In [1]:
import glob
import pandas
import seaborn
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
In [2]:
%matplotlib inline
In [3]:
pd.set_option('display.max_columns', 1000)
In [4]:
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 [5]:
pre = "/Users/weilu/Research/server/jun_week1_2020/protein_DNA_benchmark/"
In [7]:
data = pd.read_csv("/Users/weilu/Research/server/jun_week3_2020/protein_DNA/selected_extra_info.csv", index_col=0)
sampled = data.sample(6, random_state=28)
pdb_list = sampled.idcode.to_list()
In [9]:
data.hist("Chain Length")
Out[9]:
array([[<matplotlib.axes._subplots.AxesSubplot object at 0x11f68fc50>]],
dtype=object)
In [20]:
test = f"/Users/weilu/Research/server/jun_week3_2020/protein_DNA/run1_local_correct_4y60_0_energies.csv"
test_energy = pd.read_csv(test)
test_energy
Out[20]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
1082.176880
1925.405884
595.023376
166.989548
595.023376
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2.944055
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1
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0.0
1.373433e-34
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2
2
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3
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564.292603
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1.513293e-33
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107.872177
562.585693
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0.0
4.104675e-33
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0.000000
...
...
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...
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996
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997
997
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998
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999
999
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562.101807
140.512054
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140.512054
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0.000805
0.000012
0.0
4.675238e-02
1.994680e-02
0.000050
1000 rows × 34 columns
In [22]:
test_energy.plot("Unnamed: 0", "Q_protein kJ/mol")
Out[22]:
<matplotlib.axes._subplots.AxesSubplot at 0x11e9821d0>
In [21]:
test_energy.plot("Unnamed: 0", "ElectrostaticsProteinDNA kJ/mol")
Out[21]:
<matplotlib.axes._subplots.AxesSubplot at 0x11e976630>
In [16]:
test = f"/Users/weilu/Research/server/jun_week3_2020/protein_DNA/run1_local_with_DP_bonds_4y60_0_energies.csv"
test_energy = pd.read_csv(test)
test_energy
Out[16]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
2088.313965
2078.508789
905.877319
432.354156
905.877319
432.354156
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1
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1367.910400
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2
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458.755463
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3
3
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4
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...
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995
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1000 rows × 35 columns
In [17]:
test_energy.plot("Unnamed: 0", "Q_protein kJ/mol")
Out[17]:
<matplotlib.axes._subplots.AxesSubplot at 0x103ece0b8>
In [11]:
test = f"/Users/weilu/Research/server/jun_week3_2020/protein_DNA/native_with_DP_bonds_4y60_0_energies.csv"
test_energy = pd.read_csv(test)
test_energy
Out[11]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
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...
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245
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250 rows × 35 columns
In [13]:
test = f"/Users/weilu/Research/server/jun_week3_2020/protein_DNA/native_4y60_0_energies.csv"
test_energy = pd.read_csv(test)
test_energy
Out[13]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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...
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249
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250 rows × 34 columns
In [14]:
test_energy.columns
Out[14]:
Index(['Unnamed: 0', 'TotalEnergy kJ/mol', 'dna_constraint kJ/mol',
'constraint kJ/mol', 'Bond kJ/mol', 'Angle kJ/mol', 'Stacking kJ/mol',
'Dihedral kJ/mol', 'BasePair kJ/mol', 'CrossStacking kJ/mol',
'Exclusion kJ/mol', 'Electrostatics kJ/mol', 'Connectivity kJ/mol',
'Chain kJ/mol', 'Chi kJ/mol', 'Excl kJ/mol', 'rama kJ/mol',
'rama_pro kJ/mol', 'contact kJ/mol', 'beta1 kJ/mol', 'beta2 kJ/mol',
'beta3 kJ/mol', 'pap1 kJ/mol', 'pap2 kJ/mol', 'fm kJ/mol',
'ExclusionProteinDNA kJ/mol', 'ElectrostaticsProteinDNA kJ/mol',
'Q_protein kJ/mol', 'Q_value_sigma5', 'Q_value_sigma3',
'Q_value_sigma1', 'Q_value_sym_sigma5', 'Q_value_sym_sigma3',
'Q_value_sym_sigma1'],
dtype='object')
In [15]:
test_energy.plot("Unnamed: 0", "ElectrostaticsProteinDNA kJ/mol")
Out[15]:
<matplotlib.axes._subplots.AxesSubplot at 0x11f765630>
In [ ]:
In [18]:
test = f"/Users/weilu/Research/server/jun_week3_2020/protein_DNA/run1_local_4y60_0_energies.csv"
test_energy = pd.read_csv(test)
test_energy
Out[18]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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...
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1000 rows × 34 columns
In [19]:
test_energy.plot("Unnamed: 0", "Q_protein kJ/mol")
Out[19]:
<matplotlib.axes._subplots.AxesSubplot at 0x102c469b0>
In [162]:
test = f"/Users/weilu/Research/server/jun_week3_2020/protein_DNA/run1_1a1j_0_energies.csv"
test_energy = pd.read_csv(test)
test_energy
Out[162]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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In [ ]:
In [159]:
test_energy.columns
Out[159]:
Index(['Unnamed: 0', 'TotalEnergy kJ/mol', 'dna_constraint kJ/mol',
'constraint kJ/mol', 'Bond kJ/mol', 'Angle kJ/mol', 'Stacking kJ/mol',
'Dihedral kJ/mol', 'BasePair kJ/mol', 'CrossStacking kJ/mol',
'Exclusion kJ/mol', 'Electrostatics kJ/mol', 'Connectivity kJ/mol',
'Chain kJ/mol', 'Chi kJ/mol', 'Excl kJ/mol', 'rama kJ/mol',
'rama_pro kJ/mol', 'contact kJ/mol', 'beta1 kJ/mol', 'beta2 kJ/mol',
'beta3 kJ/mol', 'pap1 kJ/mol', 'pap2 kJ/mol', 'fm kJ/mol',
'ExclusionProteinDNA kJ/mol', 'ElectrostaticsProteinDNA kJ/mol',
'Q_protein kJ/mol', 'Q_value_sigma5', 'Q_value_sigma3',
'Q_value_sigma1', 'Q_value_sym_sigma5', 'Q_value_sym_sigma3',
'Q_value_sym_sigma1'],
dtype='object')
In [160]:
test_energy.plot("Unnamed: 0", "constraint kJ/mol")
Out[160]:
<matplotlib.axes._subplots.AxesSubplot at 0x12fca82b0>
In [156]:
test = f"/Users/weilu/Research/server/jun_week3_2020/protein_DNA/test_1a1j_2_energies.csv"
test_energy = pd.read_csv(test)
test_energy
Out[156]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
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250 rows × 34 columns
In [154]:
test = f"/Users/weilu/Research/server/jun_week3_2020/protein_DNA/test_1a1j_0_energies.csv"
test_energy = pd.read_csv(test)
In [155]:
test_energy
Out[155]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
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Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
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0.000000
-2.850445
0.638630
0.012762
0.001503
0.000000
0.036032
0.010604
2.962652e-04
250 rows × 34 columns
In [153]:
test_energy
Out[153]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-349.084930
2173.238770
75.407318
189.677826
-117.732140
-58.348492
-0.344947
-2.301164
3.031464
9.131438
2173.238770
2173.238770
2173.238770
2173.238770
-327.001160
-327.001160
-185.699936
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-0.072591
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0.000000
-0.400525
0.242778
0.000160
0.000001
0.0
1.498430e-02
1.217708e-03
1.468098e-14
1
1
-971.565674
2026.654541
124.595978
228.775513
-164.091049
-104.577934
-51.482243
-6.293706
0.103784
10.327463
2026.654541
2026.654541
2026.654541
2026.654541
-467.136475
-467.136475
-188.233154
-23.884880
-23.884880
-23.884880
-1.616516
-1.616516
-2354.001465
0.000000
-0.992648
0.287096
0.000092
0.000000
0.0
2.652140e-02
2.181911e-03
3.273761e-14
2
2
-973.380188
2127.672852
97.400055
215.599670
-127.804237
-114.314873
-15.291305
-3.968056
2.117152
10.252430
2127.672852
2127.672852
2127.672852
2127.672852
-470.248718
-470.248718
-222.799225
-8.911196
-8.911196
-8.911196
-0.000000
-0.000000
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-0.002686
-1.489246
0.320371
0.000260
0.000000
0.0
6.388084e-02
1.829532e-02
5.259008e-06
3
3
-858.046997
2258.286133
58.622879
242.722565
-108.770157
-76.415924
-7.846669
-3.987401
1.177509
9.105085
2258.286133
2258.286133
2258.286133
2258.286133
-463.263885
-463.263885
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-17.138174
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-17.138174
-0.000054
-0.000054
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-0.534983
-2.991436
0.360749
0.000294
0.000002
0.0
1.097542e-01
7.206161e-02
4.694553e-02
4
4
-907.980591
2019.662354
103.377312
238.520065
-133.074966
-111.043861
-8.392876
-0.656323
1.066873
8.139092
2019.662354
2019.662354
2019.662354
2019.662354
-418.661407
-418.661407
-191.200455
-9.512941
-9.512941
-9.512941
-0.000000
-0.000000
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-0.036599
-1.377616
0.326718
0.000033
0.000000
0.0
4.161120e-02
1.374123e-02
8.766719e-06
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
245
245
-4422.561035
541.814697
16.625736
48.289219
-243.639267
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-169.516693
-36.915016
0.070329
9.403797
541.814697
541.814697
541.814697
541.814697
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-238.447006
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-1.337590
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0.000000
0.000000
0.501878
0.000000
0.000000
0.0
1.542928e-25
2.747323e-66
0.000000e+00
246
246
-4376.637207
553.183105
25.222174
53.743736
-222.160065
-235.690536
-152.038742
-36.197487
0.181921
9.844149
553.183105
553.183105
553.183105
553.183105
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0.000000
0.000000
0.528659
0.000000
0.000000
