
      10
      8
      10
      31
      1
      2
      1
      1
      42
      999.0
      1.10.8.10
    
    
      14
      1tr8A02
      1
      10
      8
      10
      32
      1
      1
      1
      1
      37
      2.27
      1.10.8.10
    
    
      15
      4dbgB02
      1
      10
      8
      10
      33
      1
      1
      1
      1
      61
      2.71
      1.10.8.10
    
    
      16
      1g4aE02
      1
      10
      8
      10
      35
      1
      1
      1
      1
      47
      3.0
      1.10.8.10
    
    
      17
      1nv8B01
      1
      10
      8
      10
      36
      1
      1
      1
      1
      71
      2.2
      1.10.8.10
    
    
      18
      1bvsF03
      1
      10
      8
      10
      37
      1
      1
      1
      1
      45
      3.0
      1.10.8.10
    
    
      19
      4dbgB03
      1
      10
      8
      10
      39
      1
      1
      1
      1
      38
      2.71
      1.10.8.10
    
    
      20
      4f1iA01
      1
      10
      8
      10
      41
      1
      1
      2
      1
      78
      2.5
      1.10.8.10
    
    
      21
      1g3iF02
      1
      10
      8
      10
      43
      1
      2
      1
      1
      23
      3.41
      1.10.8.10
    
    
      22
      1q02A00
      1
      10
      8
      10
      46
      1
      1
      1
      1
      52
      999.0
      1.10.8.10
    
    
      23
      2mgwA00
      1
      10
      8
      10
      49
      1
      1
      1
      1
      52
      999.0
      1.10.8.10
    
    
      24
      1r4gA00
      1
      10
      8
      10
      50
      1
      1
      1
      1
      53
      999.0
      1.10.8.10
    
    
      25
      2knaA01
      1
      10
      8
      10
      51
      1
      1
      1
      1
      54
      999.0
      1.10.8.10
    
    
      26
      1otrA00
      1
      10
      8
      10
      53
      1
      1
      1
      1
      49
      999.0
      1.10.8.10
    
    
      27
      2jp7A00
      1
      10
      8
      10
      55
      1
      1
      1
      1
      57
      999.0
      1.10.8.10
    
    
      28
      2l4eA00
      1
      10
      8
      10
      56
      1
      1
      1
      1
      57
      999.0
      1.10.8.10
    
    
      29
      1pgyA00
      1
      10
      8
      10
      57
      1
      1
      1
      1
      47
      999.0
      1.10.8.10
    
    
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
    
    
      987
      1p94A00
      1
      10
      1220
      10
      30
      1
      1
      1
      1
      76
      999.0
      1.10.1220.10
    
    
      995
      1vq8200
      1
      10
      1620
      10
      1
      1
      1
      1
      1
      46
      2.2
      1.10.1620.10
    
    
      996
      1vq8P01
      1
      10
      1650
      10
      1
      1
      1
      1
      1
      55
      2.2
      1.10.1650.10
    
    
      997
      1m3qA02
      1
      10
      1670
      10
      1
      1
      1
      3
      1
      80
      1.9
      1.10.1670.10
    
    
      998
      1pu6A01
      1
      10
      1670
      10
      2
      1
      1
      1
      1
      93
      1.64
      1.10.1670.10
    
    
      999
      3kntC01
      1
      10
      1670
      10
      3
      2
      1
      2
      1
      95
      2.7
      1.10.1670.10
    
    
      1000
      1xg7B01
      1
      10
      1670
      10
      7
      1
      1
      1
      1
      96
      1.88
      1.10.1670.10
    
    
      1001
      1rrsA01
      1
      10
      1670
      10
      12
      1
      2
      3
      1
      111
      2.4
      1.10.1670.10
    
    
      1002
      1mpgA03
      1
      10
      1670
      10
      13
      1
      1
      1
      1
      52
      1.8
      1.10.1670.10
    
    
      1003
      4unfA01
      1
      10
      1670
      10
      14
      1
      1
      1
      1
      119
      2.15
      1.10.1670.10
    
    
      1004
      4cxfA01
      1
      10
      1740
      10
      1
      2
      1
      1
      1
      87
      1.75
      1.10.1740.10
    
    
      1005
      3czgA01
      1
      10
      1740
      10
      5
      1
      1
      1
      1
      85
      1.8
      1.10.1740.10
    
    
      1006
      1jvsA03
      1
      10
      1740
      10
      6
      1
      1
      2
      1
      85
      2.2
      1.10.1740.10
    
    
      1007
      3ucqA01
      1
      10
      1740
      10
      10
      1
      1
      1
      1
      95
      1.97
      1.10.1740.10
    
    
      1008
      1rp3A01
      1
      10
      1740
      10
      11
      1
      1
      1
      1
      85
      2.3
      1.10.1740.10
    
    
      1009
      4nqwA01
      1
      10
      1740
      10
      12
      1
      1
      1
      1
      84
      2.4
      1.10.1740.10
    
    
      1010
      3t0yA01
      1
      10
      1740
      10
      15
      1
      1
      1
      1
      65
      2.1
      1.10.1740.10
    
    
      1011
      1h19A02
      1
      10
      1740
      60
      1
      1
      1
      3
      1
      97
      2.1
      1.10.1740.60
    
    
      1012
      2gtqA02
      1
      10
      1740
      60
      2
      3
      8
      1
      1
      80
      2.05
      1.10.1740.60
    
    
      1013
      2q6fB03
      1
      10
      1840
      10
      3
      1
      1
      1
      1
      100
      2.0
      1.10.1840.10
    
    
      1018
      3kh1A00
      1
      10
      3210
      10
      7
      1
      1
      1
      1
      192
      1.37
      1.10.3210.10
    
    
      1020
      5tk8A00
      1
      10
      3210
      10
      13
      1
      1
      1
      1
      191
      1.64
      1.10.3210.10
    
    
      1021
      4n6wA00
      1
      10
      3210
      10
      19
      1
      1
      3
      1
      180
      1.85
      1.10.3210.10
    
    
      1022
      2ogiA00
      1
      10
      3210
      10
      20
      1
      1
      2
      1
      190
      1.85
      1.10.3210.10
    
    
      1024
      2pgsA01
      1
      10
      3210
      10
      23
      2
      1
      1
      1
      172
      2.35
      1.10.3210.10
    
