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 -172.685181 -190.959869 -10.722409 -6.901467 2.944055 19.519566 1925.405884 1925.405884 1925.405884 1925.405884 -323.980988 -323.980988 -272.317993 -0.115348 -0.115348 -0.115348 0.000000 0.000000 -650.195190 0.000000 0.000000 0.172975 0.000000 0.000000 0.0 2.875945e-36 2.727645e-96 0.000000
1 1 996.624634 2075.761230 549.871216 132.663055 549.871216 -210.826340 -189.028381 -3.490806 -7.186402 7.805028 19.891518 2075.761230 2075.761230 2075.761230 2075.761230 -302.742889 -302.742889 -283.210785 -8.049426 -8.049426 -8.049426 0.000000 0.000000 -785.012085 0.000000 0.000000 0.179821 0.000000 0.000000 0.0 1.373433e-34 9.565396e-92 0.000000
2 2 1102.039551 2179.960205 564.066895 176.151382 564.066895 -216.700073 -219.542679 -30.625162 -5.170397 1.031549 19.594673 2179.960205 2179.960205 2179.959961 2179.959961 -311.728912 -311.728912 -277.981323 -2.547462 -2.547462 -2.547462 0.000000 0.000000 -774.633301 0.000000 0.000000 0.164317 0.000000 0.000000 0.0 3.420950e-35 1.158427e-93 0.000000
3 3 928.742798 1919.845825 564.292603 156.906433 564.292603 -186.117188 -175.552368 -6.907540 -3.633638 3.651987 19.742455 1919.845825 1919.845825 1919.845825 1919.845825 -357.834412 -357.834412 -288.855591 -8.477329 -8.477329 -8.477329 0.000000 0.000000 -708.483765 0.000000 0.000000 0.165453 0.000000 0.000000 0.0 1.513293e-33 1.486967e-88 0.000000
4 4 541.763977 1811.974854 562.585693 107.872177 562.585693 -231.082153 -207.661545 -35.324242 -2.743639 2.565361 20.122301 1811.974854 1811.974854 1811.974854 1811.974854 -362.854065 -362.854065 -287.362762 -8.948298 -8.948298 -8.948298 0.000000 0.000000 -827.564575 0.000000 0.000000 0.184903 0.000000 0.000000 0.0 4.104675e-33 2.195320e-87 0.000000
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
995 995 -3069.083496 452.595367 152.521011 35.253174 152.521011 -360.335754 -376.429504 -219.925400 -39.317959 0.114170 19.216095 452.595367 452.595367 452.595367 452.595367 -758.286255 -758.286255 -403.096771 -80.164886 -80.164886 -80.164886 -9.449248 -9.449248 -1481.849365 -0.653029 0.112939 0.608701 0.003071 0.000343 0.0 6.748673e-02 3.887375e-02 0.004000
996 996 -3064.737793 462.006470 130.915588 38.573784 130.915588 -343.584259 -395.296692 -216.627045 -36.519203 1.288507 18.862770 462.006470 462.006470 462.006470 462.006470 -744.671814 -744.671814 -413.385681 -78.760284 -78.760284 -78.760284 -9.864801 -9.864801 -1477.479248 -0.910528 0.072205 0.639458 0.002658 0.000187 0.0 7.331867e-02 4.637758e-02 0.014211
997 997 -3032.961182 498.512939 153.732666 42.820435 153.732666 -344.704407 -396.713440 -226.427216 -40.393776 0.002420 19.085316 498.512939 498.512939 498.512939 498.512939 -739.605347 -739.605347 -429.222229 -81.162315 -81.162315 -81.162315 -11.669315 -11.669315 -1476.421875 -0.901550 -0.440871 0.545779 0.001648 0.000071 0.0 7.062980e-02 4.328375e-02 0.014114
998 998 -3057.704590 525.446655 105.362595 33.846207 105.362595 -349.397156 -379.132874 -236.260483 -42.891659 0.284987 18.913128 525.446655 525.446655 525.446655 525.446655 -756.125427 -756.125427 -400.166992 -79.370148 -79.370148 -79.370148 -9.206217 -9.206217 -1488.545898 -0.753647 -0.267141 0.557373 0.002045 0.000104 0.0 7.774580e-02 4.883582e-02 0.013521
999 999 -2965.020996 562.101807 140.512054 26.425442 140.512054 -330.774048 -389.894928 -228.543381 -40.391975 0.733526 18.849590 562.101807 562.101807 562.101807 562.101807 -750.051514 -750.051514 -408.628479 -77.578041 -77.578041 -77.578041 -12.343828 -12.343828 -1475.511475 -0.172509 -0.282126 0.527727 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 -159.737076 -163.882996 2.362528 -1.496012 8.290442 19.216988 2078.508789 2078.508789 2078.508789 2078.508789 -401.600983 -401.600983 -309.244049 -5.539253 -5.539253 -5.539253 -1.744150 -1.744150 -312.705048 13.345789 -16.040958 0.103350 0.132516 0.080403 0.031889 0.216340 0.156340 0.085151
1 1 1367.910400 2136.673828 405.895050 339.611694 405.895050 339.611694 -207.928467 -115.871429 -5.903988 -1.580091 12.857150 25.773647 2136.673828 2136.673828 2136.673828 2136.673828 -369.678711 -369.678711 -270.786438 -4.154922 -4.154922 -4.154922 -0.000000 -0.000000 -551.782166 3.190524 -29.083378 0.141578 0.284097 0.186284 0.065847 0.428425 0.311327 0.111201
2 2 779.799377 1647.184082 458.755463 366.955231 458.755463 366.955231 -164.635025 -202.601624 -19.283304 -2.219652 17.755030 22.915680 1647.184082 1647.184082 1647.184082 1647.184082 -291.468933 -291.468933 -311.880981 -3.121711 -3.121711 -3.121711 -0.000000 -0.000000 -707.001221 1.344547 -33.544758 0.197776 0.256513 0.150870 0.041542 0.486644 0.344061 0.131674
3 3 919.063110 1860.081909 435.101288 336.782104 435.101288 336.782104 -154.282532 -201.642914 -27.439941 -7.506395 11.837164 23.364021 1860.081909 1860.081909 1860.081909 1860.081909 -296.818115 -296.818115 -301.783081 -1.865732 -1.865732 -1.865732 0.000000 0.000000 -723.759094 -0.897330 -32.847511 0.182986 0.299977 0.189747 0.066603 0.572421 0.436658 0.137979
4 4 1208.641968 2203.323242 363.317749 401.466217 363.317749 401.466217 -196.059570 -189.042831 -4.841312 -2.970710 3.269238 23.414455 2203.323242 2203.323242 2203.323242 2203.323242 -376.588867 -376.588867 -301.028503 -11.005570 -11.005570 -11.005570 0.000000 0.000000 -682.237915 9.195129 -32.457779 0.197463 0.364766 0.236790 0.090012 0.632872 0.487894 0.204938
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
995 995 -3002.464355 475.683868 85.743340 95.578140 85.743340 95.578140 -350.379059 -387.553986 -222.846344 -38.363651 0.166569 19.150223 475.683868 475.683868 475.683868 475.683868 -752.016602 -752.016602 -365.157837 -73.771797 -73.771797 -73.771797 -2.354212 -2.354212 -1427.280151 -19.393969 -41.561493 0.475712 0.720508 0.509637 0.186934 0.854281 0.707813 0.322841
996 996 -2960.824463 530.802063 79.410736 70.511978 79.410736 70.511978 -322.812134 -382.872131 -226.463669 -41.853249 0.044861 19.402721 530.802063 530.802063 530.802063 530.802063 -749.161621 -749.161621 -371.261719 -73.862122 -73.862122 -73.862122 -0.978583 -0.978583 -1445.308350 -8.624689 -39.714134 0.484019 0.737605 0.520713 0.173307 0.851299 0.708986 0.360266
997 997 -2961.260742 490.864288 90.094406 106.459702 90.094406 106.459702 -338.751984 -378.603638 -226.182037 -38.953506 0.000000 19.665730 490.864288 490.864288 490.864288 490.864288 -746.534668 -746.534668 -384.111572 -66.178001 -66.178001 -66.178001 -0.588341 -0.588341 -1433.647339 -18.237103 -38.552055 0.456228 0.744819 0.550175 0.244281 0.855820 0.740453 0.420448
998 998 -2969.428223 496.591614 74.290222 82.786804 74.290222 82.786804 -342.470001 -386.838043 -223.687332 -39.992573 0.037694 18.857454 496.591614 496.591614 496.591614 496.591614 -732.593689 -732.593689 -371.058136 -64.069550 -64.069550 -64.069550 -1.527580 -1.527580 -1425.832031 -17.098616 -38.794556 0.483834 0.734634 0.532835 0.218909 0.853956 0.717178 0.292954
999 999 -3025.723633 432.977875 73.602959 103.746231 73.602959 103.746231 -340.665039 -376.611145 -236.747238 -39.262222 0.342360 18.561216 432.977875 432.977875 432.977875 432.977875 -725.507568 -725.507568 -378.355865 -72.925720 -72.925720 -72.925720 -1.355736 -1.355736 -1431.025024 -13.546547 -40.957932 0.474052 0.753371 0.554818 0.223659 0.877797 0.762915 0.386595

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 0 -2699.730713 680.539429 60.570366 132.621796 60.570366 132.621796 -341.896301 -350.991669 -225.373367 -31.557611 0.326982 19.576027 680.539429 680.539429 680.539429 680.539429 -728.190552 -728.190552 -345.795929 -66.914597 -66.914597 -66.914597 -0.000000 -0.000000 -1451.311523 -17.243395 -36.992279 0.765723 0.917707 0.811634 0.406928 0.927564 0.828057 0.420733
1 1 -2611.925537 719.089661 66.261383 136.650299 66.261383 136.650299 -329.996857 -342.179871 -200.158890 -33.334087 0.115507 19.516079 719.089661 719.089661 719.089661 719.089661 -685.073303 -685.073303 -365.712738 -65.538559 -65.538559 -65.538559 -0.463183 -0.463183 -1476.853394 -17.669903 -39.412102 0.748703 0.915583 0.801198 0.368912 0.921792 0.809887 0.326087
2 2 -2662.556641 694.320984 59.803658 123.551888 59.803658 123.551888 -321.294678 -370.048370 -203.869904 -38.536827 0.876580 20.169744 694.320984 694.320984 694.320984 694.320984 -660.942261 -660.942261 -374.608276 -74.338943 -74.338943 -74.338943 -0.791762 -0.791762 -1467.227539 -15.904264 -36.480125 0.824456 0.884470 0.748405 0.306187 0.893654 0.747196 0.270734
3 3 -2721.850342 695.070129 65.322525 121.277725 65.322525 121.277725 -333.259003 -364.631409 -219.685196 -38.292812 1.508956 21.993513 695.070129 695.070129 695.070129 695.070129 -678.553040 -678.553040 -372.802429 -70.480583 -70.480583 -70.480583 -3.619180 -3.619180 -1483.906128 -20.303032 -44.535530 0.825738 0.928502 0.832054 0.459202 0.934077 0.835899 0.386623
4 4 -2738.814453 658.747314 84.781540 140.143814 84.781540 140.143814 -328.479614 -357.212158 -218.033203 -37.900898 0.275371 20.636593 658.747314 658.747314 658.747314 658.747314 -707.661072 -707.661072 -361.196167 -77.237984 -77.237984 -77.237984 -1.573920 -1.573920 -1499.616333 -17.046160 -40.341957 0.793849 0.907026 0.794730 0.404612 0.920062 0.814239 0.406048
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
245 245 -2747.729492 711.295288 76.268761 114.554710 76.268761 114.554710 -318.049500 -370.464111 -217.579865 -36.409447 1.420260 19.285393 711.295288 711.295288 711.295288 711.295288 -738.912903 -738.912903 -380.549133 -63.967415 -63.967415 -63.967415 -2.500902 -2.500902 -1485.635010 -20.926731 -38.259956 0.709478 0.878433 0.743805 0.369372 0.902700 0.776336 0.350035
246 246 -2716.127930 704.222107 67.757370 144.353149 67.757370 144.353149 -337.592987 -361.639526 -226.498535 -35.209896 0.255442 20.533215 704.222107 704.222107 704.222107 704.222107 -701.926392 -701.926392 -382.341400 -77.719566 -77.719566 -77.719566 -3.961114 -3.961114 -1468.318359 -19.117130 -41.905422 0.781538 0.922463 0.821241 0.455791 0.922656 0.815380 0.390784
247 247 -2719.772705 695.687439 60.331821 141.465256 60.331821 141.465256 -323.605896 -363.948059 -228.967834 -35.926090 0.423843 19.229902 695.687439 695.687439 695.687439 695.687439 -709.275391 -709.275391 -351.301147 -82.362335 -82.362335 -82.362335 -2.935209 -2.935209 -1487.243774 -17.383629 -36.673634 0.765713 0.876912 0.733220 0.336138 0.903453 0.778321 0.348566
248 248 -2705.848633 680.997131 68.552170 123.740288 68.552170 123.740288 -326.217316 -367.463531 -215.130707 -37.726742 1.862479 19.366589 680.997131 680.997131 680.997131 680.997131 -701.980225 -701.980225 -379.402130 -63.905670 -63.905670 -63.905670 -3.132869 -3.132869 -1452.421387 -17.681080 -38.112457 0.758356 0.897290 0.776957 0.374258 0.894305 0.758775 0.337024
249 249 -2640.365967 756.452637 85.896439 114.379646 85.896439 114.379646 -326.478210 -379.116974 -208.333191 -36.097183 2.886812 19.405453 756.452637 756.452637 756.452637 756.452637 -715.907654 -715.907654 -370.023682 -72.633789 -72.633789 -72.633789 -0.983593 -0.983593 -1457.116821 -18.093534 -37.258293 0.691181 0.891670 0.759782 0.313327 0.883290 0.729807 0.298941