0.0
6.163170e-26
2.316834e-67
0.000000e+00
247
247
-4397.236328
505.757568
25.320171
61.190659
-236.235168
-230.297379
-157.485046
-27.071873
0.281559
9.254151
505.757568
505.757568
505.757568
505.757568
-765.278687
-765.278687
-222.603500
-117.543594
-117.543594
-117.543594
-2.742609
-2.742609
-3240.342529
0.000000
0.000000
0.560223
0.000000
0.000000
0.0
1.684637e-27
1.905496e-72
0.000000e+00
248
248
-4332.902832
555.005310
16.565491
58.772957
-223.437988
-226.699326
-160.959320
-33.683346
0.163398
9.380742
555.005310
555.005310
555.005310
555.005310
-757.398071
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-4.157536
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0.000000
0.000000
0.517034
0.000000
0.000000
0.0
4.595819e-26
1.000906e-67
0.000000e+00
249
249
-4400.042969
530.055847
22.343199
64.440956
-229.289734
-237.283600
-152.993225
-30.244156
0.114701
9.328447
530.055847
530.055847
530.055847
530.055847
-777.313721
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-232.581009
-117.963684
-117.963684
-117.963684
-2.161796
-2.161796
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0.000000
0.000000
0.544958
0.000000
0.000000
0.0
3.598062e-27
8.218646e-71
0.000000e+00
250 rows × 33 columns
In [7]:
native_file = f"{pre}/local_jun08_pdb_1a36_repetition_4_energies.csv"
native_energy = pd.read_csv(native_file)
In [40]:
native_energy
Out[40]:
Unnamed: 0
TotalEnergy kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-16226.179688
75.343147
276.041107
-404.931763
-447.719604
-191.299622
-40.055317
1.675032
33.851437
5306.451172
5306.451172
5306.451172
5306.451172
-5018.418945
-5018.418945
-3669.246094
-700.023071
-700.023071
-700.023071
-92.312622
-92.312622
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-96.125244
-162.978729
0.936808
0.849419
0.462407
0.943508
0.861644
0.477094
1
1
-16902.947266
78.837830
202.295883
-463.306152
-500.029358
-240.514221
-61.044060
4.596742
31.475451
5053.401367
5053.401855
5053.401367
5053.401367
-5036.673828
-5036.673828
-3837.937500
-722.758850
-722.758850
-722.758850
-98.811943
-98.811943
-11066.540039
-72.813553
-175.399567
0.939737
0.855479
0.478177
0.944268
0.864043
0.497012
2
2
-17401.970703
45.343399
182.227188
-466.012146
-497.576752
-246.141373
-58.878994
3.851930
30.994713
4868.971680
4868.971680
4868.971680
4868.971680
-5122.433105
-5122.433105
-3992.948730
-731.085449
-731.085449
-731.085449
-98.652359
-98.652359
-11059.136719
-97.045006
-165.617508
0.921879
0.819948
0.426885
0.927760
0.827538
0.417590
3
3
-17375.707031
64.157196
163.367340
-460.814972
-489.121033
-270.730896
-62.089310
0.573608
29.920187
4948.175293
4948.175293
4948.175293
4948.175293
-5069.142090
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-3956.500000
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-741.189331
-741.189331
-92.324829
-92.324829
-11163.900391
-98.695717
-179.610428
0.923301
0.827752
0.466873
0.937775
0.851382
0.478145
4
4
-17164.117188
63.687706
146.258926
-476.539734
-496.871429
-256.511597
-65.100105
1.010401
29.678307
5107.647949
5107.647949
5107.647461
5107.647949
-5062.104980
-5062.104980
-3953.353516
-687.670105
-687.670105
-687.670105
-99.194901
-99.194901
-11149.169922
-89.037231
-179.094177
0.926199
0.834396
0.488929
0.944327
0.866481
0.520145
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
1354
1354
-17476.857422
90.647484
192.593048
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0.528191
30.002693
5095.862305
5095.862305
5095.862305
5095.862305
-5181.652344
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-766.270447
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0.544092
0.363078
0.115236
0.824331
0.681142
0.361538
1355
1355
-17466.509766
67.424332
174.690521
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-487.781281
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4.617456
31.505203
5152.246582
5152.246094
5152.246582
5152.246582
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0.534918
0.355067
0.115245
0.811602
0.660185
0.323518
1356
1356
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76.937561
191.284973
-473.358185
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-66.500099
0.077047
30.118214
4912.732422
4912.732422
4912.732422
4912.732422
-5098.808594
-5098.808594
-4420.116211
-716.462708
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0.539219
0.369290
0.128632
0.830618
0.690483
0.354045
1357
1357
-17700.429688
76.072556
159.028076
-466.892578
-502.093323
-242.100998
-59.811329
0.785941
30.083229
4942.963867
4942.963867
4942.964355
4942.963867
-5079.197266
-5079.197266
-4377.551758
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-759.709412
-101.870842
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0.553682
0.383390
0.138519
0.839096
0.704828
0.350625
1358
1358
-17512.953125
85.468567
158.939133
-484.828430
-508.126953
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-57.349087
1.047828
30.279930
5236.811035
5236.811035
5236.811035
5236.811035
-5098.156250
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-104.880630
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-168.081055
0.566000
0.391892
0.139611
0.839462
0.706048
0.381064
1359 rows × 31 columns
In [5]:
energy_file = f"{pre}/check_unfold_no_protein_dna_long_1a36_3_energies.csv"
energy = pd.read_csv(energy_file)
In [9]:
energy_file = f"{pre}/stronger_constraint_within_DNA_1a36_3_energies.csv"
stronger_constraint = pd.read_csv(energy_file)
In [41]:
In [43]:
energy_file = f"{pre}/compare.csv"
compare = pd.read_csv(energy_file)
In [45]:
energy_file = f"{pre}/with_amhgo_quick_1a36_3_energies.csv"
with_amhgo = pd.read_csv(energy_file)
In [143]:
energy_file = f"{pre}/with_er_regular_inter_1a36_0_energies.csv"
with_er_regular_inter_1a36_0_energies = pd.read_csv(energy_file)
In [144]:
with_er_regular_inter_1a36_0_energies
Out[144]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
er kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-14000.619141
16748.166016
2563.367188
2563.367188
550.935547
-219.115402
-237.696899
-49.031216
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8.499491
27.698605
16748.167969
16748.167969
16748.167969
16748.167969
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0.063904
0.033284
0.013472
0.002596
0.074088
0.043079
0.017238
1
1
-15790.304688
17160.291016
1287.477905
1287.477905
577.592041
-193.010590
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-3.183158
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2.539808
31.779448
17160.289062
17160.291016
17160.291016
17160.289062
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0.084730
0.118270
0.066108
0.023097
0.187257
0.110600
0.041997
2
2
-16990.832031
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909.138672
909.138672
758.350952
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7.283559
27.197603
16455.714844
16455.716797
16455.714844
16455.716797
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0.093702
0.030708
0.286500
0.162603
0.036490
3
3
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802.155396
802.155396
594.262451
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37.784122
16700.445312
16700.445312
16700.445312
16700.445312
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0.107812
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0.179664
0.058437
4
4
-18204.070312
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778.743469
778.743469
664.797607
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1.613914
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16755.984375
16755.984375
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0.120737
0.213673
0.122151
0.036560
0.336356
0.212871
0.060589
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
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...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
745
745
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5543.875000
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746
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750 rows × 35 columns
In [145]:
with_dna_protein_bond_and_er_regular_inter
Out[145]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
er kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
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15213.275391
1396.384155
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542.113647
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29.914497
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2500 rows × 35 columns
In [141]:
energy_file = f"{pre}/with_dna_protein_bond_and_no_er_regular_inter_long_1a36_0_energies.csv"
with_dna_protein_bond_and_no_er_regular_inter_long = pd.read_csv(energy_file)
In [142]:
with_dna_protein_bond_and_no_er_regular_inter_long
Out[142]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
10226.996094
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2371.009277
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3750 rows × 34 columns
In [129]:
native_new
Out[129]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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0.910350
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72.628693
174.160477
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250 rows × 33 columns
In [139]:
energy_file = f"{pre}/with_dna_protein_bond_and_no_er_regular_inter_short_1a36_0_energies.csv"
with_dna_protein_bond_and_no_er_regular_inter_short = pd.read_csv(energy_file)
In [140]:
with_dna_protein_bond_and_no_er_regular_inter_short
Out[140]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
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1000 rows × 34 columns
In [130]:
energy_file = f"{pre}/with_dna_protein_bond_and_er_regular_inter_short_1a36_1_energies.csv"
with_dna_protein_bond_and_er_regular_inter_short_1 = pd.read_csv(energy_file)
In [131]:
with_dna_protein_bond_and_er_regular_inter_short_1
Out[131]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
er kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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2797.630371
2797.630371
559.293518
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500 rows × 35 columns
In [132]:
energy_file = f"{pre}/local_jun08_pdb_1a36_repetition_0_energies.csv"