    
      1025
      1yoyA00
      1
      10
      3210
      10
      24
      1
      1
      2
      1
      146
      2.0
      1.10.3210.10
    
    
      1027
      3hi0A03
      1
      10
      3210
      10
      27
      1
      1
      1
      1
      199
      2.3
      1.10.3210.10
    
    
      1028
      1vj7B01
      1
      10
      3210
      10
      29
      1
      1
      1
      1
      173
      2.1
      1.10.3210.10
    
    
      1029
      2floA03
      1
      10
      3210
      10
      30
      1
      1
      2
      1
      141
      2.2
      1.10.3210.10
    
    
      1030
      2f6sA00
      1
      10
      3290
      10
      1
      2
      1
      1
      1
      176
      2.5
      1.10.3290.10
    
  

925 rows × 13 columns



In [75]:

    
for_optimization = has_structures_small.groupby("CATH").head(1).reset_index(drop=True)



In [76]:

    
for_optimization["L"].astype(int).hist(bins=100)









    Out[76]:





<matplotlib.axes._subplots.AxesSubplot at 0x1a32047198>



In [78]:

    
for_optimization.to_csv("/Users/weilu/Research/server/dec_2019/optimization_database/for_optimization_dataset.csv")



In [80]:

    
data = pd.read_csv("/Users/weilu/Research/server/dec_2019/optimization_database/for_optimization_dataset.csv", index_col=0)
data["Protein"].to_list()



In [85]:

    
a = for_optimization["Protein"].to_list()



In [89]:

    
print(sorted(a))









    



['132lA00', '1a75A00', '1b82A02', '1b8fA01', '1bekA01', '1bqbA02', '1cpcB00', '1cscA02', '1cy5A00', '1dv5A00', '1e8yA05', '1evyA02', '1f44A01', '1fkaG00', '1fx0B03', '1g1xB00', '1gteA02', '1gu2A00', '1h19A02', '1hk5A03', '1in4A03', '1kw4A00', '1kx3D00', '1l1fA03', '1m1qA00', '1m3qA02', '1mu5A02', '1qwvA00', '1vq8200', '1vq8P01', '1xb0B00', '1xjtA00', '1xmkA00', '1z0xA01', '1zcaA02', '2cpgB00', '2f6sA00', '2grhA00', '2ii2A04', '2ptsA03', '2q6fB03', '2uxwA02', '2vqeD01', '2vyrA00', '2wh6A00', '3b89A01', '3g0vA00', '3geuA00', '3h7iA02', '3h99A03', '3hrdD02', '3ju5A01', '3k06B00', '3kh1A00', '3nasA02', '3oc7A02', '3p1wA03', '3pyoY00', '3qyhB01', '3tjtA01', '3vgjA02', '3ziaG01', '4annA00', '4bcmD01', '4cxfA01', '4du6E01', '4edmA00', '4fppB01', '4i2aA01', '4i4tB03', '4i6uB00', '4jgsE00', '4kbuK02', '4n73A00', '5fpoA01', '5hgoA01', '5kn9A02']



In [87]:

    
len(a)









    Out[87]:





77



In [56]:

    
len(s_list)









    Out[56]:





14433



In [50]:



In [39]:

    
data.shape









    Out[39]:





(60694, 13)



In [99]:

    
data = pd.read_csv("/Users/weilu/Research/server/jan_2020/multi_seq_Pfam/data_info_3.csv", index_col=0)



In [100]:

    
data.shape









    Out[100]:





(1829, 6)



In [103]:

    
data.hist("Length", bins=50)









    Out[103]:





array([[<matplotlib.axes._subplots.AxesSubplot object at 0x1a705aa828>]],
      dtype=object)



In [109]:

    
d = data.query("Length < 300").query("Problematic != 4").reset_index(drop=True)



In [118]:

    
def get_MSA_size(location):
    a = None
    with open(location) as f:
        a = f.readlines()
    return len(a)



In [117]:

    
location = "/Users/weilu/Research/server/jan_2020/multi_seq_Pfam/alignments/1Y7QB_42-131_filtered_0.05.seqs"
get_MSA_size(location)









    Out[117]:





2475



In [123]:

    
pre = "/Users/weilu/Research/server/jan_2020/multi_seq_Pfam/alignments"
d["MSA_size"] = d["FullName"].apply(lambda x:get_MSA_size(f"{pre}/{x}_filtered_0.05.seqs"))



In [124]:

    
d["Length"].hist(bins=50)









    Out[124]:





<matplotlib.axes._subplots.AxesSubplot at 0x1a6a2adba8>



In [126]:

    
d["SeqLength_diff"] = d["SeqLength"] - d["Length"]



In [132]:

    
d.shape









    Out[132]:





(1639, 8)



In [135]:

    
d2 = d.query("abs(SeqLength_diff) < 5").reset_index(drop=True)



In [140]:

    
d2.shape









    Out[140]:





(1228, 8)



In [138]:

    
d2["MSA_size"].hist(bins=50)









    Out[138]:





<matplotlib.axes._subplots.AxesSubplot at 0x1a6a62b2b0>



In [141]:

    
d2.to_csv("/Users/weilu/Research/database/pfam_selected.csv")



In [144]:

    
d2 = pd.read_csv("/Users/weilu/Research/database/pfam_selected.csv", index_col=0)



In [77]:

    
fromFile = "/Users/weilu/Research/server/feb_2020/jeff/feb04_2/original_pdbs/test10_selpro.pdb"
fixer = PDBFixer(filename=fromFile)



In [13]:

    
pd.read_pickle("/Users/weilu/Research/server/mar_2020/mass_iterative_optimization/optimization_iter0_com/decoys/openMM/1a1x_iteration_0.pkl")









    Out[13]:







  
    
      
      Steps
      Qw
      Rg
      Backbone
      Rama
      Contact
      Fragment
      Exclude_Side
      SideChain
      Exclude
      Beta
      Pap
      Helical
      Total
      Run
      Protein
      Folder
      structure
    
  
  