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 -2693.327148 667.712158 166.876556 50.261482 166.876556 -332.899963 -369.063293 -211.376114 -34.592678 1.231306 19.750187 667.712158 667.712158 667.712158 667.712158 -715.235596 -715.235596 -351.189392 -73.361115 -73.361115 -73.361115 -1.982500 -1.982500 -1460.394043 -16.416393 -35.314064 0.684516 0.892622 0.761602 0.327495 0.895080 0.754318 0.302087
1 1 -2768.368164 671.086487 129.424698 48.426983 129.424698 -334.713531 -361.882263 -232.340408 -38.304050 0.403983 19.440002 671.086487 671.086487 671.086487 671.086487 -715.766418 -715.766418 -368.017456 -59.343334 -59.343334 -59.343334 -0.247420 -0.247420 -1489.933350 -8.909724 -29.922720 0.734868 0.785442 0.565439 0.144717 0.775110 0.531099 0.090359
2 2 -2650.918945 796.540283 100.345680 73.218719 100.345680 -341.466034 -364.907867 -219.472595 -37.754959 1.469082 20.208855 796.540283 796.540283 796.540283 796.540283 -722.702209 -722.702209 -377.000549 -64.620903 -64.620903 -64.620903 -0.529005 -0.529005 -1475.985474 -12.302912 -28.365807 0.797526 0.814384 0.613756 0.180995 0.815998 0.612759 0.218198
3 3 -2774.744629 657.371155 119.771149 42.125145 119.771149 -336.720428 -381.044037 -200.905945 -34.907841 0.012123 19.019665 657.371155 657.371155 657.371155 657.371155 -733.446228 -733.446228 -359.843658 -65.249954 -65.249954 -65.249954 -0.013762 -0.013762 -1454.606689 -15.401279 -33.448601 0.690978 0.834423 0.688199 0.331119 0.933989 0.844061 0.479329
4 4 -2773.488770 698.844849 112.633728 46.912674 112.633728 -322.390839 -378.980286 -213.020660 -38.712315 0.026223 19.960886 698.844849 698.844849 698.844849 698.844849 -735.387878 -735.387878 -390.094177 -73.015915 -73.015915 -73.015915 -3.331783 -3.331783 -1445.177856 -17.768488 -36.298080 0.583997 0.822286 0.639402 0.265558 0.901826 0.775822 0.366890
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
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248 248 -2708.869385 700.398315 108.728043 61.983536 108.728043 -344.921082 -351.655457 -198.903290 -39.133198 0.052734 19.490358 700.398315 700.398315 700.398315 700.398315 -698.602356 -698.602356 -407.017700 -74.149750 -74.149750 -74.149750 -6.725941 -6.725941 -1443.357422 -9.111839 -26.923277 0.596897 0.222083 0.121978 0.037824 0.618588 0.465235 0.239471
249 249 -2696.270508 646.327820 174.891510 51.150246 174.891510 -328.904358 -370.321564 -214.202194 -35.595234 0.778098 19.459772 646.327820 646.327820 646.327820 646.327820 -728.099792 -728.099792 -374.885986 -68.691109 -68.691109 -68.691109 -0.000013 -0.000013 -1439.600342 -1.557289 -28.010269 0.577207 0.229301 0.135157 0.048495 0.547616 0.330117 0.056818

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 1149.457275 1997.370972 718.133179 162.097931 718.133179 -216.747650 -138.532837 -48.022877 -8.970857 3.401863 21.898750 1997.370972 1997.370972 1997.370972 1997.370972 -368.178467 -368.178467 -271.064148 -1.750732 -1.750732 -1.750732 -0.000000 -0.000000 -700.352966 0.000000 0.000000 0.175308 0.000000 0.000000 0.000000 2.495573e-31 1.528630e-82 0.000000e+00
1 1 796.982666 1723.353027 568.413513 175.520386 568.413513 -159.372879 -168.118637 -0.002469 -4.576169 2.925653 21.325041 1723.353027 1723.353027 1723.353027 1723.353027 -306.799316 -306.799316 -276.542938 -1.125144 -1.125144 -1.125144 0.000000 0.000000 -778.199402 0.000000 0.000000 0.181986 0.000000 0.000000 0.000000 5.344196e-31 9.954756e-82 0.000000e+00
2 2 903.166504 2006.876709 530.537048 126.919777 530.537048 -211.478638 -154.698975 -16.679733 -2.338175 0.652144 24.232115 2006.876709 2006.876587 2006.876709 2006.876709 -335.592194 -335.592194 -284.131317 -3.816046 -3.816046 -3.816046 -0.000000 -0.000000 -777.493652 0.000000 0.000000 0.177413 0.000000 0.000000 0.000000 2.583475e-25 7.916340e-66 0.000000e+00
3 3 942.549805 2031.681396 513.913940 184.522095 513.913940 -181.455933 -179.186417 -15.526243 -3.724121 2.872958 22.787895 2031.681396 2031.681396 2031.681396 2031.681396 -352.558167 -352.558167 -292.690613 -13.692242 -13.692242 -13.692242 -0.000000 -0.000000 -774.608154 0.000000 0.000000 0.213358 0.000000 0.000000 0.000000 5.896612e-21 1.414954e-53 0.000000e+00
4 4 863.594238 1924.665039 498.520203 159.361404 498.520203 -163.741058 -180.249557 -26.080467 -4.476280 13.218819 22.346138 1924.665039 1924.665039 1924.665039 1924.665039 -311.872253 -311.872253 -265.449585 -11.038004 -11.038004 -11.038004 0.000000 0.000000 -791.854492 0.000000 0.000000 0.244285 0.000000 0.000000 0.000000 1.619160e-13 6.513577e-33 2.349010e-275
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
995 995 -3158.782959 443.530365 89.397293 46.547150 89.397293 -342.140564 -394.190796 -226.920059 -41.756058 0.919186 19.981197 443.530365 443.530365 443.530365 443.530365 -744.556396 -744.556396 -431.422974 -78.339935 -78.339935 -78.339935 -10.676729 -10.676729 -1478.745239 -0.614371 -10.451429 0.549907 0.064282 0.033014 0.009213 3.058155e-01 1.914842e-01 7.321079e-02
996 996 -3151.521973 453.091309 106.974136 27.400700 106.974136 -345.788574 -383.731384 -232.920410 -35.053371 0.211685 18.827240 453.091309 453.091309 453.091309 453.091309 -736.544373 -736.544373 -433.058594 -92.765190 -92.765190 -92.765190 -5.739141 -5.739141 -1483.637573 -0.351470 -9.145006 0.612110 0.060215 0.028426 0.007386 2.642348e-01 1.409099e-01 1.772332e-02
997 997 -3073.408691 458.516937 129.758209 37.153809 129.758209 -341.534912 -386.737152 -230.942032 -38.689388 0.412992 19.427261 458.516907 458.516907 458.516907 458.516907 -736.483643 -736.483643 -435.765594 -69.039337 -69.039337 -69.039337 -9.065618 -9.065618 -1461.408569 -0.495890 -9.257893 0.623276 0.071419 0.035043 0.012456 2.674087e-01 1.393167e-01 2.321801e-02
998 998 -3155.346191 475.489105 83.757828 40.510159 83.757828 -358.029114 -390.307739 -234.718002 -42.788380 0.611248 19.458977 475.489136 475.489105 475.489136 475.489136 -736.544250 -736.544250 -444.211060 -76.259727 -76.259727 -76.259727 -9.632228 -9.632228 -1468.027100 -1.940952 -13.494979 0.606630 0.102788 0.057118 0.013374 3.306751e-01 2.090697e-01 7.994932e-02
999 999 -3100.100342 469.851685 111.367104 43.735306 111.367104 -341.732666 -389.931702 -226.465912 -41.346535 0.503911 19.991550 469.851685 469.851685 469.851685 469.851685 -750.937927 -750.937927 -434.894470 -66.545937 -66.545937 -66.545937 -8.850719 -8.850719 -1469.254761 -2.112288 -14.272167 0.598694 0.108379 0.065656 0.022157 3.667360e-01 2.154372e-01 6.732920e-02

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 0 557.021301 1841.318848 352.134155 88.465927 352.134155 -156.066864 -144.166763 -29.755480 -2.935120 1.037475 8.829189 1841.318848 1841.318848 1841.318848 1841.318848 -352.030029 -352.030029 -280.810455 -12.588223 -12.588223 -12.588223 0.000000 0.000000 -756.519836 0.0 0.000000 0.108565 0.000000 0.000000 0.000000 1.220971e-22 1.044548e-58 0.000000e+00
1 1 323.314362 1761.761963 342.547882 96.119019 342.547882 -108.764000 -149.282913 -50.909523 -7.843520 0.000000 9.650272 1761.761963 1761.761963 1761.761963 1761.761963 -419.482544 -419.482544 -294.709839 -6.013396 -6.013396 -6.013396 0.000000 0.000000 -849.871826 0.0 0.000000 0.112866 0.000000 0.000000 0.000000 1.319524e-11 5.968617e-28 7.684217e-231
2 2 -258.509155 1579.101929 251.759323 79.051964 251.759323 -181.400436 -132.744370 -101.804382 -18.078224 2.526787 9.245409 1579.101929 1579.101929 1579.101929 1579.101929 -457.150909 -457.150909 -303.228149 -4.630230 -4.630230 -4.630230 -0.000396 -0.000396 -981.237854 0.0 -0.079060 0.159608 0.000001 0.000000 0.000000 2.126187e-05 3.621002e-11 6.832865e-82
3 3 -382.805115 1368.413818 207.878860 79.655090 207.878860 -156.866974 -143.544342 -102.996727 -18.421175 0.000000 9.605591 1368.413818 1368.413818 1368.413818 1368.413818 -426.156097 -426.156097 -304.473450 -18.713223 -18.713223 -18.713223 0.000000 0.000000 -876.724670 0.0 -0.622449 0.159502 0.001080 0.000006 0.000000 2.297552e-04 4.906490e-08 3.166168e-51
4 4 -714.687012 1390.924683 192.127518 32.410713 192.127518 -192.648407 -156.898636 -85.961914 -22.800781 2.241223 9.435081 1390.924683 1390.924683 1390.924683 1390.924683 -514.470886 -514.470886 -360.048920 -14.362317 -14.362317 -14.362317 -0.000000 -0.000000 -993.368103 0.0 -1.472513 0.177161 0.022460 0.006313 0.000302 2.890206e-02 5.400355e-03 2.369197e-09
5 5 -1147.475220 1109.608765 167.376663 55.389984 167.376663 -164.782516 -165.312958 -73.844131 -21.679342 1.426584 9.457170 1109.608765 1109.608765 1109.608765 1109.608765 -559.737122 -559.737122 -366.822571 -33.216976 -33.216976 -33.216976 -1.222377 -1.222377 -1103.513794 0.0 -0.809728 0.192302 0.011894 0.002923 0.000058 1.952793e-02 3.144948e-03 1.407979e-09
6 6 -1438.475586 1019.022095 153.888336 50.101940 153.888336 -188.811951 -203.821060 -97.849152 -20.264725 2.635292 9.238403 1019.022095 1019.022095 1019.022095 1019.022095 -561.272217 -561.272217 -391.615479 -64.144478 -64.144478 -64.144478 -4.179996 -4.179996 -1140.971191 0.0 -0.648393 0.214143 0.002707 0.000162 0.000000 7.393111e-03 5.088671e-04 1.488306e-15
7 7 -2071.240967 783.810242 136.459839 35.027023 136.459839 -206.705933 -224.580063 -160.241974 -30.097418 0.277100 9.528406 783.810242 783.810242 783.810242 783.810242 -668.597290 -668.597290 -412.646027 -79.541481 -79.541481 -79.541481 -5.557109 -5.557109 -1248.316650 0.0 -0.299144 0.239067 0.000643 0.000007 0.000000 5.923379e-03 2.693021e-04 4.723084e-19
8 8 -2322.412354 682.715027 125.009567 33.928421 125.009567 -236.803558 -224.387238 -153.765839 -30.431648 0.976243 9.717251 682.715027 682.715027 682.715027 682.715027 -741.045898 -741.045898 -410.330872 -84.640297 -84.640297 -84.640297 -0.825131 -0.825131 -1292.100586 0.0 -0.678702 0.248194 0.002461 0.000150 0.000000 2.076398e-02 5.155269e-03 1.235980e-07
9 9 -2419.239014 676.057495 84.254318 34.409286 84.254318 -222.561676 -223.278336 -161.395538 -27.340906 0.000000 9.136267 676.057495 676.057495 676.057495 676.057495 -709.122681 -709.122681 -426.327393 -108.251091 -108.251091 -108.251091 -4.290016 -4.290016 -1340.071655 0.0 -0.752492 0.289888 0.004771 0.000696 0.000000 1.916066e-02 1.547578e-03 4.563461e-14

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
0 0 -4155.417969 830.338562 58.261890 28.651072 58.261890 -207.470459 -226.970825 -152.880066 -32.570721 1.908048 9.596300 830.338562 830.338562 830.338562 830.338562 -772.781006 -772.781006 -225.691803 -110.183212 -110.183212 -110.183212 -2.273163 -2.273163 -3298.538086 -24.045692 -33.866573 0.849368 0.937290 0.847751 0.463300 0.970097 0.922653 0.620028
1 1 -4337.937012 744.170776 71.145126 26.657326 71.145126 -229.045410 -226.435699 -157.297775 -37.632111 0.764863 9.708164 744.170776 744.170776 744.170776 744.170776 -796.580078 -796.580078 -233.022583 -108.647591 -108.647591 -108.647591 -0.983929 -0.983929 -3351.123535 -20.519722 -32.075783 0.909889 0.908992 0.790384 0.371417 0.948697 0.869286 0.416411
2 2 -4342.987793 668.419250 71.116913 46.362762 71.116913 -219.275528 -219.428894 -158.670624 -33.511768 0.002036 9.400763 668.419250 668.419250 668.419250 668.419250 -769.860413 -769.860413 -232.378525 -120.329308 -120.329308 -120.329308 -1.154086 -1.154086 -3342.020508 -10.202734 -34.361435 0.761183 0.898336 0.796860 0.448147 0.948731 0.883207 0.607828
3 3 -4091.565430 861.014343 81.271019 43.515457 81.271019 -222.026871 -217.853043 -145.859833 -31.615713 0.039745 9.443526 861.014343 861.014343 861.014343 861.014343 -791.975891 -791.975891 -232.579102 -87.480194 -87.480194 -87.480194 -0.114370 -0.114370 -3308.310059 -21.649879 -30.498125 0.810600 0.940155 0.860104 0.503053 0.948067 0.869729 0.448009
4 4 -4208.320801 752.978638 96.598991 34.578030 96.598991 -225.351334 -214.378540 -154.820312 -32.452229 0.081206 9.746097 752.978638 752.978638 752.978638 752.978638 -768.761475 -768.761475 -219.175903 -108.940704 -108.940704 -108.940704 -0.703225 -0.703225 -3332.721191 -16.659040 -31.351349 0.796937 0.921928 0.826259 0.466463 0.947832 0.873475 0.510040
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
245 245 -4643.930664 502.551788 45.325054 33.529053 45.325054 -226.791580 -240.839523 -169.658661 -35.626656 0.074671 9.410284 502.551788 502.551788 502.551788 502.551788 -806.163757 -806.163757 -236.552490 -105.314499 -105.314499 -105.314499 -0.256657 -0.256657 -3368.362061 -15.287663 -31.981859 0.790460 0.622708 0.439913 0.161079 0.850754 0.697607 0.322011
246 246 -4584.796875 570.234375 66.817818 29.920319 66.817818 -231.181915 -218.930542 -163.326019 -35.904003 0.176073 9.497507 570.234375 570.234375 570.234375 570.234375 -802.548767 -802.548767 -249.153412 -135.092575 -135.092575 -135.092575 -0.001071 -0.001071 -3374.953125 -19.320715 -32.978603 0.786169 0.601174 0.413374 0.147439 0.852846 0.696210 0.322700
247 247 -4553.240234 538.270996 66.985603 27.610985 66.985603 -238.337372 -235.132355 -157.373444 -33.456261 0.134577 9.542325 538.270996 538.270996 538.270996 538.270996 -784.923584 -784.923584 -231.915497 -129.483429 -129.483429 -129.483429 -1.688667 -1.688667 -3333.735840 -15.832605 -35.669086 0.769082 0.542480 0.343528 0.108159 0.876959 0.736917 0.345429
248 248 -4668.943848 505.713196 59.004738 22.448866 59.004738 -237.555267 -237.050919 -164.297607 -32.102859 0.187392 9.744363 505.713196 505.713196 505.713196 505.713196 -807.060913 -807.060913 -240.470306 -120.108070 -120.108070 -120.108070 -0.124033 -0.124033 -3375.004150 -18.413925 -35.592583 0.820160 0.496682 0.314056 0.107206 0.882302 0.739526 0.259117
249 249 -4643.302246 505.431610 49.189445 19.639977 49.189445 -235.328262 -219.110825 -153.350281 -33.157066 0.639383 9.645859 505.431610 505.431641 505.431641 505.431610 -783.147949 -783.147949 -254.170502 -126.866058 -126.866058 -126.866058 -0.001130 -0.001130 -3373.249023 -17.594696 -33.549770 0.791661 0.483118 0.304036 0.098129 0.831746 0.643636 0.229302