local_jun08_pdb_1a36_repetition_0_energies = pd.read_csv(energy_file)
In [133]:
local_jun08_pdb_1a36_repetition_0_energies
Out[133]:
Unnamed: 0
TotalEnergy kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-16320.150391
74.475220
210.609955
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4.216712
33.212463
5355.384277
5355.384277
5355.384277
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170.454681
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1352 rows × 31 columns
In [134]:
energy_file = f"{pre}/new_evalute.csv"
new_evalute = pd.read_csv(energy_file)
In [136]:
new_evalute.columns
Out[136]:
Index(['Unnamed: 0', 'TotalEnergy kJ/mol', 'Q_protein kJ/mol', 'AMH_Go kJ/mol',
'Bond kJ/mol', 'Angle kJ/mol', 'Stacking kJ/mol', 'Dihedral kJ/mol',
'BasePair kJ/mol', 'CrossStacking kJ/mol', 'Exclusion kJ/mol',
'Electrostatics kJ/mol', 'Connectivity kJ/mol', 'Chain kJ/mol',
'Chi kJ/mol', 'Excl kJ/mol', 'rama kJ/mol', 'rama_pro kJ/mol',
'contact kJ/mol', 'beta1 kJ/mol', 'beta2 kJ/mol', 'beta3 kJ/mol',
'pap1 kJ/mol', 'pap2 kJ/mol', 'fm kJ/mol', 'ExclusionProteinDNA kJ/mol',
'ElectrostaticsProteinDNA kJ/mol', 'num_contact kJ/mol',
'Q_value_sigma5', 'Q_value_sigma3', 'Q_value_sym_sigma5',
'Q_value_sym_sigma3', 'Q_value_sym_sigma1'],
dtype='object')
In [138]:
new_evalute.plot.scatter("num_contact kJ/mol", "ElectrostaticsProteinDNA kJ/mol")
Out[138]:
<matplotlib.axes._subplots.AxesSubplot at 0x1276f25c0>
In [135]:
new_evalute
Out[135]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
num_contact kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
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170.454636
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1352 rows × 33 columns
In [127]:
energy_file = f"{pre}/with_dna_protein_bond_and_er_regular_inter_short_1a36_0_energies.csv"
with_dna_protein_bond_and_er_regular_inter_short = pd.read_csv(energy_file)
In [128]:
with_dna_protein_bond_and_er_regular_inter_short
Out[128]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
er kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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15021.001953
1426.226196
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653.965576
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3.079231
33.425529
15021.001953
15021.000977
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250 rows × 35 columns
In [123]:
energy_file = f"{pre}/with_dna_protein_bond_and_er_regular_inter_1a36_0_energies.csv"
with_dna_protein_bond_and_er_regular_inter = pd.read_csv(energy_file)
In [124]:
with_dna_protein_bond_and_er_regular_inter
Out[124]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
er kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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1396.384155
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568.831421
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...
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2500 rows × 35 columns
In [125]:
with_dna_protein_bond_and_er_regular_inter.columns
Out[125]:
Index(['Unnamed: 0', 'TotalEnergy kJ/mol', 'dna_constraint kJ/mol',
'dna_protein_bond kJ/mol', 'Bond kJ/mol', 'Angle kJ/mol',
'Stacking kJ/mol', 'Dihedral kJ/mol', 'BasePair kJ/mol',
'CrossStacking kJ/mol', 'Exclusion kJ/mol', 'Electrostatics kJ/mol',
'Connectivity kJ/mol', 'Chain kJ/mol', 'Chi kJ/mol', 'Excl kJ/mol',
'rama kJ/mol', 'rama_pro kJ/mol', 'contact kJ/mol', 'beta1 kJ/mol',
'beta2 kJ/mol', 'beta3 kJ/mol', 'pap1 kJ/mol', 'pap2 kJ/mol',
'fm kJ/mol', 'er kJ/mol', 'ExclusionProteinDNA kJ/mol',
'ElectrostaticsProteinDNA kJ/mol', 'Q_protein kJ/mol', 'Q_value_sigma5',
'Q_value_sigma3', 'Q_value_sigma1', 'Q_value_sym_sigma5',
'Q_value_sym_sigma3', 'Q_value_sym_sigma1'],
dtype='object')
In [126]:
with_dna_protein_bond_and_er_regular_inter.plot("Unnamed: 0", "Q_protein kJ/mol")
Out[126]:
<matplotlib.axes._subplots.AxesSubplot at 0x127760278>
In [119]:
energy_file = f"{pre}/with_dna_protein_bond_and_er_1a36_1_energies.csv"
with_dna_protein_bond_and_er_1a36_1 = pd.read_csv(energy_file)
In [120]:
with_dna_protein_bond_and_er_1a36_1
Out[120]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
er kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
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1000 rows × 35 columns
In [122]:
native_new
Out[122]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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250 rows × 33 columns
In [117]:
energy_file = f"{pre}/with_dna_protein_bond_and_er_1a36_0_energies.csv"
with_dna_protein_bond_and_er_1a36_0 = pd.read_csv(energy_file)
In [118]:
with_dna_protein_bond_and_er_1a36_0
Out[118]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
er kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
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0
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14611.609375
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250 rows × 35 columns
In [114]:
energy_file = f"{pre}/with_dna_protein_bond_1a36_0_energies.csv"
with_dna_protein_bond = pd.read_csv(energy_file)
In [115]:
with_dna_protein_bond
Out[115]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
dna_protein_bond kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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250 rows × 34 columns
In [89]:
energy_file = f"{pre}/with_elec_PD_fm_k2_long_1a36_0_energies.csv"
with_elec_PD_fm_k2_long = pd.read_csv(energy_file)
In [90]:
with_elec_PD_fm_k2_long
Out[90]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
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1
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14894.742188
263.292175
521.607605
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0.009359
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4.474950e-02
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0.008499
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2
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15727.791016
194.440674
647.218323
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15727.791016
15727.791992
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0.006472
3
3
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14738.788086
268.273865
526.792847
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10.634282
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14738.788086
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2.682990e-02
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3750 rows × 33 columns
In [86]:
energy_file = f"{pre}/no_elec_PD_fm_k2_1a36_1_energies.csv"
no_elec_PD_fm_k2 = pd.read_csv(energy_file)
In [87]:
no_elec_PD_fm_k2
Out[87]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-2817.765625
15458.158203
254.367279
491.722076
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1
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3
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999
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0.000000
1000 rows × 33 columns
In [ ]:
In [ ]:
In [84]:
energy_file = f"{pre}/no_elec_PD_fm_k2_1a36_0_energies.csv"
no_elec_PD_fm_k2 = pd.read_csv(energy_file)
In [85]:
no_elec_PD_fm_k2
Out[85]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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750 rows × 33 columns
In [82]:
energy_file = f"{pre}/elec_k3_weak_contact_first_no_short_1a36_1_energies.csv"
elec_k3_weak_contact_first_no_short_1a36_1 = pd.read_csv(energy_file)
In [83]:
elec_k3_weak_contact_first_no_short_1a36_1
Out[83]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
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448.487030
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750 rows × 33 columns
In [81]:
elec_k3_weak_contact_first_no_short_1a36_1
Out[81]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
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750 rows × 33 columns
In [74]:
energy_file = f"{pre}/elec_k3_weak_contact_first_no_1a36_0_energies.csv"
elec_k3_weak_contact_first_no = pd.read_csv(energy_file)
In [75]:
elec_k3_weak_contact_first_no
Out[75]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
4.888317e+03
0.041506
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481.888489
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inf
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1536 rows × 33 columns
In [76]:
elec_k3_weak_contact_first_no.columns
Out[76]:
Index(['Unnamed: 0', 'TotalEnergy kJ/mol', 'Q_protein kJ/mol', 'AMH_Go kJ/mol',
'Bond kJ/mol', 'Angle kJ/mol', 'Stacking kJ/mol', 'Dihedral kJ/mol',
'BasePair kJ/mol', 'CrossStacking kJ/mol', 'Exclusion kJ/mol',
'Electrostatics kJ/mol', 'Connectivity kJ/mol', 'Chain kJ/mol',
'Chi kJ/mol', 'Excl kJ/mol', 'rama kJ/mol', 'rama_pro kJ/mol',
'contact kJ/mol', 'beta1 kJ/mol', 'beta2 kJ/mol', 'beta3 kJ/mol',
'pap1 kJ/mol', 'pap2 kJ/mol', 'fm kJ/mol', 'ExclusionProteinDNA kJ/mol',
'ElectrostaticsProteinDNA kJ/mol', 'Q_value_sigma5', 'Q_value_sigma3',
'Q_value_sigma1', 'Q_value_sym_sigma5', 'Q_value_sym_sigma3',
'Q_value_sym_sigma1'],
dtype='object')
In [78]:
elec_k3_weak_contact_first_no.plot("Unnamed: 0", "ExclusionProteinDNA kJ/mol")
plt.yscale("log")
In [72]:
energy_file = f"{pre}/elec_k3_weak_contact_1a36_0_energies.csv"
elec_k3_weak_contact = pd.read_csv(energy_file)
In [73]:
elec_k3_weak_contact
Out[73]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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0.046304
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158.260208
477.781555
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750 rows × 33 columns
In [70]:
elec_k3_weak_contact
Out[70]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
4025.972412
13280.344727
158.260162
477.781555
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750 rows × 33 columns
In [64]:
energy_file = f"{pre}/elec_k5_1a36_0_energies.csv"
elec_k5 = pd.read_csv(energy_file)
In [65]:
elec_k5
Out[65]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-1275.583984
0.044242
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213.720657
446.278412
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31.307692
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...