    
      0
      1952
      0.28
      16.38
      115.38
      -541.86
      -256.61
      -83.82
      23.25
      40.90
      1.39
      -90.52
      -31.19
      0.0
      -823.07
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      1
      1953
      0.28
      15.93
      108.30
      -537.23
      -263.13
      -79.74
      34.59
      41.74
      3.04
      -86.25
      -32.08
      0.0
      -810.76
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      2
      1954
      0.28
      16.38
      125.86
      -536.00
      -260.48
      -79.89
      26.26
      29.38
      2.66
      -90.38
      -31.90
      0.0
      -814.49
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      3
      1955
      0.29
      16.27
      108.21
      -535.76
      -260.33
      -83.02
      29.98
      30.83
      4.81
      -83.90
      -30.37
      0.0
      -819.57
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      4
      1956
      0.29
      16.38
      114.33
      -537.25
      -265.41
      -82.94
      30.12
      37.33
      5.64
      -84.92
      -31.49
      0.0
      -814.58
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      5
      1957
      0.29
      16.24
      115.07
      -538.25
      -262.33
      -82.59
      26.73
      35.34
      5.60
      -79.60
      -29.21
      0.0
      -809.23
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      6
      1958
      0.28
      16.10
      103.80
      -538.35
      -265.36
      -81.61
      31.98
      28.40
      6.43
      -85.96
      -31.67
      0.0
      -832.35
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      7
      1959
      0.28
      16.34
      125.42
      -536.45
      -257.20
      -81.81
      26.03
      36.87
      6.21
      -82.98
      -31.36
      0.0
      -795.26
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      8
      1960
      0.28
      16.56
      115.60
      -534.34
      -262.67
      -80.81
      26.81
      35.20
      2.72
      -79.91
      -30.53
      0.0
      -807.92
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      9
      1961
      0.27
      16.39
      123.69
      -540.54
      -260.08
      -80.59
      28.94
      37.83
      4.79
      -82.19
      -30.24
      0.0
      -798.39
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      10
      1962
      0.27
      16.57
      128.17
      -538.88
      -255.19
      -81.20
      24.78
      33.55
      6.02
      -87.43
      -30.68
      0.0
      -800.86
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      11
      1963
      0.27
      16.53
      98.11
      -539.14
      -258.22
      -81.69
      27.91
      37.39
      4.01
      -80.55
      -31.84
      0.0
      -824.02
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      12
      1964
      0.28
      16.17
      115.56
      -534.07
      -256.83
      -82.97
      22.78
      34.32
      2.75
      -81.20
      -33.05
      0.0
      -812.70
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      13
      1965
      0.28
      16.11
      121.31
      -538.02
      -263.90
      -82.25
      26.42
      31.60
      2.11
      -84.37
      -31.68
      0.0
      -818.79
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      14
      1966
      0.27
      16.21
      123.17
      -539.12
      -265.22
      -82.34
      29.88
      31.67
      4.52
      -84.84
      -30.83
      0.0
      -813.10
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      15
      1967
      0.28
      16.14
      102.91
      -538.77
      -264.58
      -81.11
      28.94
      34.01
      2.38
      -83.96
      -30.63
      0.0
      -830.80
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      16
      1968
      0.28
      16.21
      113.21
      -539.05
      -263.12
      -80.05
      30.35
      34.62
      4.59
      -84.61
      -33.03
      0.0
      -817.11
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      17
      1969
      0.28
      16.38
      121.67
      -539.51
      -259.51
      -81.53
      24.27
      36.89
      3.86
      -81.82
      -30.89
      0.0
      -806.57
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      18
      1970
      0.27
      16.33
      118.83
      -544.41
      -257.67
      -80.80
      27.45
      29.28
      4.71
      -83.61
      -32.65
      0.0
      -818.88
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      19
      1971
      0.27
      16.47
      114.26
      -531.71
      -266.48
      -83.53
      23.19
      36.16
      4.78
      -87.33
      -29.28
      0.0
      -819.93
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      20
      1972
      0.27
      16.69
      112.66
      -532.82
      -263.63
      -82.19
      29.09
      31.18
      3.91
      -78.67
      -29.57
      0.0
      -810.05
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      21
      1973
      0.27
      16.33
      112.61
      -542.59
      -258.33
      -80.21
      29.67
      42.25
      3.74
      -79.72
      -31.59
      0.0
      -804.17
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      22
      1974
      0.28
      16.27
      111.65
      -543.34
      -254.50
      -84.61
      23.64
      35.08
      5.88
      -88.39
      -31.36
      0.0
      -825.93
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      23
      1975
      0.28
      16.33
      114.08
      -538.72
      -257.36
      -82.70
      29.24
      35.45
      5.46
      -82.63
      -29.95
      0.0
      -807.13
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      24
      1976
      0.28
      16.40
      126.41
      -541.11
      -268.21
      -83.42
      27.49
      25.89
      3.04
      -87.21
      -29.98
      0.0
      -827.09
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      25
      1977
      0.28
      16.38
      119.15
      -541.82
      -266.71
      -82.94
      26.79
      35.97
      2.86
      -83.21
      -31.09
      0.0
      -821.01
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      26
      1978
      0.28
      16.15
      126.16
      -530.00
      -260.71
      -83.02
      26.73
      31.85
      2.24
      -83.92
      -31.69
      0.0
      -802.35
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      27
      1979
      0.29
      16.03
      114.25
      -535.64
      -262.54
      -83.83
      32.56
      25.82
      3.79
      -78.90
      -32.78
      0.0
      -817.26
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      28
      1980
      0.28
      16.32
      113.13
      -542.83
      -259.90
      -83.17
      27.37
      31.77
      4.03
      -83.65
      -30.92
      0.0
      -824.17
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      29
      1981
      0.28
      16.35
      108.58
      -535.76
      -259.02
      -79.95
      24.85
      32.39
      3.20
      -78.55
      -33.37
      0.0
      -817.63
      0
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
    