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 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 39.823486 2360.641846 299.961304 67.016731 299.961304 -121.195396 -65.336189 1.075122 -1.544315 1.773512 11.889565 2360.641846 2360.641846 2360.641846 2360.641846 -339.464905 -339.464905 -176.742371 -5.182293 -5.182293 -5.182293 0.000000 0.000000 -1989.873779 -0.009539 -3.495862 0.231610 0.050127 0.021116 0.007098 0.110910 0.057518 2.516321e-02
1 1 -698.732239 1969.341309 295.087830 98.836876 295.087830 -115.695892 -69.030624 -18.795986 -4.599777 7.335309 9.834860 1969.341309 1969.341309 1969.341309 1969.341309 -364.512573 -364.512573 -194.051010 -13.226708 -13.226708 -13.226708 -0.270397 -0.270397 -2296.844238 0.000000 -2.490843 0.322700 0.022419 0.004461 0.000000 0.038960 0.008831 1.260516e-07
2 2 -801.595154 2222.901123 257.331390 87.430458 257.331390 -167.998871 -92.219078 -21.649542 -7.202574 4.036797 9.479951 2222.901123 2222.901123 2222.901123 2222.901123 -302.696075 -302.696075 -209.000793 -8.465828 -8.465828 -8.465828 -2.053473 -2.053473 -2567.775391 -0.008224 -4.076754 0.321834 0.035818 0.013504 0.000338 0.088296 0.021671 8.184689e-07
3 3 -949.325867 2059.958984 291.460144 74.332581 291.460144 -143.539062 -108.213570 -22.348705 -8.996019 4.976562 9.774589 2059.958984 2059.958984 2059.958984 2059.958984 -372.708313 -372.708313 -216.721756 -6.296357 -6.296357 -6.296357 -0.275473 -0.275473 -2508.858643 -0.011922 -2.254035 0.366016 0.024763 0.004462 0.000000 0.123067 0.059121 1.861511e-03
4 4 -1025.987305 2059.117920 274.807404 85.999092 274.807404 -131.939636 -118.279694 -22.480148 -3.913847 0.936185 9.810230 2059.117920 2059.117920 2059.117920 2059.117920 -404.156525 -404.156525 -208.737106 -11.296759 -11.296759 -11.296759 -0.000092 -0.000092 -2555.133545 0.000000 -1.092340 0.368933 0.002794 0.000068 0.000000 0.023409 0.003410 1.759075e-09
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
245 245 -4509.291504 553.072266 85.382362 31.081087 85.382362 -223.268021 -235.113663 -162.424042 -41.547173 0.195563 9.364694 553.072266 553.072266 553.072266 553.072266 -786.812195 -786.812195 -239.778687 -135.203339 -135.203339 -135.203339 -0.657408 -0.657408 -3360.370361 -0.004550 -4.086458 0.841196 0.027243 0.009350 0.000643 0.057407 0.005872 1.631798e-09
246 246 -4519.078125 551.566223 82.523125 25.172474 82.523125 -243.365234 -236.295105 -160.547653 -32.312897 0.066495 9.874746 551.566223 551.566223 551.566223 551.566223 -800.304077 -800.304077 -244.524048 -115.462097 -115.462097 -115.462097 -0.910928 -0.910928 -3350.572021 -0.035068 -4.726903 0.741449 0.025590 0.007695 0.000124 0.075385 0.015567 5.839832e-05
247 247 -4583.382812 499.982666 69.911003 44.617153 69.911003 -237.382324 -232.918396 -163.370346 -32.344398 0.307826 9.464544 499.982666 499.982666 499.982666 499.982666 -808.151917 -808.151917 -233.967163 -116.608429 -116.608429 -116.608429 -0.022759 -0.022759 -3379.955566 -0.003313 -3.787321 0.821089 0.021251 0.003569 0.000000 0.056510 0.006365 7.836176e-10
248 248 -4520.576660 518.867920 82.211746 32.160069 82.211746 -240.931641 -229.275192 -149.423965 -32.866112 0.047689 9.640162 518.867920 518.867920 518.867920 518.867920 -786.634460 -786.634460 -229.448395 -125.048828 -125.048828 -125.048828 -2.231311 -2.231311 -3364.825195 -0.000386 -3.569661 0.720697 0.024650 0.005562 0.000006 0.042734 0.003276 1.030754e-11
249 249 -4464.675781 597.465210 88.833214 30.694790 88.833214 -229.268295 -219.706787 -166.731750 -30.443710 0.198675 9.579359 597.465210 597.465210 597.465210 597.465210 -808.778137 -808.778137 -246.836975 -135.497009 -135.497009 -135.497009 -1.045294 -1.045294 -3350.941895 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 -5.339263 -5.339263 -5.339263 -0.072591 -0.072591 -2102.574463 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 -2461.913086 -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 -187.615433 -17.138174 -17.138174 -17.138174 -0.000054 -0.000054 -2559.758057 -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 -2405.116211 -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 -237.803421 -169.516693 -36.915016 0.070329 9.403797 541.814697 541.814697 541.814697 541.814697 -775.409363 -775.409363 -238.447006 -121.044250 -121.044250 -121.044250 -1.337590 -1.337590 -3215.153809 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 -797.220276 -797.220276 -233.276489 -110.312561 -110.312561 -110.312561 -3.278319 -3.278319 -3229.166504 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 -757.398071 -220.662949 -107.955185 -107.955185 -107.955185 -4.157536 -4.157536 -3238.353760 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 -777.313721 -232.581009 -117.963684 -117.963684 -117.963684 -2.161796 -2.161796 -3247.040527 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 -11098.679688 -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 -5069.142090 -3956.500000 -741.189331 -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 -469.639832 -468.173981 -270.791748 -71.202927 0.528191 30.002693 5095.862305 5095.862305 5095.862305 5095.862305 -5181.652344 -5181.652344 -4373.848145 -766.270447 -766.270447 -766.270447 -109.655205 -109.655205 -10910.878906 -102.723877 -162.677933 0.544092 0.363078 0.115236 0.824331 0.681142 0.361538
1355 1355 -17466.509766 67.424332 174.690521 -477.919586 -487.781281 -266.450928 -60.205299 4.617456 31.505203 5152.246582 5152.246094 5152.246582 5152.246582 -5129.292969 -5129.292969 -4346.389648 -752.145630 -752.145630 -752.145630 -105.230362 -105.230362 -11011.666992 -101.783211 -159.132965 0.534918 0.355067 0.115245 0.811602 0.660185 0.323518
1356 1356 -17659.167969 76.937561 191.284973 -473.358185 -480.496826 -254.787201 -66.500099 0.077047 30.118214 4912.732422 4912.732422 4912.732422 4912.732422 -5098.808594 -5098.808594 -4420.116211 -716.462708 -716.462708 -716.462708 -108.879234 -108.879234 -10971.794922 -120.431839 -159.718735 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 -759.709412 -759.709412 -759.709412 -101.870842 -101.870842 -11024.328125 -131.442871 -165.441681 0.553682 0.383390 0.138519 0.839096 0.704828 0.350625
1358 1358 -17512.953125 85.468567 158.939133 -484.828430 -508.126953 -278.751129 -57.349087 1.047828 30.279930 5236.811035 5236.811035 5236.811035 5236.811035 -5098.156250 -5098.156250 -4395.380859 -793.282410 -793.282410 -793.282410 -104.880630 -104.880630 -11016.500000 -121.260925 -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 -18.493217 8.499491 27.698605 16748.167969 16748.167969 16748.167969 16748.167969 -1750.368896 -1750.368896 -1234.339844 -58.612610 -58.612610 -58.612610 -1.534541 -1.534541 -5261.635742 -25058.871094 -0.647152 -9.052570 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 -167.409668 -3.183158 -11.888466 2.539808 31.779448 17160.289062 17160.291016 17160.291016 17160.289062 -1627.511230 -1627.511230 -1274.558105 -45.683517 -45.683517 -45.683517 -12.318489 -12.318489 -5494.003906 -25993.480469 -12.753254 -14.473513 0.084730 0.118270 0.066108 0.023097 0.187257 0.110600 0.041997
2 2 -16990.832031 16455.716797 909.138672 909.138672 758.350952 -256.893646 -236.299500 -29.446934 -10.828147 7.283559 27.197603 16455.714844 16455.716797 16455.714844 16455.716797 -1709.427734 -1709.427734 -1339.484131 -72.881042 -72.881042 -72.881042 -6.865775 -6.865775 -5611.177734 -25848.523438 -4.122315 -22.948515 0.097037 0.160817 0.093702 0.030708 0.286500 0.162603 0.036490
3 3 -17799.298828 16700.445312 802.155396 802.155396 594.262451 -226.488617 -199.179871 -10.057462 -14.891386 4.588534 37.784122 16700.445312 16700.445312 16700.445312 16700.445312 -1670.132690 -1670.132690 -1313.989258 -73.567566 -73.567566 -73.567566 -13.398409 -13.398409 -5659.633789 -26728.314453 -5.993731 -23.352720 0.107812 0.201331 0.117052 0.039372 0.301439 0.179664 0.058437
4 4 -18204.070312 16755.984375 778.743469 778.743469 664.797607 -255.211975 -207.315308 -20.596722 -6.786825 1.613914 32.989372 16755.984375 16755.984375 16755.984375 16755.984375 -1495.672607 -1495.672607 -1388.975342 -86.376183 -86.376183 -86.376183 -9.809128 -9.809128 -5520.653809 -27396.658203 -12.391467 -38.243820 0.120737 0.213673 0.122151 0.036560 0.336356 0.212871 0.060589
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -41710.742188 5543.875000 211.059555 211.059555 213.080704 -477.956909 -480.563446 -285.286438 -65.932274 3.022510 31.707573 5543.875000 5543.875000 5543.875000 5543.875488 -3769.530273 -3769.530273 -1914.088867 -356.245300 -356.245300 -356.245300 -32.376442 -32.376442 -7188.291016 -33034.476562 -37.785030 -72.142021 0.224082 0.494975 0.336653 0.129857 0.660903 0.484253 0.182494
746 746 -41833.734375 5414.332520 214.427658 214.427658 149.601608 -483.973877 -492.562836 -285.071625 -56.379883 0.786993 32.652199 5414.333008 5414.333008 5414.333008 5414.333008 -3697.774902 -3697.774902 -1912.394043 -336.261047 -336.261047 -336.261047 -39.499722 -39.499722 -7322.418457 -32921.359375 -33.314568 -65.696655 0.226348 0.493690 0.335193 0.117416 0.669285 0.496285 0.195886
747 747 -41827.937500 5558.282715 211.470200 211.470200 163.798538 -481.616272 -496.274261 -266.222717 -68.886215 1.135251 30.620701 5558.282715 5558.282715 5558.282227 5558.282227 -3708.850586 -3708.850586 -1890.742432 -361.334869 -361.334869 -361.334869 -33.883846 -33.883846 -7243.623047 -33148.835938 -34.897552 -59.195347 0.223800 0.475852 0.314021 0.106829 0.651820 0.473985 0.186498
748 748 -42305.597656 5049.744141 249.072479 249.072479 177.006317 -492.562164 -469.891602 -272.876312 -64.300331 3.282044 31.981205 5049.744141 5049.744141 5049.744141 5049.744141 -3833.661865 -3833.661865 -1905.613281 -370.090942 -370.090942 -370.090942 -38.689526 -38.689526 -7220.023926 -33055.484375 -36.418915 -58.201149 0.223083 0.483531 0.319789 0.104951 0.675724 0.505158 0.210320
749 749 -41868.699219 5204.234863 238.780731 238.780731 186.144501 -470.977722 -491.949493 -266.520874 -70.370270 3.759845 30.516413 5204.234375 5204.234863 5204.234375 5204.234375 -3717.205566 -3717.205566 -1857.837402 -340.218323 -340.218323 -340.218323 -41.809353 -41.809353 -7205.714844 -32990.761719 -20.706787 -59.208683 0.234338 0.478285 0.318779 0.112849 0.665391 0.496395 0.199933