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750 rows × 33 columns
In [63]:
elec_k5
Out[63]:
Unnamed: 0
TotalEnergy kJ/mol
dna_constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_protein kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
2798.751221
12920.017578
213.720612
446.278381
-342.176544
-340.320770
-87.032585
-29.616756
10.055115
31.307690
12920.017578
12920.017578
12920.017578
12920.017578
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0.014584
0.008042
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0.055331
0.029833
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1
2977.150391
13306.714844
233.990997
434.423584
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7.842584
29.874681
13306.713867
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0.047039
0.006082
0.002318
0.000660
0.042173
0.019367
3.153285e-03
2
2
3570.504395
13938.670898
150.035217
456.900757
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21.840113
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13938.670898
13938.670898
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0.050780
0.002883
0.000385
0.000000
0.019886
0.003181
8.012001e-09
3
3
2501.365479
12937.806641
263.255005
549.169434
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1.726175
28.249378
12937.806641
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4
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-14.890550
0.057187
0.001625
0.000195
0.000000
0.032677
0.014008
4.615912e-03
...
...
...
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...
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...
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...
...
...
...
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...
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745
745
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0.170900
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746
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5074.129883
94.608505
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749
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156.585602
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0.171729
0.175707
0.097865
0.033931
0.669645
0.504811
2.286419e-01
750 rows × 33 columns
In [60]:
energy_file = f"{pre}/with_amhgo_cutoff16_elec_k5_1a36_0_energies.csv"
cutoff16_elec_k5 = pd.read_csv(energy_file)
In [61]:
cutoff16_elec_k5
Out[61]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-12020.449219
0.091437
-11418.078125
232.238434
413.090912
-313.558594
-306.008972
-31.621284
-18.530718
0.609952
30.964396
13667.182617
13667.183594
13667.182617
13667.182617
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0.034682
0.011836
0.002413
1
1
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0.112425
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228.072342
417.927734
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2.812229
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0.010677
0.003660
0.000615
0.053712
0.021517
0.004012
2
2
-16640.150391
0.132516
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186.258850
426.691223
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5.608495
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4.318938
30.590771
13906.835938
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13906.835938
13906.835938
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0.015267
0.006940
0.000983
0.053068
0.030309
0.010282
3
3
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163.782227
472.322388
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13418.086914
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13418.086914
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0.055361
0.023310
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4
4
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233.142395
541.981812
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0.006716
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0.069481
0.038396
0.014067
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
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745
745
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749
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72.694794
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750 rows × 33 columns
In [59]:
cutoff16_elec_k5
Out[59]:
Unnamed: 0
TotalEnergy kJ/mol
AMH_Go kJ/mol
dna_constraint kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-37038.421875
-36533.500000
13776.740234
232.238388
413.090881
-313.558594
-306.008972
-31.621319
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0.609951
30.964396
13776.740234
13776.740234
13776.740234
13776.740234
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1
1
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228.072327
417.927673
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13661.101562
13661.101562
13661.101562
13661.101562
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...
...
...
...
...
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745
745
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750 rows × 33 columns
However, it is still not perfect. and the Go term energy is not as low as expected. More importantly, the next step is to increase the protein DNA interaction strength. I will use a regular single memory, and half the regualr strength of AMH-go term. and 5 times the regualr interaction strength.
In [55]:
energy_file = f"{pre}/with_amhgo_cutoff16_1a36_0_energies.csv"
cutoff16 = pd.read_csv(energy_file)
In [56]:
cutoff16
Out[56]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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146.953308
489.531677
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33.911648
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1
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2
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...
...
...
...
...
...
...
...
...
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...
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...
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...
...
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745
745
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750 rows × 33 columns
In [ ]:
energy_file = f"{pre}/with_amhgo_k2_1a36_0_energies.csv"
with_amhgo_k2 = pd.read_csv(energy_file)
In [52]:
with_amhgo_k2.columns
Out[52]:
Index(['Unnamed: 0', 'TotalEnergy kJ/mol', 'Q_protein kJ/mol', 'AMH_Go kJ/mol',
'Bond kJ/mol', 'Angle kJ/mol', 'Stacking kJ/mol', 'Dihedral kJ/mol',
'BasePair kJ/mol', 'CrossStacking kJ/mol', 'Exclusion kJ/mol',
'Electrostatics kJ/mol', 'Connectivity kJ/mol', 'Chain kJ/mol',
'Chi kJ/mol', 'Excl kJ/mol', 'rama kJ/mol', 'rama_pro kJ/mol',
'contact kJ/mol', 'beta1 kJ/mol', 'beta2 kJ/mol', 'beta3 kJ/mol',
'pap1 kJ/mol', 'pap2 kJ/mol', 'fm kJ/mol', 'ExclusionProteinDNA kJ/mol',
'ElectrostaticsProteinDNA kJ/mol', 'Q_value_sigma5', 'Q_value_sigma3',
'Q_value_sigma1', 'Q_value_sym_sigma5', 'Q_value_sym_sigma3',
'Q_value_sym_sigma1'],
dtype='object')
In [54]:
with_amhgo_k2.plot("Unnamed: 0", "AMH_Go kJ/mol")
Out[54]:
<matplotlib.axes._subplots.AxesSubplot at 0x1287cedd8>
In [51]:
with_amhgo_k2
Out[51]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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1
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3
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...
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...
...
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...
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745
745
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0.061601
749
749
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49.127647
136.112961
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33.288712
3828.843506
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0.090514
0.029394
0.262582
0.183379
0.064309
750 rows × 33 columns
In [47]:
energy_file = f"{pre}/native_1a36_3_energies.csv"
native_new = pd.read_csv(energy_file)
In [48]:
native_new
Out[48]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
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0.910350
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72.628693
174.160477
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1.116977
32.101761
4982.414062
4982.413574
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72.544197
165.041199
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4873.564453
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0.851793
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91.083344
172.127487
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31.616669
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184.347809
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88.812004
172.881195
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31.823505
4870.122070
4870.122070
4870.122070
4870.121582
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0.961920
0.902782
0.556735
0.964789
0.908582
0.554520
...
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...
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...
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245
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32.260189
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249
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32.398632
3235.748535
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0.621944
0.227924
0.944277
0.866626
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250 rows × 33 columns
In [46]:
with_amhgo
Out[46]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-10750.947266
0.062825
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149.426193
517.377930
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1
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2
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181.505737
466.779846
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0.004356
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0.044340
0.022768
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3
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247.747009
517.660400
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153.598907
528.759277
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12933.581055
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0.000000
0.030861
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...