    
      70
      1972
      0.30
      15.56
      117.15
      -545.37
      -232.95
      -79.54
      22.77
      37.91
      2.05
      -99.76
      -36.85
      0.0
      -814.59
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      71
      1973
      0.29
      15.06
      112.71
      -538.72
      -242.68
      -76.83
      22.57
      36.53
      3.76
      -95.17
      -34.99
      0.0
      -812.83
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      72
      1974
      0.29
      15.15
      116.88
      -536.01
      -237.82
      -74.92
      25.64
      41.53
      4.69
      -98.98
      -39.40
      0.0
      -798.41
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      73
      1975
      0.29
      14.73
      110.69
      -544.25
      -234.41
      -75.79
      23.45
      29.99
      4.45
      -98.94
      -39.76
      0.0
      -824.57
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      74
      1976
      0.29
      14.77
      109.69
      -540.07
      -249.37
      -77.24
      28.82
      31.00
      5.63
      -96.06
      -35.75
      0.0
      -823.35
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      75
      1977
      0.30
      14.82
      112.14
      -545.12
      -246.79
      -75.94
      27.60
      31.36
      3.26
      -99.50
      -35.70
      0.0
      -828.69
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      76
      1978
      0.30
      15.05
      104.85
      -544.12
      -246.75
      -74.55
      23.26
      33.35
      3.39
      -92.83
      -35.24
      0.0
      -828.65
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      77
      1979
      0.29
      14.40
      106.10
      -538.87
      -238.87
      -75.44
      23.94
      31.08
      1.96
      -97.47
      -32.22
      0.0
      -819.80
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      78
      1980
      0.29
      14.46
      107.99
      -541.58
      -240.90
      -75.42
      25.00
      41.31
      5.17
      -94.71
      -36.19
      0.0
      -809.32
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      79
      1981
      0.30
      14.60
      117.03
      -545.49
      -244.84
      -78.72
      26.88
      37.48
      3.08
      -97.35
      -36.41
      0.0
      -818.34
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      80
      1982
      0.31
      14.93
      114.95
      -542.61
      -245.99
      -78.02
      22.78
      29.54
      3.61
      -92.96
      -35.33
      0.0
      -824.02
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      81
      1983
      0.30
      14.63
      115.85
      -541.57
      -246.35
      -76.37
      31.46
      46.90
      4.76
      -102.08
      -33.83
      0.0
      -801.23
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      82
      1984
      0.29
      14.88
      103.78
      -538.60
      -235.82
      -72.64
      25.76
      35.31
      2.72
      -103.76
      -39.46
      0.0
      -822.71
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      83
      1985
      0.30
      14.82
      120.02
      -540.05
      -240.84
      -75.68
      23.90
      34.32
      6.83
      -97.48
      -38.92
      0.0
      -807.90
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      84
      1986
      0.29
      15.17
      107.70
      -541.81
      -240.61
      -76.03
      26.14
      35.98
      4.86
      -98.66
      -38.53
      0.0
      -820.95
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      85
      1987
      0.30
      15.14
      123.02
      -546.00
      -242.81
      -75.74
      23.68
      32.70
      4.30
      -97.04
      -38.17
      0.0
      -816.07
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      86
      1988
      0.30
      15.01
      102.88
      -543.46
      -240.04
      -76.27
      27.47
      42.50
      3.14
      -100.65
      -36.32
      0.0
      -820.75
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      87
      1989
      0.30
      15.46
      106.49
      -544.33
      -244.29
      -74.91
      23.07
      29.72
      5.68
      -96.79
      -34.23
      0.0
      -829.58
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      88
      1990
      0.30
      15.48
      108.04
      -545.60
      -230.78
      -76.99
      24.48
      33.38
      10.17
      -98.22
      -39.25
      0.0
      -814.77
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      89
      1991
      0.30
      15.28
      109.05
      -543.42
      -242.62
      -78.86
      25.93
      37.84
      5.28
      -102.82
      -35.43
      0.0
      -825.04
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      90
      1992
      0.31
      15.57
      113.04
      -536.31
      -235.47
      -77.00
      21.80
      28.52
      3.95
      -97.71
      -37.52
      0.0
      -816.69
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      91
      1993
      0.30
      15.54
      120.31
      -540.12
      -234.42
      -75.10
      23.73
      26.86
      3.28
      -92.78
      -36.62
      0.0
      -804.86
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      92
      1994
      0.30
      15.77
      112.79
      -531.87
      -244.56
      -75.30
      23.37
      34.93
      2.83
      -93.13
      -39.53
      0.0
      -810.46
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      93
      1995
      0.29
      15.93
      101.54
      -542.05
      -239.97
      -74.11
      20.66
      41.73
      5.94
      -86.97
      -36.84
      0.0
      -810.07
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      94
      1996
      0.29
      15.93
      120.18
      -541.46
      -239.34
      -73.77
      21.46
      34.58
      2.25
      -94.14
      -39.25
      0.0
      -809.49
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      95
      1997
      0.29
      15.77
      110.02
      -543.52
      -243.36
      -73.84
      28.22
      27.17
      3.77
      -95.47
      -39.91
      0.0
      -826.93
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      96
      1998
      0.29
      15.87
      108.01
      -545.43
      -239.90
      -73.44
      28.47
      33.94
      3.39
      -96.32
      -38.91
      0.0
      -820.18
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      97
      1999
      0.29
      15.82
      112.71
      -544.04
      -244.26
      -77.21
      22.30
      31.79
      3.64
      -98.00
      -37.06
      0.0
      -830.14
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      98
      2000
      0.29
      16.02
      109.64
      -542.37
      -240.94
      -77.22
      22.48
      41.26
      3.16
      -96.75
      -38.12
      0.0
      -818.87
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
    
      99
      2001
      0.28
      16.03
      113.90
      -536.30
      -232.76
      -76.58
      24.44
      37.30
      3.44
      -93.48
      -39.78
      0.0
      -799.82
      1
      1a1x
      iteration_0
      (((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
    
  

100 rows × 18 columns



In [ ]:



In [ ]:



In [15]:

    
ls









    