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
0 0 -25113.011719 15213.275391 1396.384155 1396.384155 568.831421 -254.716675 -208.203766 -11.446313 -10.360762 12.430771 28.383865 15213.275391 15213.275391 15213.275391 15213.275391 -2006.858398 -2006.858398 -1311.020508 -114.078659 -114.078659 -114.078659 -23.889977 -23.889977 -14022.275391 -24330.773438 -3.938205 -35.256489 0.098108 0.229125 0.134808 0.043674 0.314859 0.198710 0.052288
1 1 -27233.019531 15671.946289 830.277039 830.277039 700.534607 -289.423981 -213.242661 -26.910570 -7.485239 10.097235 30.497986 15671.945312 15671.945312 15671.945312 15671.945312 -2103.403809 -2103.403809 -1322.070312 -106.755981 -106.755981 -106.755981 -48.669987 -48.669987 -14926.272461 -25365.072266 -15.848166 -51.922600 0.114297 0.326635 0.202694 0.064840 0.455060 0.321058 0.119914
2 2 -29412.171875 14884.777344 681.438416 681.438416 689.653870 -293.755493 -231.623169 -42.849586 -18.094606 1.321061 32.943748 14884.777344 14884.777344 14884.777344 14884.777344 -2212.348145 -2212.348145 -1424.661621 -98.073677 -98.073677 -98.073677 -41.496658 -41.496658 -15664.468750 -25598.054688 -30.550636 -47.123726 0.122675 0.359847 0.231283 0.080323 0.486493 0.344262 0.107309
3 3 -30445.765625 15459.026367 676.766479 676.766479 542.113647 -296.310425 -255.682785 -57.522942 -9.102396 7.696231 29.914497 15459.025391 15459.026367 15459.025391 15459.025391 -2068.183105 -2068.183105 -1420.056274 -138.799286 -138.799286 -138.799286 -49.381828 -49.381828 -16365.539062 -26432.148438 -13.933872 -55.519943 0.139296 0.403858 0.262963 0.091190 0.537068 0.403004 0.172659
4 4 -31220.523438 15123.919922 829.743713 829.743713 538.306824 -228.928253 -236.550522 -15.065624 -9.895781 33.727947 34.547218 15123.919922 15123.919922 15123.920898 15123.919922 -2320.590088 -2320.590088 -1449.679077 -136.157806 -136.157806 -136.157806 -35.716927 -35.716927 -16856.062500 -26418.031250 -15.670280 -59.280117 0.141892 0.391163 0.247138 0.080156 0.514053 0.363557 0.145905
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
2495 2495 -53475.191406 5437.392090 164.572510 164.572510 165.457443 -477.048065 -511.165619 -242.537964 -54.973854 1.879056 31.301361 5437.391602 5437.391602 5437.392090 5437.392090 -4616.214844 -4616.214844 -2063.680664 -570.688721 -570.688721 -570.688721 -89.135315 -89.135315 -21413.382812 -29130.757812 -24.871449 -83.684990 0.457792 0.851996 0.708565 0.328269 0.880591 0.755263 0.376886
2496 2496 -53520.351562 5175.629883 154.459518 154.459518 152.555496 -486.757507 -500.540131 -269.931396 -63.669117 1.586104 31.530334 5175.629883 5175.629883 5175.629395 5175.629883 -4522.477539 -4522.477539 -2041.882324 -564.579285 -564.579285 -564.579285 -79.343590 -79.343590 -21510.435547 -28898.789062 -22.918919 -77.096138 0.462405 0.846018 0.698053 0.302183 0.867402 0.726392 0.320461
2497 2497 -53638.917969 5122.781250 206.524231 206.524231 158.441833 -490.239624 -488.299042 -293.155457 -67.977005 7.043468 30.395050 5122.780762 5122.781250 5122.781250 5122.781250 -4569.411133 -4569.411133 -2059.089355 -568.095093 -568.095093 -568.095093 -83.955185 -83.955185 -21381.626953 -29062.070312 -20.984013 -81.548218 0.468497 0.851702 0.707081 0.320519 0.883860 0.752358 0.366204
2498 2498 -53591.886719 5266.937012 169.046600 169.046600 204.129654 -461.154663 -506.339172 -266.694275 -63.712521 3.694311 30.305124 5266.937500 5266.937012 5266.937500 5266.937012 -4597.342285 -4597.342285 -2070.128906 -548.405273 -548.405273 -548.405273 -92.388741 -92.388741 -21429.570312 -29113.556641 -43.914787 -75.149956 0.480770 0.844070 0.702612 0.333865 0.884566 0.755895 0.355177
2499 2499 -53582.320312 5117.964844 175.550415 175.550415 204.601837 -479.894745 -484.111603 -282.617310 -61.933254 0.919242 30.016945 5117.964844 5117.964844 5117.964844 5117.964844 -4558.850586 -4558.850586 -2031.912842 -604.608887 -604.608887 -604.608887 -91.409164 -91.409164 -21395.230469 -29015.673828 -32.791344 -74.681427 0.459197 0.850982 0.709164 0.320147 0.880967 0.754800 0.367179

2500 rows × 35 columns

this one, without AMH-go, and ER. doesn't fold well. even with 1.5e7 steps.


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 16373.279297 2371.009277 2371.009277 603.912659 -258.299774 -247.249954 -53.013573 -17.335554 8.711543 28.566280 16373.279297 16373.279297 16373.278320 16373.278320 -2039.092529 -2039.092529 -1200.275635 -38.625572 -38.625572 -38.625572 -19.125645 -19.125645 -5279.178711 -2.127504 -4.288480 0.054175 0.045593 0.023058 0.007462 0.060618 0.027018 0.004372
1 1 8802.133789 16178.447266 1227.702881 1227.702881 485.050232 -272.594299 -209.265594 -14.792652 -9.640638 11.250684 28.565052 16178.447266 16178.446289 16178.447266 16178.448242 -1891.509399 -1891.509399 -1243.427979 -26.218863 -26.218863 -26.218863 -9.936148 -9.936148 -5452.228516 20.571758 -20.089567 0.067756 0.108359 0.056283 0.016960 0.154522 0.081260 0.024892
2 2 8531.545898 16419.931641 855.906128 855.906128 491.065704 -279.433807 -212.408554 -22.828575 -2.128881 2.845388 30.721703 16419.933594 16419.933594 16419.933594 16419.933594 -2150.773926 -2150.773926 -1300.429321 -11.167533 -11.167533 -11.167533 -0.268728 -0.268728 -5281.723633 19.572933 -27.656490 0.076872 0.141937 0.075942 0.026986 0.223987 0.141195 0.051848
3 3 9093.503906 16778.125000 669.767334 669.767334 622.687439 -211.305252 -179.581497 -15.840036 -8.842993 4.059708 33.195301 16778.125000 16778.125000 16778.126953 16778.125000 -1986.462158 -1986.462158 -1224.745117 -16.622852 -16.622852 -16.622852 -0.012140 -0.012140 -5326.045410 -15.379452 -29.891922 0.083164 0.186886 0.100533 0.027269 0.277944 0.178969 0.055758
4 4 9221.838867 16491.808594 712.419678 712.419678 803.970154 -259.659790 -158.128494 -0.842916 -8.221447 8.970200 32.478909 16491.808594 16491.808594 16491.808594 16491.808594 -2138.400879 -2138.400879 -1213.401123 -17.088501 -17.088501 -17.088501 -0.019363 -0.019363 -5007.484375 -1.152154 -23.857128 0.082899 0.208354 0.118147 0.037757 0.306309 0.175980 0.042434
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
3745 3745 -15152.976562 5026.809570 105.480354 105.480354 177.659927 -481.165771 -508.989380 -269.131775 -62.344807 2.830058 31.588661 5026.809570 5026.809082 5026.809570 5026.809570 -5104.049805 -5104.049805 -1966.191406 -723.939697 -723.939697 -723.939697 -80.145592 -80.145592 -11175.029297 -43.100037 -85.234177 0.334913 0.764483 0.609958 0.267467 0.799451 0.656054 0.306156
3746 3746 -15058.488281 5007.347168 137.184692 137.184692 151.237885 -464.431641 -501.786377 -301.797180 -71.039284 0.921664 29.679722 5007.346680 5007.346680 5007.346680 5007.346680 -5055.144531 -5055.144531 -1887.488525 -733.286865 -733.286865 -733.286865 -83.206451 -83.206451 -11154.650391 -45.250614 -88.771599 0.360740 0.763277 0.608225 0.262473 0.799621 0.654915 0.307883
3747 3747 -14862.297852 5225.870605 139.996582 139.996582 168.836304 -508.743652 -517.134827 -300.156525 -70.109322 3.077751 30.356539 5225.870117 5225.871094 5225.870605 5225.870605 -5075.645020 -5075.645020 -1958.456299 -718.547852 -718.547852 -718.547852 -81.013435 -81.013435 -11074.173828 -41.106262 -87.459641 0.357352 0.787428 0.652687 0.313533 0.802933 0.669114 0.322161
3748 3748 -15043.521484 5163.494141 106.586151 106.586151 199.503784 -504.391785 -513.653870 -281.031250 -72.862152 0.264688 30.463551 5163.494141 5163.494141 5163.494141 5163.494141 -5086.955566 -5086.955566 -1939.042847 -693.738159 -693.738159 -693.738159 -72.416946 -72.416946 -11249.943359 -47.755924 -84.191139 0.369756 0.786037 0.660237 0.333773 0.816678 0.705483 0.391332
3749 3749 -14907.193359 5182.839844 119.547516 119.547516 209.879044 -483.834839 -500.966553 -290.469543 -65.607857 1.369849 30.317133 5182.839844 5182.839844 5182.839844 5182.839844 -5046.087891 -5046.087891 -1946.559082 -691.997070 -691.997070 -691.997070 -64.968430 -64.968430 -11221.057617 -51.910072 -89.765594 0.350344 0.775076 0.641087 0.311674 0.805075 0.679524 0.338528

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 -41761.898438 0.910350 -24148.511719 72.628693 174.160477 -492.280762 -496.281281 -299.294342 -65.298683 1.116977 32.101761 4982.414062 4982.413574 4982.414062 4982.413574 -5116.578125 -5116.578125 -3372.669434 -788.578857 -788.578857 -788.578857 -87.048683 -87.048683 -11913.384766 -74.894501 -172.878815 0.967220 0.916209 0.598239 0.972316 0.928374 0.626994
1 1 -41800.851562 0.925077 -24174.560547 72.544197 165.041199 -480.148041 -500.106628 -274.647064 -63.609055 0.172277 30.470150 4873.564453 4873.563965 4873.564453 4873.564453 -5086.610840 -5086.610840 -3325.110840 -782.810059 -782.810059 -782.810059 -82.263390 -82.263390 -11943.054688 -62.340652 -170.711533 0.961359 0.901237 0.553961 0.959051 0.895604 0.541304
2 2 -41745.632812 0.851793 -24189.828125 91.083344 172.127487 -461.366455 -494.880646 -291.325989 -64.341721 0.568332 31.616669 5072.878906 5072.878906 5072.878906 5072.878906 -5138.804688 -5138.804688 -3395.028320 -788.807373 -788.807373 -788.807373 -79.207420 -79.207420 -11924.847656 -110.780952 -177.901993 0.956154 0.888922 0.523362 0.959400 0.896102 0.538825
3 3 -41892.742188 0.886018 -24129.302734 51.578461 184.347809 -506.004578 -479.178986 -276.171234 -59.279732 1.358014 31.211781 4813.846680 4813.846680 4813.846680 4813.846680 -5095.519531 -5095.519531 -3352.770020 -804.503418 -804.503418 -804.503418 -84.143646 -84.143646 -11909.226562 -111.979210 -170.268646 0.958449 0.894621 0.536966 0.965112 0.908757 0.528775
4 4 -41876.664062 0.916250 -24161.134766 88.812004 172.881195 -492.063080 -504.710785 -276.787720 -68.570572 2.135250 31.823505 4870.122070 4870.122070 4870.122070 4870.121582 -5147.251953 -5147.251953 -3358.418945 -787.141235 -787.141235 -787.141235 -80.618805 -80.618805 -11920.861328 -82.409134 -165.794693 0.961920 0.902782 0.556735 0.964789 0.908582 0.554520
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
245 245 -44218.445312 0.910282 -24328.419922 53.136841 105.146851 -508.894928 -512.151855 -310.310913 -76.330750 1.095423 32.260189 3308.041260 3308.041016 3308.041016 3308.041260 -5325.213867 -5325.213867 -3454.216309 -854.620117 -854.620117 -854.620117 -80.490845 -80.490845 -11994.501953 -103.738083 -171.799683 0.811682 0.621376 0.232360 0.960487 0.898759 0.543176
246 246 -44081.304688 0.869112 -24308.099609 58.100685 124.604019 -516.636841 -512.087708 -298.018494 -66.826683 0.774467 31.588593 3324.935547 3324.935547 3324.935303 3324.935547 -5292.588867 -5292.588867 -3438.642822 -846.340088 -846.340088 -846.340088 -80.363419 -80.363419 -11994.630859 -101.965279 -167.570999 0.791153 0.591524 0.220003 0.954601 0.887171 0.539565
247 247 -43920.828125 0.884810 -24328.154297 56.388245 144.464966 -480.523895 -513.313965 -315.142426 -69.884544 0.503394 31.224329 3461.500488 3461.500732 3461.500488 3461.500488 -5305.854004 -5305.854004 -3445.930420 -833.889404 -833.889404 -833.889404 -89.813217 -89.813217 -11970.527344 -95.103828 -169.201202 0.787529 0.580062 0.186515 0.943319 0.861994 0.483121
248 248 -44173.488281 0.905386 -24323.910156 47.034550 116.440445 -496.897888 -512.915588 -299.912720 -70.170296 0.917068 32.955006 3295.433594 3295.433350 3295.433350 3295.433594 -5339.147949 -5339.147949 -3465.430420 -837.304932 -837.304932 -837.304932 -79.374741 -79.374741 -11985.265625 -90.838982 -167.697739 0.819279 0.636080 0.250024 0.955081 0.885529 0.497608
249 249 -44217.929688 0.881131 -24323.048828 57.388577 98.314499 -520.283386 -528.126709 -308.141663 -77.708755 0.809490 32.398632 3235.748535 3235.749023 3235.748779 3235.749023 -5325.193848 -5325.193848 -3415.360840 -816.455688 -816.455688 -816.455688 -80.864258 -80.864258 -11989.242188 -102.605324 -158.091797 0.811218 0.621944 0.227924 0.944277 0.866626 0.491240