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245
245
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3564.943359
3564.943359
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246
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247
247
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248
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250 rows × 33 columns
In [44]:
compare
Out[44]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-37504.875000
0.825722
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75.343140
276.041138
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0.477094
1
1
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2
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...
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1356
1356
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0.412031
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191.284973
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4912.732910
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85.468567
158.939087
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1359 rows × 33 columns
In [ ]:
energy_file = f"{pre}/stronger_constraint_within_DNA_long_2_1a36_3_energies.csv"
stronger_constraint_fold = pd.read_csv(energy_file)
In [42]:
stronger_constraint_fold
Out[42]:
Unnamed: 0
TotalEnergy kJ/mol
Q_protein kJ/mol
AMH_Go kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
-4963.160156
0.054905
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193.614624
389.494141
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0.020081
31.347294
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0.000562
1
1
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519.555725
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3.636368e-02
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0.000390
2
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478.538879
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181.355347
514.997986
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29.101568
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0.002121
0.000272
6.036279e-02
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4
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217.547180
591.753052
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30.445271
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0.008621
0.003056
0.000858
6.992062e-02
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0.019951
...
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0.000000
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0.000000
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55.518173
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0.091450
30.793739
3463.173340
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0.000000
9.465677e-29
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0.000000
2500 rows × 33 columns
In [39]:
stronger_constraint_fold
Out[39]:
Unnamed: 0
TotalEnergy kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Q_protein kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
1516.460449
193.614624
389.494141
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0.020081
31.347294
0.054905
13908.466797
13908.466797
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1
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0.000390
2
2
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307.757141
478.538879
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12746.143555
12746.143555
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0.004084
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5.672172e-02
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0.006587
3
3
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181.355347
514.997986
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6.992062e-02
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2500 rows × 32 columns
In [15]:
stronger_constraint_fold
Out[15]:
Unnamed: 0
TotalEnergy kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
Connectivity kJ/mol
Chain kJ/mol
Chi kJ/mol
Excl kJ/mol
rama kJ/mol
rama_pro kJ/mol
contact kJ/mol
beta1 kJ/mol
beta2 kJ/mol
beta3 kJ/mol
pap1 kJ/mol
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
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0.020081
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0.000000
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2
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514.997925
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0.000000
2496
2496
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56.799328
146.473892
-515.979736
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-75.415527
0.854753
30.287868
3462.849609
3462.849609
3462.849609
3462.849609
-5263.055664
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-4828.315918
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-76.535439
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0.000000
0.000000
0.000000
0.000000
0.000000
2.743599e-27
6.183768e-70
0.000000
2497
2497
-20111.171875
48.113892
84.582458
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0.400839
30.814110
3461.849854
3461.849854
3461.850098
3461.849854
-5211.725586
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0.000000
0.000000
0.000000
0.000000
0.000000
3.428768e-28
1.894132e-72
0.000000
2498
2498
-20281.796875
50.091408
120.050140
-523.828125
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1.107744
31.206522
3345.334473
3345.334717
3345.334961
3345.334961
-5216.617188
-5216.617188
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0.000000
0.000000
0.000000
0.000000
0.000000
9.521503e-30
9.106016e-77
0.000000
2499
2499
-20118.857422
55.518166
116.415886
-505.374084
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0.091450
30.793739
3463.173340
3463.173340
3463.173340
3463.173340
-5209.401855
-5209.401855
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0.000000
0.000000
0.000000
0.000000
0.000000
9.465677e-29
5.377658e-74
0.000000
2500 rows × 31 columns
In [10]:
stronger_constraint
Out[10]:
Unnamed: 0
TotalEnergy kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
...
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
2751.756104
187.043335
472.385925
-279.620728
-285.180359
-37.666931
-20.094942
14.769954
28.938948
...
-0.000885
-5653.264648
-0.016492
-15.730292
0.010448
0.003916
0.000161
0.045830
0.015680
0.000553
1
1
3344.220459
206.967651
495.209229
-351.113556
-282.360382
-27.561464
-14.128434
5.213923
32.944870
...
-0.000000
-5666.094727
-0.626513
-10.067689
0.020576
0.011143
0.005402
0.064746
0.038197
0.012049
2
2
3570.406738
174.872589
604.908325
-326.279358
-241.867004
-11.380614
-15.850067
9.216265
32.884300
...
-0.000000
-5505.086914
-3.493746
-9.414020
0.025760
0.016287
0.005430
0.054612
0.036158
0.012272
3
3
3260.695557
173.167938
481.796509
-310.534882
-282.409485
-52.986652
-23.804586
8.019660
35.213364
...
-0.834329
-5608.276367
-1.571845
-12.561926
0.030074
0.018290
0.004887
0.064057
0.041900
0.013772
4
4
3448.626465
213.952820
528.470642
-322.784332
-301.791901
-36.606747
-16.725708
3.138205
29.116264
...
-0.000001
-5764.266113
-5.332120
-19.371002
0.022172
0.014490
0.005562
0.053415
0.025048
0.004745
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
745
745
-13794.053711
81.198723
208.947205
-461.315857
-486.655334
-266.447876
-68.230888
6.431051
31.506172
...
-44.248390
-9825.283203
-43.558395
-147.625443
0.081011
0.046731
0.015926
0.264246
0.167895
0.061185
746
746
-13679.349609
123.038223
221.537964
-472.415436
-488.727600
-258.686768
-59.512806
2.693787
31.207396
...
-54.073891
-9862.950195
-62.270706
-146.033951
0.084354
0.046297
0.011088
0.277929
0.179796
0.063191
747
747
-13966.784180
89.602585
235.601700
-459.807861
-440.669617
-250.781738
-55.060417
4.970407
33.288662
...
-47.779346
-9893.587891
-54.356178
-149.513885
0.081224
0.046133
0.013062
0.274974
0.176941
0.064224
748
748
-13611.095703
80.808060
273.054688
-455.670074
-459.646973
-201.079102
-56.204491
1.246781
30.025082
...
-38.545300
-9978.288086
-49.563362
-162.994598
0.089252
0.051221
0.017675
0.299104
0.188173
0.065845
749
749
-13771.947266
123.044830
266.527527
-446.666687
-440.401855
-195.184113
-53.572548
0.614097
32.546722
...
-56.634232
-9792.927734
-51.947975
-167.630646
0.080752
0.048326
0.015890
0.276278
0.172286
0.053290
750 rows × 31 columns
In [6]:
energy
Out[6]:
Unnamed: 0
TotalEnergy kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
...
pap2 kJ/mol
fm kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
0
0
3305.783691
239.759033
506.615448
-229.517700
-300.989807
-35.822762
-12.156846
5.389489
33.854439
...
-0.000001
-5597.865234
-0.053774
-0.105683
0.018308
0.010644
0.004147
5.417059e-02
3.142258e-02
1.002480e-02
1
1
3268.414062
243.954346
483.564545
-184.352783
-97.142609
-2.403640
-2.931943
4.148345
32.477295
...
-0.001313
-5966.361328
-0.122402
-3.881339
0.011060
0.004317
0.000850
5.433777e-02
2.906103e-02
7.522326e-03
2
2
2957.700928
199.026550
625.448914
-101.639122
-138.101379
-0.019470
-1.554419
0.608642
33.851032
...
-12.305786
-5961.482422
-3.258794
-10.635117
0.010988
0.004684
0.000637
6.502639e-02
3.841384e-02
1.185867e-02
3
3
3500.243164
218.979370
646.042480
-146.134369
-82.631851
-0.009582
-0.445503
4.168328
32.623455
...
-0.001030
-5814.566406
-2.266489
-11.704278
0.009701
0.004103
0.001575
6.035545e-02
2.972190e-02
1.107600e-02
4
4
3810.185791
240.551346
481.391937
-152.146133
-15.086666
-13.307845
-0.436618
5.167522
35.620865
...
-0.000000
-5927.345703
-4.454960
-18.650276
0.026752
0.014347
0.004243
1.048964e-01
6.801796e-02
2.377536e-02
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
1495
1495
-13895.026367
127.764664
270.320953
-335.433380
-334.371521
-1.294995
-1.651048
0.909865
12.673875
...
-83.489944
-10305.003906
0.000000
-0.088717
0.000001
0.000000
0.000000
1.195113e-06
5.905640e-13
3.127160e-90
1496
1496
-14001.965820
96.780586
296.236633
-359.190857
-354.874023
-0.001035
-1.077930
0.759880
13.328664
...
-74.435699
-10195.861328
0.000000
-0.000549
0.000000
0.000000
0.000000
3.860616e-08
4.888146e-17
5.777858e-127
1497
1497
-13191.241211
83.388748
288.018829
-340.293152
-326.422363
-0.000335
-0.315053
0.019772
12.806475
...