18-02-28 Parsing PFAM database.ipynb
CPU_openAWSEM_benchmark.ipynb
Contact_Optimization_feb26.ipynb
Contact_Optimization_mar02.ipynb
Contact_Optimization_mar26.ipynb
Cornichon.ipynb
Curate_optimization_dataset.ipynb
Cys_energy_term.ipynb
DMP_contact_visual_contact_map_oct04.ipynb
ER_rnative_visual.ipynb
ER_rnative_visual_Agu08.ipynb
Expand_contact_table.ipynb
Experiment_LSTM.ipynb
FourBody.ipynb
Group_Contact_Optimization_apr23.ipynb
HybridDatabase.ipynb
Hybrid_contact.ipynb
LSTM.ipynb
LSTM_test.ipynb
MembraneProteinDatabase.ipynb
MembraneProteinDatabase_largeData.ipynb
MembraneProteinDatabase_moredata.ipynb
MembraneProteinDatabase_oct16.ipynb
Membrane_contact.ipynb
Membrane_contact_Optimization_helperFunctions_Oct17.ipynb
Membrane_pore_and_disulfide_bond.ipynb
Multi_Seq.ipynb
Optimization_helperFunctions.ipynb
Optimization_helperFunctions_Sep20.ipynb
Optimization_helperFunctions_Sep23.ipynb
Optimization_helperFunctions_Sep24.ipynb
Optimization_helperFunctions_Sep25.ipynb
Optimization_helperFunctions_Sep26.ipynb
Optimization_helperFunctions_Sep27.ipynb
Optimization_helperFunctions_Sep27_clean.ipynb
Optimization_helperFunctions_Sep28.ipynb
Optimization_helperFunctions_setup-Copy1.ipynb
Optimization_helperFunctions_setup.ipynb
Optimization_helperFunctions_setup_clean.ipynb
Optimization_helperFunctions_setup_oct08.ipynb
Optimization_helperFunctions_setup_specific_decoy_structures_nov03.ipynb
PCA_exploration.ipynb
Select_frames_apr12.ipynb
Validate_hamiltonian.ipynb
Z_score_evaluation.ipynb
analyze_membrane_simulation_data_jun07.ipynb
analyze_simulation_data_apr17.ipynb
analyze_simulation_data_mar30.ipynb
analyze_simulation_data_may05.ipynb
analyze_simulation_data_nov18.ipynb
benchmark_side_chain_effect.ipynb
cb_cb_distance_database_check.ipynb
cleaned_pdbs/
com_com_exclude_volume_term_parameters.ipynb
combine_raptor_ER_map.ipynb
compute_energy.ipynb
contact_optimization_lagrange_multiplier.ipynb
convert_multi_chain_lammps_to_openmm.ipynb
cys_openMM_figures_plot.ipynb
cys_protein_simulation_analysis_aug13.ipynb
cys_protein_simulation_analysis_aug15.ipynb
cys_protein_simulation_analysis_nov12.ipynb
data_jan20.csv
diffusion_timescale.ipynb
diffusion_timescale_dec03.ipynb
direct_contact.pdf
domain_separation_and_recombine.ipynb
experiment_with_openMM.ipynb
extract_info_from_slurms_out_and_pdb_seqres.ipynb
family_fold_may11.ipynb
frag_predict_cluster.ipynb
frag_predict_cluster_feb26.ipynb
fragment_optimization.ipynb
fragment_optimization_data_analysis.ipynb
frags.mem
hamiltonian_averaging.ipynb
helperFunction_palyGround.ipynb
hybrid_simulation_analysis_aug05.ipynb
hybrid_simulation_analysis_aug11.ipynb
hybrid_simulation_analysis_aug12.ipynb
hybrid_simulation_analysis_aug18.ipynb
hybrid_simulation_analysis_dec07.ipynb
hybrid_simulation_analysis_jul01.ipynb
hybrid_simulation_analysis_jul12.ipynb
hybrid_simulation_analysis_jun29.ipynb
hybrid_simulation_analysis_nov25.ipynb
interaction_well.ipynb
iris.html
iter0.ipynb
iterative_optimization_simulations.ipynb
iterative_optimization_simulations_fragmemory.ipynb
mass_iterative_optimization_simulations_feb07.ipynb
max_Q_wat_frame_202.pdb
multi_chain_support.ipynb
multi_seq_iteration.ipynb
new_old_beta_prediction_comparision.ipynb
nov16_run_openmm.ipynb
nov17_lammps_to_openmm.ipynb
obsolete/
openAWSEM.ipynb
openAWSEM_benchmark.ipynb
openmmReading.ipynb
optimization.ipynb
optimization_dec09.ipynb
optimization_dec28.ipynb
optimization_feb07.ipynb
optimization_feb14.ipynb
optimization_z_score_feb06.ipynb
out.pdb
pap_term_python_with_abit_beta_term.ipynb
plot_explore.ipynb
porter5_ssweight.ipynb
protein_mediated.pdf
read_gamma.ipynb
read_pdbs.ipynb
read_topology_prediction.ipynb
real_contact_cbd_cbd_exclude_volume_term_parameters.ipynb
relative_k.ipynb
relative_k_nov04_clean.ipynb
relative_k_oct16.ipynb
relative_k_oct31.ipynb
represent_center_of_mass_of_side_chain.ipynb
represent_center_of_mass_of_side_chain_convert_to_openMM_feb15.ipynb
rewrite_phis_computation_reading_format.ipynb
secondary_prediction_software_test_netsurfp2.ipynb
shift_z_optimization.ipynb
simulation_analysis_membrane_oct19.ipynb
small_molecular.ipynb
structure_prediction_analysis_another_set_jan17.ipynb
structure_prediction_analysis_combined_mar31.ipynb
structure_prediction_analysis_combined_mar31_with_frag.ipynb
structure_prediction_analysis_membrane_protein_jun08.ipynb
structure_prediction_analysis_old_set.ipynb
structure_prediction_analysis_single_apr30.ipynb
structure_prediction_analysis_test_apr18.ipynb
structure_prediction_analysis_test_may06.ipynb
structure_prediction_analysis_test_set_mar29.ipynb
structure_prediction_frag_memory.ipynb
survey_density_info_for_database.ipynb
survey_density_info_for_database_jan31.ipynb
toLocation
topoogy_prediction_comparision_dec04.ipynb
understand_frag_memory_generation.ipynb
visual_check_of_all_19_amino_acid_gmm.ipynb
zimPosition



In [ ]:

	Protein	Length
26	1BAJ	71
27	1HOE	74
28	1HYP	75
29	1TIF	76
30	1VCC	77
31	1BY9	80
32	1BDO	80
33	451C	82
34	1CC5	83
35	1BB9	83
36	1PHT	83
37	1OPD	85
38	1A32	85
39	1PTF	87
40	1GVP	87
41	1CYO	88
42	1TIG	88
43	1CTJ	89
44	1FNA	91
45	1RZL	91
46	1WHO	94
47	2CBP	96
48	2ACY	98
49	1PLC	99
50	1BM8	99
51	1OPC	99
52	1PUC	101
53	3VUB	101
54	1TUL	102
55	1FMB	104
...	...	...
95	1CPQ	129
96	1PDO	129
97	3LZT	129
98	1MSC	129
99	1HMT	131
100	1HTP	131
101	1C52	131
102	1KUH	132
103	1CRB	134
104	1POC	134
105	1AQT	135
106	2END	137
107	5NUL	138
108	1PNE	139
109	1LCL	141
110	2SNS	141
111	1FLP	142
112	1TFE	142
113	1AX8	144
114	1PKP	145
115	1RSS	145
116	1JON	146
117	1VLS	146
118	1LBA	146
119	1ALY	146
120	1MBA	146
121	2HBG	147
122	1AKR	147
123	1OSA	148
124	1DIV	149

	Protein	Length
0	1AIE	31
1	1PPT	36
2	1AJJ	37
3	2ERL	40
4	4HB1	44
5	1BHP	45
6	1CBN	46
7	1PTQ	50
8	1BX7	51
9	1RB9	52
10	1MOF	53
11	2FDN	55
12	2KNT	58
13	1FXD	58
14	1NKD	59
15	1VIE	60
16	1TUD	60
17	4MT2	61
18	2IGD	61
19	1FAS	61
20	1AHO	64
21	2SN3	65
22	1MSI	66
23	1MJC	69
24	1AIL	70
25	1UTG	70
26	1BAJ	71
27	1HOE	74
28	1HYP	75
29	1TIF	76
...	...	...
349	1AB4	493
350	1A8H	500
351	1DPE	507
352	1TDJ	510
353	1BFD	523
354	1USH	525
355	5EAU	528
356	1DDT	535
357	1CTN	538
358	1AYL	540
359	1LCI	541
360	1TYV	554
361	1UOK	558
362	1VNS	574
363	1CIY	577
364	1XWL	580
365	1ECL	589
366	1CII	602
367	1SQC	619
368	1FCE	629
369	1GOF	639
370	1PJR	651
371	1ACC	722
372	1VOM	746
373	1BF2	750
374	1KIT	757
375	1DMR	779
376	1YGE	839
377	1FIY	881
378	1KCW	1040

	Protein	C	A	T	H	S1	S2	S3	S4	S5	L	resolution	CATH
0	3b89A01	1	10	8	10	2	1	1	2	1	54	2.6	1.10.8.10
1	1oksA00	1	10	8	10	6	1	1	1	1	51	1.8	1.10.8.10
2	2ltuA00	1	10	8	10	7	2	1	1	1	62	999.0	1.10.8.10
3	1zv1A00	1	10	8	10	8	1	1	1	1	59	1.6	1.10.8.10
4	1cukA03	1	10	8	10	11	1	1	1	1	48	1.9	1.10.8.10
5	2oo9A00	1	10	8	10	13	2	1	1	1	44	2.1	1.10.8.10
6	3lcuA01	1	10	8	10	14	1	1	2	1	57	2.1	1.10.8.10
7	1p3qQ00	1	10	8	10	15	1	1	1	1	43	1.7	1.10.8.10
8	3bbzA00	1	10	8	10	16	1	1	1	1	48	2.1	1.10.8.10
9	1y8gA03	1	10	8	10	21	2	2	1	1	39	2.5	1.10.8.10
10	3ihpB05	1	10	8	10	27	1	1	1	1	54	2.8	1.10.8.10
11	1a5tA02	1	10	8	10	28	1	1	1	1	40	2.2	1.10.8.10
12	2hwjA02	1	10	8	10	30	1	1	1	1	59	2.61	1.10.8.10
13	2lbcA01	1	10	8	10	31	1	2	1	1	42	999.0	1.10.8.10
14	1tr8A02	1	10	8	10	32	1	1	1	1	37	2.27	1.10.8.10
15	4dbgB02	1	10	8	10	33	1	1	1	1	61	2.71	1.10.8.10
16	1g4aE02	1	10	8	10	35	1	1	1	1	47	3.0	1.10.8.10
17	1nv8B01	1	10	8	10	36	1	1	1	1	71	2.2	1.10.8.10
18	1bvsF03	1	10	8	10	37	1	1	1	1	45	3.0	1.10.8.10
19	4dbgB03	1	10	8	10	39	1	1	1	1	38	2.71	1.10.8.10
20	4f1iA01	1	10	8	10	41	1	1	2	1	78	2.5	1.10.8.10
21	1g3iF02	1	10	8	10	43	1	2	1	1	23	3.41	1.10.8.10
22	1q02A00	1	10	8	10	46	1	1	1	1	52	999.0	1.10.8.10
23	2mgwA00	1	10	8	10	49	1	1	1	1	52	999.0	1.10.8.10
24	1r4gA00	1	10	8	10	50	1	1	1	1	53	999.0	1.10.8.10
25	2knaA01	1	10	8	10	51	1	1	1	1	54	999.0	1.10.8.10
26	1otrA00	1	10	8	10	53	1	1	1	1	49	999.0	1.10.8.10
27	2jp7A00	1	10	8	10	55	1	1	1	1	57	999.0	1.10.8.10
28	2l4eA00	1	10	8	10	56	1	1	1	1	57	999.0	1.10.8.10
29	1pgyA00	1	10	8	10	57	1	1	1	1	47	999.0	1.10.8.10
...	...	...	...	...	...	...	...	...	...	...	...	...	...
987	1p94A00	1	10	1220	10	30	1	1	1	1	76	999.0	1.10.1220.10
995	1vq8200	1	10	1620	10	1	1	1	1	1	46	2.2	1.10.1620.10
996	1vq8P01	1	10	1650	10	1	1	1	1	1	55	2.2	1.10.1650.10
997	1m3qA02	1	10	1670	10	1	1	1	3	1	80	1.9	1.10.1670.10
998	1pu6A01	1	10	1670	10	2	1	1	1	1	93	1.64	1.10.1670.10
999	3kntC01	1	10	1670	10	3	2	1	2	1	95	2.7	1.10.1670.10
1000	1xg7B01	1	10	1670	10	7	1	1	1	1	96	1.88	1.10.1670.10
1001	1rrsA01	1	10	1670	10	12	1	2	3	1	111	2.4	1.10.1670.10
1002	1mpgA03	1	10	1670	10	13	1	1	1	1	52	1.8	1.10.1670.10
1003	4unfA01	1	10	1670	10	14	1	1	1	1	119	2.15	1.10.1670.10
1004	4cxfA01	1	10	1740	10	1	2	1	1	1	87	1.75	1.10.1740.10
1005	3czgA01	1	10	1740	10	5	1	1	1	1	85	1.8	1.10.1740.10
1006	1jvsA03	1	10	1740	10	6	1	1	2	1	85	2.2	1.10.1740.10
1007	3ucqA01	1	10	1740	10	10	1	1	1	1	95	1.97	1.10.1740.10
1008	1rp3A01	1	10	1740	10	11	1	1	1	1	85	2.3	1.10.1740.10
1009	4nqwA01	1	10	1740	10	12	1	1	1	1	84	2.4	1.10.1740.10
1010	3t0yA01	1	10	1740	10	15	1	1	1	1	65	2.1	1.10.1740.10
1011	1h19A02	1	10	1740	60	1	1	1	3	1	97	2.1	1.10.1740.60
1012	2gtqA02	1	10	1740	60	2	3	8	1	1	80	2.05	1.10.1740.60
1013	2q6fB03	1	10	1840	10	3	1	1	1	1	100	2.0	1.10.1840.10
1018	3kh1A00	1	10	3210	10	7	1	1	1	1	192	1.37	1.10.3210.10
1020	5tk8A00	1	10	3210	10	13	1	1	1	1	191	1.64	1.10.3210.10
1021	4n6wA00	1	10	3210	10	19	1	1	3	1	180	1.85	1.10.3210.10
1022	2ogiA00	1	10	3210	10	20	1	1	2	1	190	1.85	1.10.3210.10
1024	2pgsA01	1	10	3210	10	23	2	1	1	1	172	2.35	1.10.3210.10
1025	1yoyA00	1	10	3210	10	24	1	1	2	1	146	2.0	1.10.3210.10
1027	3hi0A03	1	10	3210	10	27	1	1	1	1	199	2.3	1.10.3210.10
1028	1vj7B01	1	10	3210	10	29	1	1	1	1	173	2.1	1.10.3210.10
1029	2floA03	1	10	3210	10	30	1	1	2	1	141	2.2	1.10.3210.10
1030	2f6sA00	1	10	3290	10	1	2	1	1	1	176	2.5	1.10.3290.10