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
0 0 9127.415039 14525.158203 2697.747070 2697.747070 605.406738 -250.368103 -233.610504 -41.521984 -9.966216 5.151029 28.869446 14525.158203 14525.159180 14525.160156 14525.160156 -2175.564453 -2175.564453 -1197.665771 -31.779808 -31.779808 -31.779808 -0.177427 -0.177427 -4789.038574 -0.981598 -4.339045 0.054651 0.029679 0.010088 0.001085 0.051204 0.018654 0.003344
1 1 8957.602539 16086.345703 1492.339355 1492.339355 622.997681 -297.531128 -200.324631 -22.809326 -18.524002 3.602570 27.225203 16086.345703 16086.346680 16086.345703 16086.345703 -1979.145264 -1979.145264 -1201.169189 -26.634792 -26.634792 -26.634792 -1.409769 -1.409769 -5510.653809 -4.584737 -12.361418 0.063628 0.102130 0.055747 0.019565 0.143721 0.072717 0.020329
2 2 6365.622070 14607.689453 914.850647 914.850647 467.844910 -291.474945 -231.439346 -16.779318 -8.683804 26.855642 36.504627 14607.689453 14607.689453 14607.689453 14607.689453 -2299.407471 -2299.407471 -1234.374634 -19.632896 -19.632896 -19.632896 -2.628139 -2.628139 -5548.616211 -0.296653 -35.145493 0.073305 0.165300 0.089303 0.028352 0.243340 0.155865 0.058185
3 3 6973.531250 14913.457031 808.598022 808.598022 655.385010 -214.178085 -187.189514 -23.428823 -15.153639 3.709998 36.819572 14913.457031 14913.457031 14913.457031 14913.457031 -2082.257812 -2082.257812 -1264.408447 -37.454704 -37.454704 -37.454704 -9.766295 -9.766295 -5570.606445 -12.026272 -28.363443 0.079866 0.182289 0.101562 0.031119 0.294055 0.198602 0.076960
4 4 7065.994141 15212.683594 744.216248 744.216248 570.235657 -225.186844 -238.246704 -13.037592 -12.802148 23.964462 30.252686 15212.685547 15212.683594 15212.683594 15212.684570 -2066.539062 -2066.539062 -1285.417969 -16.265472 -16.265472 -16.265472 -0.000856 -0.000856 -5631.441406 6.921254 -33.774734 0.087499 0.196792 0.111549 0.036106 0.322984 0.212760 0.087024
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
995 995 -14696.871094 5114.482422 158.847580 158.847580 182.141876 -494.844879 -477.735504 -291.245911 -64.160713 1.589803 32.420090 5114.482422 5114.481934 5114.481934 5114.481934 -5076.694824 -5076.694824 -2041.663574 -697.065491 -697.065491 -697.065491 -81.710114 -81.710114 -10855.673828 -29.450251 -77.686317 0.262784 0.649866 0.485165 0.180313 0.744715 0.581817 0.221068
996 996 -14825.744141 5007.963379 164.670258 164.670258 157.856369 -484.206482 -509.903412 -280.313751 -70.066917 0.875295 30.529055 5007.962891 5007.963379 5007.963379 5007.963379 -5113.803223 -5113.803223 -1996.901123 -688.512451 -688.512451 -688.512451 -85.338631 -85.338631 -10847.662109 -38.349861 -74.165291 0.261530 0.652430 0.486509 0.184524 0.765132 0.599577 0.240082
997 997 -14522.886719 5245.998535 160.487213 160.487213 142.549515 -493.587158 -497.342804 -277.600494 -69.676651 0.582503 31.153845 5245.999023 5245.999023 5245.999023 5245.999023 -4917.850586 -4917.850586 -2046.813477 -704.642334 -704.642334 -704.642334 -86.588562 -86.588562 -10896.574219 -39.043560 -75.498253 0.245903 0.648927 0.480359 0.185115 0.773798 0.624696 0.282405
998 998 -14749.774414 5146.747070 185.451508 185.451508 178.919022 -485.103516 -503.149506 -282.831055 -73.892326 0.497496 32.872646 5146.747070 5146.747070 5146.747070 5146.747070 -5069.239746 -5069.239746 -2067.640137 -690.271240 -690.271240 -690.271240 -87.587128 -87.587128 -10930.884766 -29.884817 -75.302322 0.248928 0.634937 0.462288 0.178069 0.746470 0.580989 0.255107
999 999 -14519.336914 5120.292969 188.783798 188.783798 165.138657 -484.363068 -505.516846 -289.386902 -64.020615 0.700149 30.205866 5120.292969 5120.292969 5120.292969 5120.292969 -5003.158203 -5003.158203 -1961.615479 -658.404419 -658.404419 -658.404419 -79.418137 -79.418137 -10863.561523 -39.971642 -76.511055 0.247876 0.614292 0.444649 0.162642 0.725882 0.561273 0.237754

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 -24055.808594 15301.533203 2797.630371 2797.630371 559.293518 -259.372284 -264.448639 -29.994204 -17.911156 7.567412 29.695469 15301.533203 15301.534180 15301.533203 15301.534180 -2242.792969 -2242.792969 -1283.301758 -88.794456 -88.794456 -88.794456 -18.132706 -18.132706 -14257.455078 -24278.773438 -1.513863 -9.156893 0.065719 0.033450 0.015709 0.005006 0.084116 0.049470 0.018399
1 1 -27723.984375 14802.665039 1365.441650 1365.441650 670.968750 -281.478271 -238.248215 -22.932543 -20.631466 3.381753 30.097397 14802.664062 14802.666016 14802.665039 14802.665039 -2043.829590 -2043.829590 -1360.717285 -114.404617 -114.404617 -114.404617 -40.565720 -40.565720 -15036.800781 -25418.845703 -3.291100 -15.036631 0.084652 0.092687 0.051488 0.016004 0.165459 0.099788 0.032215
2 2 -29697.339844 14742.403320 966.706604 966.706604 517.745911 -332.201447 -289.065338 -46.351055 -14.245848 1.437738 30.617626 14742.403320 14742.403320 14742.404297 14742.403320 -2057.126953 -2057.126953 -1413.422241 -96.418633 -96.418633 -96.418633 -50.780052 -50.780052 -15339.055664 -26292.496094 -0.246501 -25.224152 0.104046 0.164236 0.087394 0.028070 0.241254 0.128368 0.033147
3 3 -29613.158203 15617.820312 754.815247 754.815247 535.740906 -264.623108 -278.848755 -5.299677 -6.972278 3.022138 30.112740 15617.820312 15617.820312 15617.820312 15617.820312 -2198.784668 -2198.784668 -1401.806641 -114.289642 -114.289642 -114.289642 -34.086609 -34.086609 -16027.731445 -26181.625000 -17.087696 -23.979996 0.112081 0.200152 0.116292 0.040458 0.338779 0.206617 0.057794
4 4 -30916.828125 15003.067383 643.818359 643.818359 484.299286 -247.284470 -212.410370 -6.111562 -11.521433 2.622487 35.091660 15003.067383 15003.066406 15003.068359 15003.067383 -2405.519043 -2405.519043 -1344.385986 -148.800827 -148.800827 -148.800827 -42.640041 -42.640041 -16243.251953 -26382.351562 -8.826256 -33.114677 0.113731 0.223870 0.119482 0.037588 0.353558 0.218535 0.082911
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
495 495 -49905.824219 6775.476562 162.165680 162.165680 348.025909 -460.278534 -480.046082 -185.099731 -44.686455 1.606389 29.996651 6775.476562 6775.476562 6775.476562 6775.476562 -4365.019531 -4365.019531 -1827.620850 -392.334625 -392.334625 -392.334625 -47.814808 -47.814808 -21053.173828 -28270.117188 -28.012320 -70.371841 0.248786 0.626244 0.443768 0.159897 0.730397 0.557733 0.210691
496 496 -49538.171875 7015.426758 192.819733 192.819733 304.291199 -482.066132 -467.533295 -205.297180 -55.169079 3.280465 30.493914 7015.426758 7015.427246 7015.427246 7015.427246 -4326.797852 -4326.797852 -1856.780518 -398.400269 -398.400269 -398.400269 -56.552834 -56.552834 -20835.732422 -28297.742188 -37.569191 -66.284325 0.249174 0.619775 0.428265 0.149033 0.750434 0.582214 0.223114
497 497 -50388.179688 6449.608398 196.859283 196.859283 205.569397 -467.076080 -469.940521 -236.848404 -58.437943 0.635657 30.519222 6449.608398 6449.607910 6449.608398 6449.608398 -4403.699707 -4403.699707 -1846.312744 -336.679352 -336.679352 -336.679352 -64.339142 -64.339142 -21038.230469 -28283.644531 -9.071424 -58.498173 0.242541 0.604384 0.419320 0.141893 0.691891 0.500374 0.174530
498 498 -50168.972656 6541.162109 232.708344 232.708344 224.630798 -466.797333 -484.339294 -268.989258 -61.733963 4.929641 29.515995 6541.162598 6541.162109 6541.162109 6541.162109 -4122.917969 -4122.917969 -1820.471558 -365.039185 -365.039185 -365.039185 -57.048592 -57.048592 -21098.750000 -28375.226562 -15.914689 -66.101669 0.241055 0.610398 0.423413 0.139322 0.691830 0.504349 0.177894
499 499 -50197.085938 6746.481445 191.180450 191.180450 203.548492 -477.579285 -480.196503 -253.372345 -53.599365 5.167786 32.869297 6746.481445 6746.481445 6746.480957 6746.481445 -4243.308105 -4243.308105 -1842.252319 -370.058655 -370.058655 -370.058655 -64.026794 -64.026794 -21036.369141 -28469.324219 -20.680696 -66.984497 0.241440 0.616428 0.424845 0.140141 0.694343 0.497676 0.174693

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 -392.763519 -469.106354 -157.546158 -38.410599 4.216712 33.212463 5355.384277 5355.384277 5355.384277 5355.384766 -4940.760742 -4940.760742 -3838.023682 -720.704956 -720.704956 -720.704956 -103.133423 -103.133423 -11082.034180 -97.947983 -159.917664 0.942605 0.861538 0.495228 0.950446 0.878951 0.540868
1 1 -16727.988281 105.296135 164.350174 -454.326996 -458.210724 -205.394699 -52.416176 1.369517 31.705673 5250.726562 5250.726562 5250.726562 5250.726562 -5014.828125 -5014.828125 -3910.713867 -725.014282 -725.014282 -725.014282 -87.351898 -87.351898 -11109.675781 -95.857376 -169.929001 0.941039 0.857769 0.484938 0.949925 0.876747 0.520582
2 2 -17066.710938 72.720604 147.385223 -452.154327 -482.814850 -250.886322 -62.619217 0.485088 30.012085 5135.125977 5135.125977 5135.125977 5135.125977 -4991.761230 -4991.761230 -3883.658203 -745.737976 -745.737976 -745.737976 -96.754745 -96.754745 -11230.724609 -92.207108 -165.392548 0.936035 0.848508 0.485147 0.938360 0.850782 0.488478
3 3 -17468.425781 80.091873 197.759094 -464.373169 -491.921661 -259.558838 -57.891171 2.858864 29.756275 4897.955566 4897.955566 4897.955566 4897.956055 -5151.034180 -5151.034180 -3997.531006 -737.855225 -737.855225 -737.855225 -85.441666 -85.441666 -11178.132812 -86.502281 -168.871765 0.929334 0.841026 0.495872 0.939038 0.855826 0.506194
4 4 -16705.625000 76.169281 160.586716 -470.116486 -492.720490 -277.024078 -59.199928 1.816934 29.753113 5378.410156 5378.410156 5378.409668 5378.410156 -4941.544922 -4941.544922 -3958.017090 -688.917114 -688.917114 -688.917114 -92.798706 -92.798706 -11101.974609 -113.317917 -158.883972 0.912180 0.807174 0.434527 0.925959 0.828665 0.443302
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
1347 1347 -17272.636719 58.789490 137.027802 -466.996399 -491.325348 -286.931213 -62.402119 2.976237 31.393959 5405.324219 5405.323730 5405.323730 5405.323730 -4995.520020 -4995.520020 -4550.981934 -716.453796 -716.453796 -716.453796 -109.522766 -109.522766 -10923.883789 -103.686157 -201.505478 0.544408 0.376315 0.140518 0.794283 0.643964 0.315931
1348 1348 -17272.820312 73.538147 160.681412 -468.127136 -480.733856 -280.583740 -62.032452 3.921861 32.144428 5369.016113 5369.015625 5369.016113 5369.016113 -5030.248535 -5030.248535 -4467.886719 -710.185242 -710.185242 -710.185242 -106.545517 -106.545517 -11022.460938 -94.871704 -189.492767 0.532824 0.367764 0.145284 0.796841 0.645310 0.308549
1349 1349 -17234.392578 73.686440 145.862000 -476.791382 -507.396545 -257.636108 -61.765190 1.093132 31.936871 5399.900391 5399.900879 5399.900879 5399.900879 -5047.286133 -5047.286133 -4482.777344 -700.921631 -700.921631 -700.921631 -98.674751 -98.674751 -10961.904297 -106.253914 -186.525284 0.540856 0.371297 0.148312 0.811498 0.668159 0.319919
1350 1350 -17608.339844 55.219597 203.999298 -487.359497 -472.829437 -269.801270 -64.448120 0.890099 33.351913 5085.490723 5085.490723 5085.490723 5085.490723 -4999.078613 -4999.078613 -4517.480469 -723.782776 -723.782776 -723.782776 -106.283325 -106.283325 -11071.834961 -97.212646 -178.238602 0.544760 0.374307 0.138902 0.793933 0.640368 0.269225
1351 1351 -17294.462891 64.212326 170.454681 -482.677307 -490.268250 -265.353516 -64.491074 1.272023 31.911182 5245.522461 5245.522949 5245.522949 5245.522949 -5015.397949 -5015.397949 -4469.151367 -770.711365 -770.711365 -770.711365 -103.847534 -103.847534 -10872.309570 -86.013214 -188.686432 0.548965 0.379796 0.142881 0.792669 0.642194 0.291382