-77.932861
-10182.134766
0.000000
-0.022824
0.000000
0.000000
0.000000
7.447466e-08
3.360901e-16
2.061122e-119
1498
1498
-14020.452148
131.711029
232.028412
-349.804321
-345.736359
0.000000
-0.056315
0.255597
12.082605
...
-75.535828
-10370.130859
0.000000
-0.021400
0.000000
0.000000
0.000000
1.428192e-07
1.783523e-15
6.650291e-113
1499
1499
-13470.135742
95.700760
246.400162
-335.066681
-298.478821
-0.000002
-0.053539
2.335101
11.861460
...
-72.454460
-10248.289062
0.000000
-0.021326
0.000000
0.000000
0.000000
3.100745e-07
7.614935e-15
1.686316e-108
1500 rows × 31 columns
In [10]:
all_energies
Out[10]:
TotalEnergy kJ/mol
Bond kJ/mol
Angle kJ/mol
Stacking kJ/mol
Dihedral kJ/mol
BasePair kJ/mol
CrossStacking kJ/mol
Exclusion kJ/mol
Electrostatics kJ/mol
ExclusionProteinDNA kJ/mol
ElectrostaticsProteinDNA kJ/mol
Q_value_sigma5
Q_value_sigma3
Q_value_sigma1
Q_value_sym_sigma5
Q_value_sym_sigma3
Q_value_sym_sigma1
Frame
Repetition
0
-579.956187
30.034379
55.576137
-236.216455
-197.643073
-168.099165
-19.031443
0.174821
11.422789
-12.473771
-46.067273
0.953503
0.883798
0.529567
0.960756
0.900067
0.557033
0
0
1
-562.156997
39.764986
69.553571
-235.920273
-202.864152
-155.138428
-20.380014
0.321760
12.088811
-23.412640
-48.544412
0.952031
0.881245
0.540520
0.966318
0.914261
0.603573
1
0
2
-563.423157
42.565791
89.690582
-255.192209
-209.413393
-171.520337
-22.155608
1.645880
12.308197
-5.117595
-48.601390
0.951902
0.882430
0.532592
0.960807
0.902798
0.586058
2
0
3
-514.230684
35.016136
111.395315
-239.041864
-181.228089
-161.712875
-18.269944
0.000000
11.087300
-27.326799
-46.502775
0.945481
0.871140
0.536289
0.962326
0.905865
0.589554
3
0
4
-562.644147
37.246923
72.924086
-250.273912
-193.951326
-155.298453
-17.644028
1.517006
10.809981
-21.970781
-48.296910
0.942463
0.860939
0.489864
0.952847
0.884054
0.541758
4
0
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
1417
-562.872924
29.985269
68.880045
-258.416188
-197.371733
-165.780367
-23.927309
0.388246
11.164529
-7.152417
-20.750824
0.068095
0.032055
0.007676
0.297275
0.140731
0.026941
1417
0
1418
-480.715832
48.445864
115.587048
-252.116772
-188.624121
-171.766329
-17.827105
0.243118
11.416885
-5.952100
-20.220776
0.062427
0.029212
0.006816
0.281279
0.124022
0.019764
1418
0
1419
-529.079808
31.689233
74.986257
-259.405059
-187.150954
-157.696625
-18.488982
1.287880
11.339750
-4.808696
-20.934107
0.062060
0.030204
0.009231
0.275546
0.124143
0.021917
1419
0
1420
-509.725327
48.118250
82.329313
-253.216857
-183.815660
-166.723617
-19.424492
0.235718
10.214656
-6.853522
-20.697462
0.068749
0.032440
0.007157
0.319733
0.162285
0.032661
1420
0
1421
-505.517641
32.458037
93.116197
-249.932257
-194.661925
-150.585107
-18.376587
1.146029
11.017838
-8.405581
-21.412435
0.074683
0.035435
0.008030
0.325141
0.168198
0.028708
1421
0
1422 rows × 19 columns
In [13]:
energy_file = f"{pre}/local_jun08_pdb_1svc_dimer_repetition_0_energies.csv"
energy = pd.read_csv(energy_file)
In [15]:
energy.columns
Out[15]:
Index(['Unnamed: 0', 'TotalEnergy kJ/mol', 'Bond kJ/mol', 'Angle kJ/mol',
'Stacking kJ/mol', 'Dihedral kJ/mol', 'BasePair kJ/mol',
'CrossStacking kJ/mol', 'Exclusion kJ/mol', 'Electrostatics kJ/mol',
'Connectivity kJ/mol', 'Chain kJ/mol', 'Chi kJ/mol', 'Excl kJ/mol',
'rama kJ/mol', 'rama_pro kJ/mol', 'contact kJ/mol', 'beta1 kJ/mol',
'beta2 kJ/mol', 'beta3 kJ/mol', 'pap1 kJ/mol', 'pap2 kJ/mol',
'fm kJ/mol', 'ExclusionProteinDNA kJ/mol',
'ElectrostaticsProteinDNA kJ/mol', 'Q_value_sigma5', 'Q_value_sigma3',
'Q_value_sigma1', 'Q_value_sym_sigma5', 'Q_value_sym_sigma3',
'Q_value_sym_sigma1'],
dtype='object')
In [16]:
energy["fm kJ/mol"]
Out[16]:
0 -2883.662598
1 -3092.789551
2 -3276.278809
3 -3354.642090
4 -3495.340576
...
88 -4912.582031
89 -4911.849609
90 -4932.357910
91 -4969.287109
92 -4876.708984
Name: fm kJ/mol, Length: 93, dtype: float64
In [17]:
pdb_file = f"{pre}/DNAProtein_Platform_OpenCL_date_20200226_pdb_1a3q_repetition_0_clean.pdb"
seq_file = f"{pre}/DNAProtein_Platform_OpenCL_date_20200226_pdb_1a3q_repetition_0_protein.seq"
dcd_file = f"{pre}/local_jun08_pdb_1a3q_repetition_0_output.dcd"
trajectory_files=glob.glob(dcd_file[:-12]+'*.dcd')
energy_files=glob.glob(dcd_file[:-12]+'*.csv')
trajectory_files.sort()
energy_files.sort()
all_energies=[]
for i,e in enumerate(energy_files):
e=pandas.read_csv(e,index_col=0)
e['Frame']=e.index
e['Repetition']=i
all_energies+=[e]
all_energies=pandas.concat(all_energies)
plt.figure()
seaborn.lineplot(data=all_energies,x='Frame',y='Q_value_sigma5',hue='Repetition')
plt.legend([0,1,2,3,4])
pdb_name=pdb_file.split('/')[-1].split('_')[-4]
seaborn.lineplot(data=all_energies,x='Frame',y='Q_value_sigma5',hue='Repetition',)
seaborn.despine()
plt.legend([0,1,2,3,4],title="Repetition",loc=1)
plt.ylabel("Q")
plt.ylim(0,1)
plt.suptitle(f'Protein-DNA Q value [PDBid:{pdb_name}]')
# plt.savefig(f'{pdb_name}_fig1_Qvalue.png')
Out[17]:
Text(0.5, 0.98, 'Protein-DNA Q value [PDBid:1a3q]')
In [18]:
plt.figure()
seaborn.lineplot(data=all_energies,x='Frame',y='Q_value_sym_sigma5',hue='Repetition',)
seaborn.despine()
plt.legend([0,1,2,3,4],title="Repetition",loc=1)
plt.ylabel("Q (DNA symmetric)")
plt.ylim(0,1)
plt.suptitle(f'Protein-DNA Q value (DNA symmetric) [PDBid:{pdb_name}]')
Out[18]:
Text(0.5, 0.98, 'Protein-DNA Q value (DNA symmetric) [PDBid:1a3q]')
In [19]:
Rep0=all_energies[all_energies['Repetition']==0]
fig,ax=plt.subplots(1)
ax.plot(Rep0['Q_value_sym_sigma5'])
ax.plot(Rep0['Q_value_sigma5'])
#plt.plot(out2.sum(axis=0)/len(protein_contacts))
#plt.plot(all_energies['Q_value2 kJ/mol'])
#plt.plot(out3.sum(axis=0)/len(protein_contacts))
#plt.plot(all_energies['Q_value3 kJ/mol'])
ax.set_xlabel('Frame')
ax.set_ylabel('Q')
ax.set_ylim(-1,1)
ax.set_xlim(0,len(Rep0))
ax2=ax.twinx()
ax2.plot(Rep0['ExclusionProteinDNA kJ/mol']+Rep0['ElectrostaticsProteinDNA kJ/mol'],'r')
minimum=(Rep0['ExclusionProteinDNA kJ/mol']+Rep0['ElectrostaticsProteinDNA kJ/mol']).min()
ax2.set_ylim(minimum,-minimum)
ax.legend(['Q_interface (DNA symmetric)','Q_interface'],loc=1)
ax2.legend(['Protein - DNA interaction (kJ/mol)'],loc=4)
ax2.set_ylabel('Energy (kJ/mol)')
plt.suptitle(f'Q values and Interface Energy (PDBid:{pdb_name}, Repetition 0)')
Out[19]:
Text(0.5, 0.98, 'Q values and Interface Energy (PDBid:1a3q, Repetition 0)')
In [20]:
plt.figure()
interface_energy=all_energies['ExclusionProteinDNA kJ/mol']+all_energies['ElectrostaticsProteinDNA kJ/mol']
seaborn.kdeplot(interface_energy,all_energies['Q_value_sym_sigma5'],shade=True,shade_lowest=False,n_levels=10)
plt.xlabel('Interface energy (kJ/mol)')
plt.ylabel('Q_value (DNA_symmetric)')
plt.ylim(0,1)
plt.xlim(interface_energy.min(),interface_energy.max())
plt.suptitle(f'Q value vs Energy (PDBid:{pdb_name})')
seaborn.despine()
In [21]:
plt.figure()
plt.scatter(interface_energy,all_energies['Q_value_sym_sigma5'],s=1,alpha=0.5)