	Steps	Qw	Rg	Backbone	Rama	Contact	Fragment	Exclude_Side	SideChain	Exclude	Beta	Pap	Helical	Total	Run	Protein	Folder	structure
0	1952	0.28	16.38	115.38	-541.86	-256.61	-83.82	23.25	40.90	1.39	-90.52	-31.19	0.0	-823.07	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
1	1953	0.28	15.93	108.30	-537.23	-263.13	-79.74	34.59	41.74	3.04	-86.25	-32.08	0.0	-810.76	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
2	1954	0.28	16.38	125.86	-536.00	-260.48	-79.89	26.26	29.38	2.66	-90.38	-31.90	0.0	-814.49	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
3	1955	0.29	16.27	108.21	-535.76	-260.33	-83.02	29.98	30.83	4.81	-83.90	-30.37	0.0	-819.57	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
4	1956	0.29	16.38	114.33	-537.25	-265.41	-82.94	30.12	37.33	5.64	-84.92	-31.49	0.0	-814.58	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
5	1957	0.29	16.24	115.07	-538.25	-262.33	-82.59	26.73	35.34	5.60	-79.60	-29.21	0.0	-809.23	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
6	1958	0.28	16.10	103.80	-538.35	-265.36	-81.61	31.98	28.40	6.43	-85.96	-31.67	0.0	-832.35	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
7	1959	0.28	16.34	125.42	-536.45	-257.20	-81.81	26.03	36.87	6.21	-82.98	-31.36	0.0	-795.26	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
8	1960	0.28	16.56	115.60	-534.34	-262.67	-80.81	26.81	35.20	2.72	-79.91	-30.53	0.0	-807.92	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
9	1961	0.27	16.39	123.69	-540.54	-260.08	-80.59	28.94	37.83	4.79	-82.19	-30.24	0.0	-798.39	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
10	1962	0.27	16.57	128.17	-538.88	-255.19	-81.20	24.78	33.55	6.02	-87.43	-30.68	0.0	-800.86	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
11	1963	0.27	16.53	98.11	-539.14	-258.22	-81.69	27.91	37.39	4.01	-80.55	-31.84	0.0	-824.02	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
12	1964	0.28	16.17	115.56	-534.07	-256.83	-82.97	22.78	34.32	2.75	-81.20	-33.05	0.0	-812.70	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
13	1965	0.28	16.11	121.31	-538.02	-263.90	-82.25	26.42	31.60	2.11	-84.37	-31.68	0.0	-818.79	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
14	1966	0.27	16.21	123.17	-539.12	-265.22	-82.34	29.88	31.67	4.52	-84.84	-30.83	0.0	-813.10	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
15	1967	0.28	16.14	102.91	-538.77	-264.58	-81.11	28.94	34.01	2.38	-83.96	-30.63	0.0	-830.80	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
16	1968	0.28	16.21	113.21	-539.05	-263.12	-80.05	30.35	34.62	4.59	-84.61	-33.03	0.0	-817.11	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
17	1969	0.28	16.38	121.67	-539.51	-259.51	-81.53	24.27	36.89	3.86	-81.82	-30.89	0.0	-806.57	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
18	1970	0.27	16.33	118.83	-544.41	-257.67	-80.80	27.45	29.28	4.71	-83.61	-32.65	0.0	-818.88	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
19	1971	0.27	16.47	114.26	-531.71	-266.48	-83.53	23.19	36.16	4.78	-87.33	-29.28	0.0	-819.93	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
20	1972	0.27	16.69	112.66	-532.82	-263.63	-82.19	29.09	31.18	3.91	-78.67	-29.57	0.0	-810.05	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
21	1973	0.27	16.33	112.61	-542.59	-258.33	-80.21	29.67	42.25	3.74	-79.72	-31.59	0.0	-804.17	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
22	1974	0.28	16.27	111.65	-543.34	-254.50	-84.61	23.64	35.08	5.88	-88.39	-31.36	0.0	-825.93	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
23	1975	0.28	16.33	114.08	-538.72	-257.36	-82.70	29.24	35.45	5.46	-82.63	-29.95	0.0	-807.13	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
24	1976	0.28	16.40	126.41	-541.11	-268.21	-83.42	27.49	25.89	3.04	-87.21	-29.98	0.0	-827.09	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
25	1977	0.28	16.38	119.15	-541.82	-266.71	-82.94	26.79	35.97	2.86	-83.21	-31.09	0.0	-821.01	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
26	1978	0.28	16.15	126.16	-530.00	-260.71	-83.02	26.73	31.85	2.24	-83.92	-31.69	0.0	-802.35	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
27	1979	0.29	16.03	114.25	-535.64	-262.54	-83.83	32.56	25.82	3.79	-78.90	-32.78	0.0	-817.26	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
28	1980	0.28	16.32	113.13	-542.83	-259.90	-83.17	27.37	31.77	4.03	-83.65	-30.92	0.0	-824.17	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
29	1981	0.28	16.35	108.58	-535.76	-259.02	-79.95	24.85	32.39	3.20	-78.55	-33.37	0.0	-817.63	0	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