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
0 0 -35742.613281 0.817115 -21180.789062 74.475235 210.609955 -392.763519 -469.106415 -157.546173 -38.410610 4.216719 33.212463 5355.384766 5355.385254 5355.385254 5355.385254 -4940.760742 -4940.760742 -3838.023438 -720.704956 -720.704956 -720.704956 -103.133423 -103.133423 -11082.032227 -97.947968 -159.917648 1758.0 0.942605 0.861538 0.950446 0.878951 0.540868
1 1 -36282.210938 0.799650 -21279.539062 105.296127 164.350159 -454.326996 -458.210754 -205.394714 -52.416176 1.369517 31.705673 5250.727539 5250.727539 5250.727539 5250.727539 -5014.829102 -5014.829102 -3910.713623 -725.014282 -725.014282 -725.014282 -87.351898 -87.351898 -11109.675781 -95.857384 -169.929016 1725.0 0.941039 0.857769 0.949925 0.876747 0.520582
2 2 -36646.601562 0.799917 -21287.203125 72.720612 147.385193 -452.154358 -482.814880 -250.886307 -62.619205 0.485089 30.012089 5135.126953 5135.126953 5135.126953 5135.126953 -4991.761719 -4991.761719 -3883.658203 -745.737915 -745.737915 -745.737915 -96.754745 -96.754745 -11230.724609 -92.207108 -165.392563 1707.0 0.936035 0.848508 0.938360 0.850782 0.488478
3 3 -37012.773438 0.792599 -21260.644531 80.091888 197.759125 -464.373169 -491.921631 -259.558838 -57.891163 2.858867 29.756277 4897.955566 4897.955566 4897.956055 4897.955566 -5151.034180 -5151.034180 -3997.531006 -737.855347 -737.855347 -737.855347 -85.441666 -85.441666 -11178.130859 -86.502274 -168.871796 1716.0 0.929334 0.841026 0.939038 0.855826 0.506194
4 4 -35947.656250 0.783824 -20918.382812 76.169296 160.586700 -470.116486 -492.720520 -277.024048 -59.199924 1.816933 29.753113 5378.410156 5378.410156 5378.410156 5378.410156 -4941.545410 -4941.545410 -3958.017090 -688.917114 -688.917114 -688.917114 -92.798691 -92.798691 -11101.972656 -113.317917 -158.883942 1676.0 0.912180 0.807174 0.925959 0.828665 0.443302
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
1347 1347 -35565.031250 0.376207 -19291.630859 58.789482 137.027802 -466.996429 -491.325348 -286.931183 -62.402122 2.976238 31.393963 5405.324707 5405.324219 5405.324707 5405.324707 -4995.520508 -4995.520508 -4550.981445 -716.453857 -716.453857 -716.453857 -109.522766 -109.522766 -10923.883789 -103.686157 -201.505524 999.0 0.544408 0.376315 0.794283 0.643964 0.315931
1348 1348 -35487.343750 0.391762 -19194.771484 73.538170 160.681442 -468.127167 -480.733887 -280.583740 -62.032436 3.921859 32.144428 5369.016602 5369.016602 5369.016602 5369.016602 -5030.249023 -5030.249023 -4467.886230 -710.185303 -710.185303 -710.185303 -106.545517 -106.545517 -11022.458984 -94.871704 -189.492767 980.0 0.532824 0.367764 0.796841 0.645310 0.308549
1349 1349 -35572.609375 0.398252 -19324.468750 73.686447 145.862000 -476.791351 -507.396545 -257.636139 -61.765186 1.093132 31.936869 5399.901367 5399.900879 5399.900879 5399.901367 -5047.286133 -5047.286133 -4482.777344 -700.921692 -700.921692 -700.921692 -98.674759 -98.674759 -10961.902344 -106.253906 -186.525299 986.0 0.540856 0.371297 0.811498 0.668159 0.319919
1350 1350 -35979.250000 0.381592 -19376.152344 55.219601 203.999329 -487.359528 -472.829407 -269.801270 -64.448105 0.890099 33.351913 5085.491211 5085.491211 5085.491211 5085.491211 -4999.079102 -4999.079102 -4517.479980 -723.782837 -723.782837 -723.782837 -106.283333 -106.283333 -11071.833984 -97.212646 -178.238586 1005.0 0.544760 0.374307 0.793933 0.640368 0.269225
1351 1351 -35345.847656 0.360881 -19048.601562 64.212341 170.454636 -482.677307 -490.268250 -265.353516 -64.491066 1.272023 31.911182 5245.523438 5245.523438 5245.523438 5245.523438 -5015.398438 -5015.398438 -4469.151855 -770.711426 -770.711426 -770.711426 -103.847565 -103.847565 -10872.310547 -86.013222 -188.686432 997.0 0.548965 0.379796 0.792669 0.642194 0.291382

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 -24693.507812 15021.001953 1426.226196 1426.226196 653.965576 -269.549194 -177.473129 -23.259935 -12.476166 3.079231 33.425529 15021.001953 15021.000977 15021.001953 15021.001953 -2048.901123 -2048.901123 -1311.678711 -77.829529 -77.829529 -77.829529 -28.320200 -28.320200 -13289.615234 -24585.464844 21.033781 -28.199675 0.098140 0.247011 0.143459 0.040964 0.354637 0.226255 0.065237
1 1 -26831.142578 15772.398438 985.953003 985.953003 580.098877 -229.292511 -187.259567 -21.188015 -8.945752 11.731072 36.439121 15772.397461 15772.397461 15772.398438 15772.397461 -2082.229004 -2082.229004 -1316.234375 -98.935181 -98.935181 -98.935181 -46.210831 -46.210831 -14871.353516 -25304.708984 -19.964371 -32.103142 0.116976 0.305413 0.183149 0.058641 0.435973 0.296897 0.115421
2 2 -29290.984375 14878.052734 974.952515 974.952515 571.402344 -275.302124 -206.076157 13.662031 -15.313881 3.975441 39.543850 14878.052734 14878.052734 14878.052734 14878.051758 -2223.881348 -2223.881348 -1389.048584 -99.523308 -99.523308 -99.523308 -37.039822 -37.039822 -15360.232422 -26144.539062 18.358547 -40.733231 0.131193 0.333168 0.213642 0.082297 0.469937 0.336542 0.133099
3 3 -29915.574219 15087.328125 748.272461 748.272461 617.961914 -264.035339 -162.975586 -14.057974 -10.640308 5.654045 37.940441 15087.328125 15087.327148 15087.328125 15087.327148 -2189.303223 -2189.303223 -1468.953857 -133.416000 -133.416000 -133.416000 -34.383888 -34.383888 -15493.484375 -26551.511719 -11.452255 -79.358719 0.152431 0.388793 0.236488 0.063058 0.548329 0.378136 0.120927
4 4 -29745.451172 15486.254883 839.339111 839.339111 577.150757 -254.674545 -215.078430 -16.816208 -12.174308 17.847595 34.704056 15486.255859 15486.254883 15486.254883 15486.254883 -2215.494141 -2215.494141 -1454.466553 -140.081696 -140.081696 -140.081696 -37.148663 -37.148663 -15671.684570 -26655.482422 36.126568 -64.598839 0.152475 0.372030 0.227461 0.076107 0.550777 0.376521 0.124283
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
245 245 -44151.082031 10038.781250 429.294861 429.294861 331.506958 -364.676025 -350.539764 -102.115341 -21.681091 9.721833 34.137527 10038.781250 10038.782227 10038.781250 10038.781250 -3628.467041 -3628.467041 -1672.040771 -302.024353 -302.024353 -302.024353 -64.108490 -64.108490 -19918.525391 -28491.171875 -8.815675 -71.689362 0.217262 0.564357 0.396532 0.152355 0.687506 0.513273 0.175144
246 246 -44481.257812 9818.949219 369.002014 369.002014 281.116486 -356.319336 -321.343903 -96.108353 -28.963867 2.142846 31.738731 9818.949219 9818.949219 9818.949219 9818.949219 -3510.029785 -3510.029785 -1683.321045 -300.150391 -300.150391 -300.150391 -63.794270 -63.794270 -19860.781250 -28699.349609 1.726063 -67.105560 0.228385 0.568329 0.396430 0.141393 0.697848 0.549338 0.243749
247 247 -44308.308594 10134.249023 361.416718 361.416718 316.134186 -380.495697 -352.242035 -95.688438 -31.113920 14.038322 32.697540 10134.248047 10134.249023 10134.249023 10134.250000 -3737.285645 -3737.285645 -1700.219971 -333.444366 -333.444366 -333.444366 -55.316238 -55.316238 -20129.564453 -28279.601562 -7.066272 -66.087189 0.219427 0.546322 0.384213 0.129749 0.688269 0.536299 0.200712
248 248 -43744.273438 10229.148438 376.918335 376.918335 379.432007 -386.202637 -277.075989 -150.307205 -31.207958 10.502914 33.137932 10229.148438 10229.148438 10229.148438 10229.148438 -3447.447754 -3447.447754 -1655.148438 -277.847687 -277.847687 -277.847687 -68.417465 -68.417465 -19952.535156 -28439.179688 -26.890865 -62.429482 0.213887 0.544880 0.380091 0.136122 0.674422 0.513951 0.198367
249 249 -44351.437500 9891.104492 415.926117 415.926117 354.594360 -367.543701 -383.383240 -114.245262 -36.028046 17.048773 31.219267 9891.103516 9891.104492 9891.103516 9891.103516 -3641.780273 -3641.780273 -1697.130127 -305.633148 -305.633148 -305.633148 -67.528931 -67.528931 -20016.509766 -28360.269531 -11.889153 -60.714817 0.213830 0.564537 0.400078 0.150668 0.668708 0.525276 0.232051

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 -25113.011719 15213.275391 1396.384155 1396.384155 568.831421 -254.716675 -208.203766 -11.446313 -10.360762 12.430771 28.383865 15213.275391 15213.275391 15213.275391 15213.275391 -2006.858398 -2006.858398 -1311.020508 -114.078659 -114.078659 -114.078659 -23.889977 -23.889977 -14022.275391 -24330.773438 -3.938205 -35.256489 0.098108 0.229125 0.134808 0.043674 0.314859 0.198710 0.052288
1 1 -27233.019531 15671.946289 830.277039 830.277039 700.534607 -289.423981 -213.242661 -26.910570 -7.485239 10.097235 30.497986 15671.945312 15671.945312 15671.945312 15671.945312 -2103.403809 -2103.403809 -1322.070312 -106.755981 -106.755981 -106.755981 -48.669987 -48.669987 -14926.272461 -25365.072266 -15.848166 -51.922600 0.114297 0.326635 0.202694 0.064840 0.455060 0.321058 0.119914
2 2 -29412.171875 14884.777344 681.438416 681.438416 689.653870 -293.755493 -231.623169 -42.849586 -18.094606 1.321061 32.943748 14884.777344 14884.777344 14884.777344 14884.777344 -2212.348145 -2212.348145 -1424.661621 -98.073677 -98.073677 -98.073677 -41.496658 -41.496658 -15664.468750 -25598.054688 -30.550636 -47.123726 0.122675 0.359847 0.231283 0.080323 0.486493 0.344262 0.107309
3 3 -30445.765625 15459.026367 676.766479 676.766479 542.113647 -296.310425 -255.682785 -57.522942 -9.102396 7.696231 29.914497 15459.025391 15459.026367 15459.025391 15459.025391 -2068.183105 -2068.183105 -1420.056274 -138.799286 -138.799286 -138.799286 -49.381828 -49.381828 -16365.539062 -26432.148438 -13.933872 -55.519943 0.139296 0.403858 0.262963 0.091190 0.537068 0.403004 0.172659
4 4 -31220.523438 15123.919922 829.743713 829.743713 538.306824 -228.928253 -236.550522 -15.065624 -9.895781 33.727947 34.547218 15123.919922 15123.919922 15123.920898 15123.919922 -2320.590088 -2320.590088 -1449.679077 -136.157806 -136.157806 -136.157806 -35.716927 -35.716927 -16856.062500 -26418.031250 -15.670280 -59.280117 0.141892 0.391163 0.247138 0.080156 0.514053 0.363557 0.145905
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
2495 2495 -53475.191406 5437.392090 164.572510 164.572510 165.457443 -477.048065 -511.165619 -242.537964 -54.973854 1.879056 31.301361 5437.391602 5437.391602 5437.392090 5437.392090 -4616.214844 -4616.214844 -2063.680664 -570.688721 -570.688721 -570.688721 -89.135315 -89.135315 -21413.382812 -29130.757812 -24.871449 -83.684990 0.457792 0.851996 0.708565 0.328269 0.880591 0.755263 0.376886
2496 2496 -53520.351562 5175.629883 154.459518 154.459518 152.555496 -486.757507 -500.540131 -269.931396 -63.669117 1.586104 31.530334 5175.629883 5175.629883 5175.629395 5175.629883 -4522.477539 -4522.477539 -2041.882324 -564.579285 -564.579285 -564.579285 -79.343590 -79.343590 -21510.435547 -28898.789062 -22.918919 -77.096138 0.462405 0.846018 0.698053 0.302183 0.867402 0.726392 0.320461
2497 2497 -53638.917969 5122.781250 206.524231 206.524231 158.441833 -490.239624 -488.299042 -293.155457 -67.977005 7.043468 30.395050 5122.780762 5122.781250 5122.781250 5122.781250 -4569.411133 -4569.411133 -2059.089355 -568.095093 -568.095093 -568.095093 -83.955185 -83.955185 -21381.626953 -29062.070312 -20.984013 -81.548218 0.468497 0.851702 0.707081 0.320519 0.883860 0.752358 0.366204
2498 2498 -53591.886719 5266.937012 169.046600 169.046600 204.129654 -461.154663 -506.339172 -266.694275 -63.712521 3.694311 30.305124 5266.937500 5266.937012 5266.937500 5266.937012 -4597.342285 -4597.342285 -2070.128906 -548.405273 -548.405273 -548.405273 -92.388741 -92.388741 -21429.570312 -29113.556641 -43.914787 -75.149956 0.480770 0.844070 0.702612 0.333865 0.884566 0.755895 0.355177
2499 2499 -53582.320312 5117.964844 175.550415 175.550415 204.601837 -479.894745 -484.111603 -282.617310 -61.933254 0.919242 30.016945 5117.964844 5117.964844 5117.964844 5117.964844 -4558.850586 -4558.850586 -2031.912842 -604.608887 -604.608887 -604.608887 -91.409164 -91.409164 -21395.230469 -29015.673828 -32.791344 -74.681427 0.459197 0.850982 0.709164 0.320147 0.880967 0.754800 0.367179