plt.xlabel('Interface energy (kJ/mol)')
plt.ylabel('Q_value (DNA_symmetric)')
plt.suptitle(f'Q_value (DNA_symmetric) vs Interface Energy (PDBid:{pdb_name})')
plt.ylim(0,1)
plt.xlim(interface_energy.min()-1,interface_energy.max()+1)
seaborn.despine()
In [ ]:
for dcd_file in glob.glob('/media/cab22/My Book/protein_DNA_selected_openmm/DNAProtein_Platform_OpenCL_date_20200226_pdb_*0_output.dcd'):
pdb_file=dcd_file[:-12]+'0_clean.pdb'
seq_file=dcd_file[:-12]+'0_protein.seq'
trajectory_files=glob.glob(dcd_file[:-12]+'*.dcd')
energy_files=glob.glob(dcd_file[:-12]+'*.csv')
trajectory_files.sort()
energy_files.sort()
all_energies=[]
for i,e in enumerate(energy_files):
e=pandas.read_csv(e,index_col=0)
e['Frame']=e.index
e['Repetition']=i
all_energies+=[e]
all_energies=pandas.concat(all_energies)
plt.figure()
seaborn.lineplot(data=all_energies,x='Frame',y='Q_value_sigma5',hue='Repetition')
plt.legend([0,1,2,3,4])
pdb_name=pdb_file.split('/')[-1].split('_')[-4]
seaborn.lineplot(data=all_energies,x='Frame',y='Q_value_sigma5',hue='Repetition',)
seaborn.despine()
plt.legend([0,1,2,3,4],title="Repetition",loc=1)
plt.ylabel("Q")
plt.ylim(0,1)
plt.suptitle(f'Protein-DNA Q value [PDBid:{pdb_name}]')
plt.savefig(f'{pdb_name}_fig1_Qvalue.png')
plt.figure()
seaborn.lineplot(data=all_energies,x='Frame',y='Q_value_sym_sigma5',hue='Repetition',)
seaborn.despine()
plt.legend([0,1,2,3,4],title="Repetition",loc=1)
plt.ylabel("Q (DNA symmetric)")
plt.ylim(0,1)
plt.suptitle(f'Protein-DNA Q value (DNA symmetric) [PDBid:{pdb_name}]')
plt.savefig(f'{pdb_name}_fig2_Qvaluesym.png')
Rep0=all_energies[all_energies['Repetition']==0]
fig,ax=plt.subplots(1)
ax.plot(Rep0['Q_value_sym_sigma5'])
ax.plot(Rep0['Q_value_sigma5'])
#plt.plot(out2.sum(axis=0)/len(protein_contacts))
#plt.plot(all_energies['Q_value2 kJ/mol'])
#plt.plot(out3.sum(axis=0)/len(protein_contacts))
#plt.plot(all_energies['Q_value3 kJ/mol'])
ax.set_xlabel('Frame')
ax.set_ylabel('Q')
ax.set_ylim(-1,1)
ax.set_xlim(0,len(Rep0))
ax2=ax.twinx()
ax2.plot(Rep0['ExclusionProteinDNA kJ/mol']+Rep0['ElectrostaticsProteinDNA kJ/mol'],'r')
minimum=(Rep0['ExclusionProteinDNA kJ/mol']+Rep0['ElectrostaticsProteinDNA kJ/mol']).min()
ax2.set_ylim(minimum,-minimum)
ax.legend(['Q_interface (DNA symmetric)','Q_interface'],loc=1)
ax2.legend(['Protein - DNA interaction (kJ/mol)'],loc=4)
ax2.set_ylabel('Energy (kJ/mol)')
plt.suptitle(f'Q values and Interface Energy (PDBid:{pdb_name}, Repetition 0)')
plt.savefig(f'{pdb_name}_fig3_QandEnergy.png')
plt.figure()
interface_energy=all_energies['ExclusionProteinDNA kJ/mol']+all_energies['ElectrostaticsProteinDNA kJ/mol']
seaborn.kdeplot(interface_energy,all_energies['Q_value_sym_sigma5'],shade=True,shade_lowest=False,n_levels=10)
plt.xlabel('Interface energy (kJ/mol)')
plt.ylabel('Q_value (DNA_symmetric)')
plt.ylim(0,1)
plt.xlim(interface_energy.min(),interface_energy.max())
plt.suptitle(f'Q value vs Energy (PDBid:{pdb_name})')
seaborn.despine()
plt.savefig(f'{pdb_name}_fig5_kde.png')
plt.figure()
plt.scatter(interface_energy,all_energies['Q_value_sym_sigma5'],s=1,alpha=0.5)
plt.xlabel('Interface energy (kJ/mol)')
plt.ylabel('Q_value (DNA_symmetric)')
plt.suptitle(f'Q_value (DNA_symmetric) vs Interface Energy (PDBid:{pdb_name})')
plt.ylim(0,1)
plt.xlim(interface_energy.min()-1,interface_energy.max()+1)
seaborn.despine()
plt.savefig(f'{pdb_name}_fig4_scatter.png')
In [33]:
import numpy as np
from Bio.PDB.PDBParser import PDBParser
parser = PDBParser()
structure = parser.get_structure('X', "/Users/weilu/Research/server/jun_week1_2020/protein_DNA_benchmark/DNAProtein_Platform_OpenCL_date_20200226_pdb_1a36_repetition_0_clean.pdb")
model = structure[0]
In [34]:
chain_start = 0
count = 0
proteinResidues = ['ALA', 'ASN', 'CYS', 'GLU', 'HIS', 'LEU', 'MET', 'PRO', 'THR', 'TYR', 'ARG', 'ASP', 'GLN', 'GLY', 'ILE', 'LYS', 'PHE', 'SER', 'TRP', 'VAL']
rnaResidues = ['A', 'G', 'C', 'U', 'I']
dnaResidues = ['DA', 'DG', 'DC', 'DT', 'DI']
removeDNAchains = True
for chain in model.get_chains():
chain_start += count
count = 0
if removeDNAchains and np.alltrue([a.get_resname().strip() in dnaResidues for a in chain.get_residues()]):
print(f"chain {chain.id} is a DNA chain. will be ignored for Q evaluation")
continue
print(chain)
chain A is a DNA chain. will be ignored for Q evaluation
chain B is a DNA chain. will be ignored for Q evaluation
<Chain id=C>
In [35]:
a = list(chain.get_residues())
In [36]:
b = a[0]
In [37]:
b.get_resname().strip()
Out[37]:
'NGP'
In [102]:
from simtk.openmm.app import *
# from simtk.openmm import *
from simtk.unit import *
In [103]:
type(AWSEM_xml) == list
Out[103]:
True
In [ ]:
In [106]:
def compute_dis(pos1, pos2):
dis = pos1 - pos2
dis = dis.value_in_unit(nanometer)
r = (dis[0]**2 + dis[1]**2 + dis[2]**2)**0.5
return r
# def get_het_bonds_info(fileLocation="5x2r-openmmawsem.pdb", AWSEM_xml="awsem.xml", pre="./"):
fileLocation = "/Users/weilu/Research/server/jun_week1_2020/protein_DNA_benchmark/DNAProtein_Platform_OpenCL_date_20200226_pdb_1a36_repetition_0_clean.pdb"
AWSEM_xml = ["/Users/weilu/openmmawsem/awsem.xml", "/Users/weilu/open3spn2/open3SPN2/3SPN2.xml"]
pdb = PDBFile(fileLocation)
res_list = list(pdb.topology.residues())
atom_list = list(pdb.topology.atoms())
protein_resNames = ["NGP", "IGL", "IPR", "NTER", "CTER"]
DNA_resNames = ["DA", "DC", "DT", "DG"]
protein_res_list = []
DNA_res_list = []
ligand_res_list = []
for res in res_list:
if res.name in protein_resNames:
protein_res_list.append(res)
elif res.name in DNA_resNames:
DNA_res_list.append(res)
else:
ligand_res_list.append(res)
protein_atom_list = []
DNA_atom_list = []
ligand_atom_list = []
for atom in atom_list:
if atom.residue.name in protein_resNames:
protein_atom_list.append(atom)
elif atom.residue.name in DNA_resNames:
DNA_atom_list.append(atom)
else:
ligand_atom_list.append(atom)
if type(AWSEM_xml) == list:
forcefield = ForceField(*AWSEM_xml)
else:
forcefield = ForceField(AWSEM_xml)
[templates, names] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
for a in templates:
for a1 in a.atoms:
a1.type = a1.name
forcefield.registerResidueTemplate(a)
system = forcefield.createSystem(pdb.topology)
info = []
for DNA_atom in DNA_atom_list:
pos1 = pdb.positions[DNA_atom.index]
for protein_atom in protein_atom_list:
if protein_atom.name != "CB":
continue
protein_chain = protein_atom.residue.chain.id
pos2 = pdb.positions[protein_atom.index]
r = compute_dis(pos1, pos2)
if r < 0.65:
# print(ligand_atom, protein_atom, "in contact", r)
info.append([DNA_atom.index, protein_atom.index, r, protein_chain])
data = pd.DataFrame(info, columns=["DNA_atom_index", "Protein_atom_index", "r", "Protein_chain"])
# data.to_csv(f"{pre}/het_protein_bonds.csv", index=False)
In [107]:
data
Out[107]:
DNA_atom_index
Protein_atom_index
r
Protein_chain
0
16
1364
0.642480
C
1
18
1281
0.556150
C
2
18
1364
0.642990
C
3
19
1281
0.548340
C
4
21
1281
0.420549
C
...