70	1972	0.30	15.56	117.15	-545.37	-232.95	-79.54	22.77	37.91	2.05	-99.76	-36.85	0.0	-814.59	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
71	1973	0.29	15.06	112.71	-538.72	-242.68	-76.83	22.57	36.53	3.76	-95.17	-34.99	0.0	-812.83	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
72	1974	0.29	15.15	116.88	-536.01	-237.82	-74.92	25.64	41.53	4.69	-98.98	-39.40	0.0	-798.41	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
73	1975	0.29	14.73	110.69	-544.25	-234.41	-75.79	23.45	29.99	4.45	-98.94	-39.76	0.0	-824.57	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
74	1976	0.29	14.77	109.69	-540.07	-249.37	-77.24	28.82	31.00	5.63	-96.06	-35.75	0.0	-823.35	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
75	1977	0.30	14.82	112.14	-545.12	-246.79	-75.94	27.60	31.36	3.26	-99.50	-35.70	0.0	-828.69	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
76	1978	0.30	15.05	104.85	-544.12	-246.75	-74.55	23.26	33.35	3.39	-92.83	-35.24	0.0	-828.65	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
77	1979	0.29	14.40	106.10	-538.87	-238.87	-75.44	23.94	31.08	1.96	-97.47	-32.22	0.0	-819.80	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
78	1980	0.29	14.46	107.99	-541.58	-240.90	-75.42	25.00	41.31	5.17	-94.71	-36.19	0.0	-809.32	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
79	1981	0.30	14.60	117.03	-545.49	-244.84	-78.72	26.88	37.48	3.08	-97.35	-36.41	0.0	-818.34	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
80	1982	0.31	14.93	114.95	-542.61	-245.99	-78.02	22.78	29.54	3.61	-92.96	-35.33	0.0	-824.02	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
81	1983	0.30	14.63	115.85	-541.57	-246.35	-76.37	31.46	46.90	4.76	-102.08	-33.83	0.0	-801.23	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
82	1984	0.29	14.88	103.78	-538.60	-235.82	-72.64	25.76	35.31	2.72	-103.76	-39.46	0.0	-822.71	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
83	1985	0.30	14.82	120.02	-540.05	-240.84	-75.68	23.90	34.32	6.83	-97.48	-38.92	0.0	-807.90	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
84	1986	0.29	15.17	107.70	-541.81	-240.61	-76.03	26.14	35.98	4.86	-98.66	-38.53	0.0	-820.95	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
85	1987	0.30	15.14	123.02	-546.00	-242.81	-75.74	23.68	32.70	4.30	-97.04	-38.17	0.0	-816.07	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
86	1988	0.30	15.01	102.88	-543.46	-240.04	-76.27	27.47	42.50	3.14	-100.65	-36.32	0.0	-820.75	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
87	1989	0.30	15.46	106.49	-544.33	-244.29	-74.91	23.07	29.72	5.68	-96.79	-34.23	0.0	-829.58	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
88	1990	0.30	15.48	108.04	-545.60	-230.78	-76.99	24.48	33.38	10.17	-98.22	-39.25	0.0	-814.77	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
89	1991	0.30	15.28	109.05	-543.42	-242.62	-78.86	25.93	37.84	5.28	-102.82	-35.43	0.0	-825.04	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
90	1992	0.31	15.57	113.04	-536.31	-235.47	-77.00	21.80	28.52	3.95	-97.71	-37.52	0.0	-816.69	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
91	1993	0.30	15.54	120.31	-540.12	-234.42	-75.10	23.73	26.86	3.28	-92.78	-36.62	0.0	-804.86	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
92	1994	0.30	15.77	112.79	-531.87	-244.56	-75.30	23.37	34.93	2.83	-93.13	-39.53	0.0	-810.46	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
93	1995	0.29	15.93	101.54	-542.05	-239.97	-74.11	20.66	41.73	5.94	-86.97	-36.84	0.0	-810.07	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
94	1996	0.29	15.93	120.18	-541.46	-239.34	-73.77	21.46	34.58	2.25	-94.14	-39.25	0.0	-809.49	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
95	1997	0.29	15.77	110.02	-543.52	-243.36	-73.84	28.22	27.17	3.77	-95.47	-39.91	0.0	-826.93	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
96	1998	0.29	15.87	108.01	-545.43	-239.90	-73.44	28.47	33.94	3.39	-96.32	-38.91	0.0	-820.18	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
97	1999	0.29	15.82	112.71	-544.04	-244.26	-77.21	22.30	31.79	3.64	-98.00	-37.06	0.0	-830.14	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
98	2000	0.29	16.02	109.64	-542.37	-240.94	-77.22	22.48	41.26	3.16	-96.75	-38.12	0.0	-818.87	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...
99	2001	0.28	16.03	113.90	-536.30	-232.76	-76.58	24.44	37.30	3.44	-93.48	-39.78	0.0	-799.82	1	1a1x	iteration_0	(((<Atom CA>, <Atom C>, <Atom O>, <Atom CB>), ...