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
0 0 -25206.402344 14888.933594 1622.723999 1622.723999 443.290894 -259.304504 -249.766312 -12.799174 -10.329629 2.744922 30.028885 14888.933594 14888.933594 14888.933594 14888.933594 -1916.531494 -1916.531494 -1303.225342 -69.902802 -69.902802 -69.902802 -7.506907 -7.506907 -13970.867188 -24372.476562 -6.486084 -15.478305 0.099870 0.251631 0.151126 0.048272 0.344290 0.236592 0.092049
1 1 -27761.199219 15331.582031 1174.520386 1174.520386 593.834534 -245.702209 -210.734802 -28.006517 -10.816239 12.800676 32.368805 15331.582031 15331.582031 15331.582031 15331.583008 -2242.398438 -2242.398438 -1347.305054 -99.174316 -99.174316 -99.174316 -36.497581 -36.497581 -15000.968750 -25675.363281 6.906437 -16.853191 0.109846 0.287311 0.162975 0.050025 0.405244 0.260847 0.095157
2 2 -28298.675781 15438.144531 781.317261 781.317261 540.262451 -234.477036 -179.699356 -1.169111 -8.965717 27.860428 32.922264 15438.144531 15438.144531 15438.144531 15438.144531 -1967.528564 -1967.528564 -1366.320679 -103.664429 -103.664429 -103.664429 -42.383156 -42.383156 -15317.267578 -25896.791016 19.896770 -21.560810 0.127003 0.342649 0.208825 0.069164 0.530185 0.374857 0.138005
3 3 -29871.166016 15298.605469 700.552734 700.552734 575.032043 -254.174164 -194.817719 -5.042788 -16.217186 20.364546 36.145622 15298.606445 15298.605469 15298.606445 15298.605469 -1984.553833 -1984.553833 -1432.021240 -110.527596 -110.527596 -110.527596 -45.969475 -45.969475 -16087.461914 -26326.476562 -18.894012 -26.506451 0.139922 0.365916 0.224699 0.066224 0.531097 0.368005 0.116271
4 4 -30875.324219 15038.380859 808.278076 808.278076 587.150940 -270.358521 -232.139450 -9.437372 -16.307322 5.817956 35.441593 15038.380859 15038.380859 15038.380859 15038.380859 -2128.158203 -2128.158203 -1444.239014 -117.985840 -117.985840 -117.985840 -38.357944 -38.357944 -16175.599609 -26875.613281 -13.213889 -29.843327 0.144770 0.383350 0.245386 0.087162 0.562494 0.399500 0.133647
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
995 995 -53198.312500 5141.760254 183.002487 183.002487 157.588364 -490.311707 -503.223999 -276.239899 -63.831264 2.226560 29.742519 5141.760254 5141.760254 5141.759766 5141.760254 -4694.799805 -4694.799805 -1885.715210 -466.015045 -466.015045 -466.015045 -75.979294 -75.979294 -21452.902344 -28758.511719 -7.969313 -38.946800 0.285235 0.702510 0.558483 0.264023 0.811989 0.691368 0.371213
996 996 -53369.546875 5013.210938 165.501556 165.501556 151.824554 -486.544006 -509.940674 -245.161346 -64.738823 1.771675 29.964407 5013.210938 5013.210938 5013.210938 5013.210938 -4684.027344 -4684.027344 -1923.932373 -453.642761 -453.642761 -453.642761 -64.485168 -64.485168 -21528.726562 -28727.812500 -3.793143 -40.812061 0.271834 0.713309 0.562752 0.250169 0.815138 0.681213 0.320452
997 997 -53290.480469 5028.659668 172.207855 172.207855 157.845108 -489.188110 -500.046631 -271.910889 -61.530422 1.522354 29.801796 5028.659668 5028.659668 5028.660156 5028.659668 -4547.985352 -4547.985352 -1923.587036 -445.587585 -445.587585 -445.587585 -68.435013 -68.435013 -21466.832031 -28836.519531 -32.346874 -38.352791 0.268783 0.719337 0.571652 0.241989 0.835272 0.706192 0.324867
998 998 -53161.734375 5122.421875 195.892181 195.892181 180.739471 -488.787628 -507.089752 -274.461761 -67.300316 0.631500 29.636150 5122.421875 5122.421387 5122.421875 5122.421875 -4684.926758 -4684.926758 -1913.003296 -477.447021 -477.447021 -477.447021 -71.018867 -71.018867 -21506.976562 -28633.685547 -30.891853 -37.316353 0.270821 0.720973 0.579961 0.275394 0.850386 0.732792 0.374412
999 999 -53434.363281 4853.821289 219.476242 219.476242 145.100464 -461.787689 -498.320587 -273.035126 -63.263905 0.471262 29.242758 4853.820801 4853.820801 4853.820801 4853.820801 -4697.026367 -4697.026367 -1886.687500 -455.190308 -455.190308 -455.190308 -80.925522 -80.925522 -21472.685547 -28714.750000 -42.153587 -38.456421 0.261609 0.716819 0.571952 0.257853 0.837364 0.708632 0.333209

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 -41761.898438 0.910350 -24148.511719 72.628693 174.160477 -492.280762 -496.281281 -299.294342 -65.298683 1.116977 32.101761 4982.414062 4982.413574 4982.414062 4982.413574 -5116.578125 -5116.578125 -3372.669434 -788.578857 -788.578857 -788.578857 -87.048683 -87.048683 -11913.384766 -74.894501 -172.878815 0.967220 0.916209 0.598239 0.972316 0.928374 0.626994
1 1 -41800.851562 0.925077 -24174.560547 72.544197 165.041199 -480.148041 -500.106628 -274.647064 -63.609055 0.172277 30.470150 4873.564453 4873.563965 4873.564453 4873.564453 -5086.610840 -5086.610840 -3325.110840 -782.810059 -782.810059 -782.810059 -82.263390 -82.263390 -11943.054688 -62.340652 -170.711533 0.961359 0.901237 0.553961 0.959051 0.895604 0.541304
2 2 -41745.632812 0.851793 -24189.828125 91.083344 172.127487 -461.366455 -494.880646 -291.325989 -64.341721 0.568332 31.616669 5072.878906 5072.878906 5072.878906 5072.878906 -5138.804688 -5138.804688 -3395.028320 -788.807373 -788.807373 -788.807373 -79.207420 -79.207420 -11924.847656 -110.780952 -177.901993 0.956154 0.888922 0.523362 0.959400 0.896102 0.538825
3 3 -41892.742188 0.886018 -24129.302734 51.578461 184.347809 -506.004578 -479.178986 -276.171234 -59.279732 1.358014 31.211781 4813.846680 4813.846680 4813.846680 4813.846680 -5095.519531 -5095.519531 -3352.770020 -804.503418 -804.503418 -804.503418 -84.143646 -84.143646 -11909.226562 -111.979210 -170.268646 0.958449 0.894621 0.536966 0.965112 0.908757 0.528775
4 4 -41876.664062 0.916250 -24161.134766 88.812004 172.881195 -492.063080 -504.710785 -276.787720 -68.570572 2.135250 31.823505 4870.122070 4870.122070 4870.122070 4870.121582 -5147.251953 -5147.251953 -3358.418945 -787.141235 -787.141235 -787.141235 -80.618805 -80.618805 -11920.861328 -82.409134 -165.794693 0.961920 0.902782 0.556735 0.964789 0.908582 0.554520
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
245 245 -44218.445312 0.910282 -24328.419922 53.136841 105.146851 -508.894928 -512.151855 -310.310913 -76.330750 1.095423 32.260189 3308.041260 3308.041016 3308.041016 3308.041260 -5325.213867 -5325.213867 -3454.216309 -854.620117 -854.620117 -854.620117 -80.490845 -80.490845 -11994.501953 -103.738083 -171.799683 0.811682 0.621376 0.232360 0.960487 0.898759 0.543176
246 246 -44081.304688 0.869112 -24308.099609 58.100685 124.604019 -516.636841 -512.087708 -298.018494 -66.826683 0.774467 31.588593 3324.935547 3324.935547 3324.935303 3324.935547 -5292.588867 -5292.588867 -3438.642822 -846.340088 -846.340088 -846.340088 -80.363419 -80.363419 -11994.630859 -101.965279 -167.570999 0.791153 0.591524 0.220003 0.954601 0.887171 0.539565
247 247 -43920.828125 0.884810 -24328.154297 56.388245 144.464966 -480.523895 -513.313965 -315.142426 -69.884544 0.503394 31.224329 3461.500488 3461.500732 3461.500488 3461.500488 -5305.854004 -5305.854004 -3445.930420 -833.889404 -833.889404 -833.889404 -89.813217 -89.813217 -11970.527344 -95.103828 -169.201202 0.787529 0.580062 0.186515 0.943319 0.861994 0.483121
248 248 -44173.488281 0.905386 -24323.910156 47.034550 116.440445 -496.897888 -512.915588 -299.912720 -70.170296 0.917068 32.955006 3295.433594 3295.433350 3295.433350 3295.433594 -5339.147949 -5339.147949 -3465.430420 -837.304932 -837.304932 -837.304932 -79.374741 -79.374741 -11985.265625 -90.838982 -167.697739 0.819279 0.636080 0.250024 0.955081 0.885529 0.497608
249 249 -44217.929688 0.881131 -24323.048828 57.388577 98.314499 -520.283386 -528.126709 -308.141663 -77.708755 0.809490 32.398632 3235.748535 3235.749023 3235.748779 3235.749023 -5325.193848 -5325.193848 -3415.360840 -816.455688 -816.455688 -816.455688 -80.864258 -80.864258 -11989.242188 -102.605324 -158.091797 0.811218 0.621944 0.227924 0.944277 0.866626 0.491240

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
0 0 -26055.074219 14611.609375 1475.164307 1475.164307 486.222717 -278.954285 -289.858887 2.202472 -13.879367 3.509465 30.581259 14611.609375 14611.609375 14611.609375 14611.609375 -2161.553223 -2161.553223 -1372.686157 -110.347130 -110.347130 -110.347130 -24.860693 -24.860693 -13740.677734 -24665.437500 8.046674 -14.651911 0.095393 0.232327 0.130396 0.041287 0.327289 0.213114 0.065137
1 1 -28105.531250 14708.051758 1085.279053 1085.279053 597.548157 -256.803162 -163.553772 -10.235674 -15.704374 14.783965 31.881634 14708.050781 14708.050781 14708.050781 14708.050781 -1990.168701 -1990.168701 -1425.000732 -91.456085 -91.456085 -91.456085 -28.129639 -28.129639 -15248.490234 -25296.992188 3.433063 -20.598919 0.124835 0.290810 0.162915 0.046031 0.429931 0.282840 0.090656
2 2 -30737.076172 14977.237305 761.495178 761.495178 474.626617 -269.960083 -176.069122 -45.432426 -10.508386 10.123620 34.676281 14977.237305 14977.237305 14977.237305 14977.236328 -2387.196045 -2387.196045 -1527.652954 -131.600739 -131.600739 -131.600739 -34.940502 -34.940502 -16225.667969 -26149.013672 -10.941273 -27.034817 0.136867 0.363640 0.216452 0.065606 0.515217 0.356856 0.131220
3 3 -31992.298828 14479.767578 827.625122 827.625122 488.996155 -287.505127 -163.447815 -24.378351 -11.416314 7.240215 35.883739 14479.767578 14479.767578 14479.767578 14479.768555 -2599.467041 -2599.467041 -1503.030029 -186.050934 -186.050934 -186.050934 -44.119576 -44.119576 -16509.542969 -26469.945312 -6.948917 -26.797983 0.150112 0.381188 0.234538 0.076792 0.567518 0.407102 0.142915
4 4 -32408.623047 15038.445312 790.083191 790.083191 465.865448 -170.492569 -201.070404 -26.923603 -8.823274 9.521983 35.753136 15038.445312 15038.445312 15038.445312 15038.445312 -2484.333740 -2484.333740 -1530.595947 -170.920425 -170.920425 -170.920425 -48.405529 -48.405529 -17118.199219 -26945.984375 -4.346951 -39.110825 0.164606 0.411845 0.260689 0.077279 0.594433 0.418193 0.153263
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
245 245 -52805.187500 5356.251953 241.396469 241.396469 189.596176 -495.454498 -510.843353 -293.967560 -68.695358 0.072573 31.251450 5356.251953 5356.251953 5356.251953 5356.251953 -4565.055664 -4565.055664 -1862.156738 -561.549194 -561.549194 -561.549194 -78.134995 -78.134995 -21301.222656 -28807.894531 -32.113346 -48.690205 0.360319 0.765857 0.617882 0.277626 0.833808 0.678485 0.314656
246 246 -52704.945312 5457.871094 246.697586 246.697586 141.143295 -478.458130 -495.206543 -246.147720 -62.075897 1.654974 31.483849 5457.871582 5457.871094 5457.871094 5457.871094 -4567.626953 -4567.626953 -1952.933228 -588.681030 -588.681030 -588.681030 -80.563721 -80.563721 -21582.324219 -28452.466797 -33.545326 -45.767868 0.350887 0.756922 0.610712 0.281962 0.836410 0.682069 0.301495
247 247 -52878.089844 5300.280762 227.284409 227.284409 155.245255 -496.128326 -511.833344 -282.354828 -66.476852 0.410354 30.191788 5300.280762 5300.280762 5300.281250 5300.280762 -4488.004883 -4488.004883 -1902.074951 -542.840210 -542.840210 -542.840210 -74.322380 -74.322380 -21498.025391 -28654.859375 -29.571220 -47.016464 0.354038 0.752613 0.609176 0.288911 0.827491 0.673209 0.313865
248 248 -52802.250000 5291.218750 218.353119 218.353119 194.409546 -491.582214 -520.871887 -269.095306 -70.452377 0.228974 31.114557 5291.219238 5291.219238 5291.219238 5291.218750 -4590.050293 -4590.050293 -1939.538330 -526.504639 -526.504639 -526.504639 -85.839371 -85.839371 -21523.953125 -28465.417969 -7.857483 -48.392517 0.347248 0.762764 0.607580 0.260169 0.840591 0.680742 0.294070
249 249 -53092.933594 5280.054688 219.372131 219.372131 156.199158 -494.391846 -498.909271 -280.819458 -65.666443 0.121710 31.841377 5280.054688 5280.055176 5280.055176 5280.054688 -4638.664062 -4638.664062 -1940.112305 -561.190186 -561.190186 -561.190186 -80.491272 -80.491272 -21599.785156 -28550.140625 -23.714056 -48.617424 0.366824 0.746549 0.598196 0.268912 0.814138 0.652709 0.283848

250 rows × 35 columns

add the bond between protein and DNA. to ensure they are in native contact.