...
...
...
...
60
113
2324
0.427642
C
61
113
2330
0.381089
C
62
114
2318
0.527796
C
63
116
2253
0.630645
C
64
116
2318
0.565779
C
65 rows × 4 columns
In [112]:
save_name = "/Users/weilu/Research/server/jun_week1_2020/protein_DNA_benchmark/1a36_DNA_protein_bonds.csv"
fileLocation = "/Users/weilu/Research/server/jun_week1_2020/protein_DNA_benchmark/DNAProtein_Platform_OpenCL_date_20200226_pdb_1a36_repetition_0_clean.pdb"
AWSEM_xml = ["/Users/weilu/openmmawsem/awsem.xml", "/Users/weilu/open3spn2/open3SPN2/3SPN2.xml"]
data = get_in_contact_bonds_info(fileLocation=fileLocation, AWSEM_xml=AWSEM_xml, interaction_atom="DNA", save_name=save_name)
In [113]:
data
Out[113]:
DNA_atom_index
Protein_atom_index
r
Protein_chain
0
16
1364
0.642480
C
1
18
1281
0.556150
C
2
18
1364
0.642990
C
3
19
1281
0.548340
C
4
21
1281
0.420549
C
...
...
...
...
...
60
113
2324
0.427642
C
61
113
2330
0.381089
C
62
114
2318
0.527796
C
63
116
2253
0.630645
C
64
116
2318
0.565779
C
65 rows × 4 columns
In [111]:
def get_in_contact_bonds_info(fileLocation="5x2r-openmmawsem.pdb", AWSEM_xml="awsem.xml", interaction_atom="DNA", save_name="./DNA_protein_bonds.csv", save_dir="./"):
# interaction_atom could be DNA or ligand
# save_name = "/Users/weilu/Research/server/jun_week1_2020/protein_DNA_benchmark/1a36_DNA_protein_bonds.csv"
# fileLocation = "/Users/weilu/Research/server/jun_week1_2020/protein_DNA_benchmark/DNAProtein_Platform_OpenCL_date_20200226_pdb_1a36_repetition_0_clean.pdb"
# AWSEM_xml = ["/Users/weilu/openmmawsem/awsem.xml", "/Users/weilu/open3spn2/open3SPN2/3SPN2.xml"]
pdb = PDBFile(fileLocation)
res_list = list(pdb.topology.residues())
atom_list = list(pdb.topology.atoms())
protein_resNames = ["NGP", "IGL", "IPR", "NTER", "CTER"]
DNA_resNames = ["DA", "DC", "DT", "DG"]
protein_res_list = []
DNA_res_list = []
ligand_res_list = []
for res in res_list:
if res.name in protein_resNames:
protein_res_list.append(res)
elif res.name in DNA_resNames:
DNA_res_list.append(res)
else:
ligand_res_list.append(res)
protein_atom_list = []
DNA_atom_list = []
ligand_atom_list = []
for atom in atom_list:
if atom.residue.name in protein_resNames:
protein_atom_list.append(atom)
elif atom.residue.name in DNA_resNames:
DNA_atom_list.append(atom)
else:
ligand_atom_list.append(atom)
if type(AWSEM_xml) == list:
forcefield = ForceField(*AWSEM_xml)
else:
forcefield = ForceField(AWSEM_xml)
[templates, names] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
for a in templates:
for a1 in a.atoms:
a1.type = a1.name
forcefield.registerResidueTemplate(a)
system = forcefield.createSystem(pdb.topology)
info = []
if interaction_atom == "DNA":
for DNA_atom in DNA_atom_list:
pos1 = pdb.positions[DNA_atom.index]
for protein_atom in protein_atom_list:
if protein_atom.name != "CB":
continue
protein_chain = protein_atom.residue.chain.id
pos2 = pdb.positions[protein_atom.index]
r = compute_dis(pos1, pos2)
if r < 0.65:
# print(ligand_atom, protein_atom, "in contact", r)
info.append([DNA_atom.index, protein_atom.index, r, protein_chain])
data = pd.DataFrame(info, columns=[f"DNA_atom_index", "Protein_atom_index", "r", "Protein_chain"])
data.to_csv(save_name, index=False)
elif interaction_atom == "Ligand":
info = []
for ligand_atom in ligand_atom_list:
pos1 = pdb.positions[ligand_atom.index]
for protein_atom in protein_atom_list:
if protein_atom.name != "CB":
continue
protein_chain = protein_atom.residue.chain.id
pos2 = pdb.positions[protein_atom.index]
r = compute_dis(pos1, pos2)
if r < 0.65:
# print(ligand_atom, protein_atom, "in contact", r)
info.append([ligand_atom.index, protein_atom.index, r, protein_chain])
data = pd.DataFrame(info, columns=["Ligand_atom_index", "Protein_atom_index", "r", "Protein_chain"])
data.to_csv(f"{save_dir}/het_protein_bonds.csv", index=False)
res_list = list(pdb.topology.residues())
atom_list = list(pdb.topology.atoms())
protein_resNames = ["NGP", "IGL", "IPR", "NTER", "CTER"]
DNA_resNames = ["DA", "DC", "DT", "DG"]
protein_res_list = []
DNA_res_list = []
ligand_res_list = []
for res in res_list:
if res.name in protein_resNames:
protein_res_list.append(res)
elif res.name in DNA_resNames:
DNA_res_list.append(res)
else:
ligand_res_list.append(res)
protein_atom_list = []
DNA_atom_list = []
ligand_atom_list = []
for atom in atom_list:
if atom.residue.name in protein_resNames:
protein_atom_list.append(atom)
elif atom.residue.name in DNA_resNames:
DNA_atom_list.append(atom)
else:
ligand_atom_list.append(atom)
ligand_res_list
info = []
for res in ligand_res_list:
atoms = list(res.atoms())
n_atoms = len(atoms)
for i in range(n_atoms):
atom1 = atoms[i]
pos1 = pdb.positions[atom1.index]
for j in range(i+1, n_atoms):
atom2 = atoms[j]
pos2 = pdb.positions[atom2.index]
dis = pos1 - pos2
dis = dis.value_in_unit(nanometer)
r = (dis[0]**2 + dis[1]**2 + dis[2]**2)**0.5
# print(atom1.index, atom2.index, round(r, 3))
info.append([res.name, atom1.index, atom2.index, atom1.name, atom2.name, atom1.element.symbol, atom2.element.symbol, round(r, 3)])
data = pd.DataFrame(info, columns=["Name", "Atom1", "Atom2", "Name1", "Name2", "Symbol1", "Symbol2", "r"])
data.to_csv(f"{save_dir}/het_frag.csv", index=False)
return data
In [ ]:
Content source: luwei0917/awsemmd_script
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