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 -467.744507 15207.207031 1520.193359 1520.193359 579.519226 -268.620789 -194.005508 -14.522429 -12.689537 10.890283 33.702301 15207.207031 15207.205078 15207.206055 15207.206055 -2289.256836 -2289.256836 -1271.702148 -49.685577 -49.685577 -49.685577 -8.200542 -8.200542 -13690.828125 -3.311884 -16.881588 0.090526 0.211695 0.114064 0.032346 0.287664 0.184878 0.070790
1 1 -2798.031982 15377.487305 998.145203 998.145203 599.738159 -250.527512 -221.077362 -0.449299 -9.358805 3.007111 31.417149 15377.488281 15377.488281 15377.487305 15377.488281 -2309.317871 -2309.317871 -1352.401123 -108.884064 -108.884064 -108.884064 -16.436724 -16.436724 -15522.000000 -7.321196 -10.672285 0.105448 0.292093 0.170604 0.051475 0.405013 0.264687 0.091932
2 2 -3857.514648 15497.428711 625.153137 625.153137 640.194763 -299.430054 -213.524994 -35.315254 -11.355023 7.521466 31.429810 15497.429688 15497.429688 15497.429688 15497.428711 -2363.800293 -2363.800293 -1356.808716 -131.373459 -131.373459 -131.373459 -25.262691 -25.262691 -16218.927734 22.374834 -26.619638 0.122706 0.367372 0.235668 0.074226 0.516698 0.385708 0.146474
3 3 -4783.910156 14987.666016 653.489563 653.489563 568.696106 -251.788544 -274.831451 -18.307970 -12.378512 24.416430 34.140175 14987.666016 14987.666016 14987.666016 14987.666016 -2451.455566 -2451.455566 -1369.601074 -145.328888 -145.328888 -145.328888 -21.942541 -21.942541 -16503.544922 23.778734 -27.755821 0.125613 0.392918 0.245352 0.075107 0.533347 0.388480 0.131591
4 4 -6164.950684 14548.517578 584.299255 584.299255 571.186218 -278.178009 -252.683212 -42.726120 -14.628922 8.432912 31.980976 14548.517578 14548.516602 14548.516602 14548.516602 -2719.712158 -2719.712158 -1389.759033 -170.839462 -170.839462 -170.839462 -19.496864 -19.496864 -16964.777344 -28.531132 -28.971828 0.136800 0.424902 0.282727 0.093390 0.592163 0.446515 0.167316
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
245 245 -25648.447266 5185.463867 262.024719 262.024719 204.918793 -472.856964 -424.063934 -244.047012 -41.686195 1.618226 30.529890 5185.464355 5185.463867 5185.464355 5185.463867 -4939.442383 -4939.442383 -1719.309326 -566.983643 -566.983643 -566.983643 -49.886520 -49.886520 -22796.486328 -35.186382 -44.623322 0.237804 0.640490 0.488910 0.201616 0.731321 0.593087 0.286350
246 246 -25657.988281 5115.803711 278.873291 278.873291 182.550201 -487.786346 -448.062256 -232.840027 -45.712330 1.841576 31.543209 5115.804199 5115.803711 5115.804199 5115.803711 -4837.254883 -4837.254883 -1689.188721 -591.437744 -591.437744 -591.437744 -51.857822 -51.857822 -22800.410156 -41.508408 -44.138500 0.232322 0.650281 0.502783 0.211200 0.734672 0.598982 0.273802
247 247 -25624.839844 5297.968262 268.407379 268.407379 185.669815 -480.746216 -452.739044 -248.372147 -43.957413 6.348877 30.705921 5297.968750 5297.968750 5297.968750 5297.968750 -4977.410156 -4977.410156 -1736.390381 -600.064331 -600.064331 -600.064331 -57.784294 -57.784294 -22727.710938 -44.206558 -46.211796 0.241285 0.663697 0.520233 0.229631 0.742955 0.617334 0.306413
248 248 -26098.644531 4936.685547 264.826477 264.826477 214.620193 -499.446625 -431.650757 -239.861221 -43.219990 16.882938 32.271507 4936.685547 4936.685547 4936.686035 4936.685547 -5063.604492 -5063.604492 -1759.790039 -572.662720 -572.662720 -572.662720 -45.878147 -45.878147 -22812.609375 -49.320580 -47.499310 0.245363 0.649832 0.500868 0.216060 0.720795 0.584979 0.271957
249 249 -26010.326172 4996.624023 226.313263 226.313263 182.577637 -471.651550 -436.782349 -245.364853 -40.691994 1.751009 31.328274 4996.624023 4996.624512 4996.624023 4996.624023 -4926.836914 -4926.836914 -1747.076904 -619.638855 -619.638855 -619.638855 -37.095051 -37.095051 -22826.738281 -54.773743 -43.887894 0.239968 0.653474 0.509276 0.215111 0.735776 0.601679 0.266586

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
0 0 -2538.068604 14986.912109 249.780426 589.105530 -220.482941 -271.074249 -53.770676 -23.907406 4.144581 36.603165 14986.912109 14986.912109 14986.912109 14986.912109 -2194.646973 -2194.646973 -1196.337646 -67.790588 -67.790588 -67.790588 -0.000000 -0.000000 -14376.100586 -0.151445 -0.404284 0.050053 0.002496 0.000258 0.000000 2.517432e-02 0.007734 0.001945
1 1 -4030.669922 14894.742188 263.292175 521.607605 -220.119904 -259.365967 -20.630465 -7.958625 2.017937 31.728765 14894.742188 14894.742188 14894.742188 14894.742188 -2355.711670 -2355.711670 -1205.842407 -84.849312 -84.849312 -84.849312 -0.000014 -0.000014 -15586.259766 -1.052077 -2.338029 0.055656 0.009359 0.003951 0.000836 4.474950e-02 0.024538 0.008499
2 2 -4048.184570 15727.791016 194.440674 647.218323 -317.517609 -278.889038 -14.401599 -7.779828 7.600757 28.845783 15727.791016 15727.791992 15727.792969 15727.791016 -2468.952637 -2468.952637 -1187.520630 -121.524826 -121.524826 -121.524826 -0.000000 -0.000000 -16252.882812 -1.606207 -3.079109 0.058463 0.008853 0.003818 0.001052 3.657156e-02 0.015639 0.006472
3 3 -5612.025879 14738.788086 268.273865 526.792847 -271.898621 -205.735336 -21.480417 -4.720959 10.634282 30.609665 14738.788086 14738.788086 14738.788086 14738.789062 -2659.316895 -2659.316895 -1211.271606 -132.490753 -132.490753 -132.490753 -5.180204 -5.180204 -16673.375000 -0.411722 -1.306422 0.058423 0.004342 0.000798 0.000001 2.682990e-02 0.009082 0.001930
4 4 -6499.157227 15152.313477 193.379486 526.643921 -316.522858 -247.433395 -14.709517 -6.676085 0.159797 31.299288 15152.313477 15152.313477 15152.312500 15152.314453 -2874.054443 -2874.054443 -1247.669189 -165.306396 -165.306396 -165.306396 -10.483606 -10.483606 -17517.556641 -0.057370 -2.562263 0.067962 0.007466 0.002941 0.000246 3.707107e-02 0.016892 0.005725
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
3745 3745 -27188.796875 5101.370117 94.965935 147.976257 -490.117493 -507.364319 -290.380859 -66.310608 2.939061 31.392286 5101.370117 5101.370605 5101.370605 5101.370117 -5057.494141 -5057.494141 -1986.205322 -760.203003 -760.203003 -760.203003 -79.727715 -79.727715 -23330.058594 0.000000 0.000000 0.421944 0.000000 0.000000 0.000000 1.023572e-123 0.000000 0.000000
3746 3746 -27511.511719 4888.036133 60.601658 157.436279 -479.589111 -494.821686 -294.324799 -61.335056 0.567451 30.713554 4888.036133 4888.036133 4888.036133 4888.036133 -5092.290039 -5092.290039 -2061.340332 -753.228027 -753.228027 -753.228027 -88.688499 -88.688499 -23323.662109 0.000000 0.000000 0.414109 0.000000 0.000000 0.000000 3.673208e-127 0.000000 0.000000
3747 3747 -27604.695312 4885.696289 69.465485 163.667725 -496.187195 -509.731812 -271.164398 -67.123581 0.669205 31.481956 4885.696289 4885.696289 4885.696289 4885.696289 -5105.923828 -5105.923828 -2008.518799 -803.723511 -803.723511 -803.723511 -84.795166 -84.795166 -23408.925781 0.000000 0.000000 0.417003 0.000000 0.000000 0.000000 2.812107e-125 0.000000 0.000000
3748 3748 -27200.857422 5020.501953 86.356964 151.850235 -473.954956 -521.767456 -252.832153 -63.002563 2.266031 29.502819 5020.501953 5020.501953 5020.501953 5020.501953 -5060.547852 -5060.547852 -1987.681641 -739.483276 -739.483276 -739.483276 -79.938858 -79.938858 -23312.521484 0.000000 0.000000 0.394255 0.000000 0.000000 0.000000 9.930814e-125 0.000000 0.000000
3749 3749 -27501.417969 4946.089844 79.462135 145.748306 -490.710022 -523.619873 -295.614136 -69.890907 3.562120 29.753006 4946.089355 4946.089844 4946.089844 4946.089844 -5087.288086 -5087.288086 -2011.557129 -789.530396 -789.530396 -789.530396 -77.314934 -77.314934 -23360.912109 0.000000 0.000000 0.407119 0.000000 0.000000 0.000000 2.926768e-124 0.000000 0.000000

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 -311.528137 -278.608307 -75.776825 -24.425158 10.696676 34.154716 15458.159180 15458.158203 15458.159180 15458.158203 -2261.000977 -2261.000977 -1173.311890 -86.364052 -86.364052 -86.364052 -3.678096 -3.678096 -14852.208984 -0.024233 0.0 0.055139 0.004966 0.001255 0.000035 3.215528e-02 1.247164e-02 0.001705
1 1 -4856.808594 15053.111328 280.692322 529.039185 -284.241699 -297.870117 -43.890682 -16.672424 34.260136 29.634205 15053.111328 15053.111328 15053.111328 15053.111328 -2533.397949 -2533.397949 -1182.528564 -107.517365 -107.517365 -107.517365 -1.013446 -1.013446 -16316.458984 -0.038448 0.0 0.063291 0.013534 0.005608 0.001226 5.294800e-02 2.107635e-02 0.003382
2 2 -6045.305664 14766.082031 342.805603 564.643494 -327.364502 -279.434326 5.788673 -12.714335 7.471346 27.266710 14766.082031 14766.082031 14766.082031 14766.081055 -2727.257080 -2727.257080 -1239.440674 -152.309570 -152.309570 -152.309570 -0.008998 -0.008998 -17020.804688 -0.126714 0.0 0.068554 0.018992 0.009338 0.002568 5.895488e-02 2.252176e-02 0.004478
3 3 -5234.680664 15804.160156 227.210083 430.859741 -264.294556 -266.601837 -27.231817 -9.361356 3.832142 27.980145 15804.161133 15804.161133 15804.160156 15804.161133 -2330.283203 -2330.283203 -1235.837646 -134.893738 -134.893738 -134.893738 -0.000034 -0.000034 -17460.164062 -0.154700 0.0 0.076801 0.014377 0.006719 0.001563 6.721424e-02 3.208169e-02 0.008095
4 4 -7113.800781 15141.484375 216.128510 614.363892 -268.998718 -309.322662 -31.835688 -8.322509 4.489673 28.239109 15141.483398 15141.483398 15141.482422 15141.482422 -2955.866699 -2955.866699 -1274.805054 -179.790817 -179.790817 -179.790817 -2.232126 -2.232126 -18086.855469 -0.608338 0.0 0.086556 0.024114 0.014345 0.005613 8.800613e-02 4.455577e-02 0.010323
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
995 995 -27147.880859 4931.836914 103.192078 172.973129 -493.601959 -503.158936 -297.705078 -67.222214 1.240260 30.747005 4931.836914 4931.836914 4931.836914 4931.836914 -5077.621094 -5077.621094 -1965.320190 -734.552368 -734.552368 -734.552368 -74.725517 -74.725517 -23174.175781 0.000000 0.0 0.213662 0.000000 0.000000 0.000000 7.922485e-24 2.179693e-60 0.000000
996 996 -27026.101562 5110.825195 88.514496 174.461517 -487.750732 -498.453522 -278.084595 -72.909920 3.643381 30.995527 5110.825195 5110.825195 5110.825195 5110.825684 -5099.282227 -5099.282227 -1974.555664 -683.314453 -683.314453 -683.314453 -84.415817 -84.415817 -23255.986328 0.000000 0.0 0.212019 0.000000 0.000000 0.000000 1.962429e-22 1.614620e-56 0.000000
997 997 -27201.800781 4946.042480 93.343201 180.743912 -484.308777 -504.591522 -266.799957 -59.651524 3.094773 31.844486 4946.042480 4946.042480 4946.041992 4946.042480 -5145.367188 -5145.367188 -1993.890869 -710.146729 -710.146729 -710.146729 -80.763527 -80.763527 -23211.566406 0.000000 0.0 0.216058 0.000000 0.000000 0.000000 2.988445e-24 9.024876e-62 0.000000
998 998 -26719.044922 5396.250977 73.735046 140.999588 -490.173889 -503.805237 -262.737915 -61.965893 1.378956 31.983120 5396.250977 5396.251465 5396.250977 5396.250977 -5053.323242 -5053.323242 -1982.187378 -726.015869 -726.015869 -726.015869 -75.201401 -75.201401 -23208.195312 0.000000 0.0 0.212536 0.000000 0.000000 0.000000 8.730197e-25 1.854451e-63 0.000000
999 999 -26852.597656 5124.725586 77.237061 192.921860 -479.260010 -515.713684 -287.638824 -61.810482 2.197131 30.146061 5124.725098 5124.725586 5124.725586 5124.725586 -5041.493164 -5041.493164 -1981.614502 -705.420654 -705.420654 -705.420654 -73.504845 -73.504845 -23133.582031 0.000000 0.0 0.212500 0.000000 0.000000 0.000000 8.523705e-24 1.062988e-60 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 -2665.194092 15103.355469 222.010651 567.488281 -236.233765 -295.434540 -48.607677 -15.259773 30.949139 30.157701 15103.356445 15103.356445 15103.356445 15103.356445 -2268.554443 -2268.554443 -1162.637939 -46.586327 -46.586327 -46.586327 0.000000 0.000000 -14545.910156 -0.005724 0.0 0.050982 0.015000 0.006443 0.002086 0.056451 0.023838 0.002671
1 1 -4376.646484 14708.171875 252.368164 486.690155 -288.714661 -210.117615 -31.429754 -10.748849 1.837250 31.463348 14708.171875 14708.171875 14708.171875 14708.171875 -2428.259766 -2428.259766 -1209.350586 -91.300095 -91.300095 -91.300095 -0.000389 -0.000389 -15587.253906 -0.085095 0.0 0.052593 0.018345 0.010604 0.002929 0.062168 0.029153 0.007352
2 2 -5651.489258 14816.953125 253.354813 537.718506 -288.788666 -324.398102 -22.928154 -10.653888 1.819814 30.481457 14816.953125 14816.953125 14816.953125 14816.952148 -2711.393555 -2711.393555 -1212.394287 -134.685745 -134.685745 -134.685745 -0.000000 -0.000000 -16585.753906 -0.895276 0.0 0.060133 0.009598 0.004047 0.001075 0.035339 0.013064 0.004509
3 3 -6229.262695 14835.302734 253.330063 531.099609 -288.926697 -237.968445 -17.738323 -12.508602 3.792984 30.654873 14835.302734 14835.302734 14835.302734 14835.302734 -2744.128418 -2744.128418 -1230.319214 -152.523010 -152.523010 -152.523010 0.000000 0.000000 -17199.398438 -0.000713 0.0 0.063260 0.004749 0.001234 0.000226 0.025993 0.009554 0.002868
4 4 -5733.814941 14955.227539 209.262573 658.260132 -271.505859 -235.037003 -1.215147 -6.876260 2.102283 27.037155 14955.226562 14955.226562 14955.227539 14955.228516 -2761.312500 -2761.312500 -1221.755127 -145.201508 -145.201508 -145.201508 -2.058842 -2.058842 -16940.798828 -0.017111 0.0 0.065850 0.006835 0.001878 0.000066 0.028084 0.012798 0.002621
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -26764.734375 5119.753418 74.306915 134.677322 -497.534180 -497.357208 -267.745514 -61.020782 0.920776 33.410576 5119.753418 5119.753418 5119.753906 5119.753418 -5020.172852 -5020.172852 -1937.115723 -642.216797 -642.216797 -642.216797 -60.463142 -60.463142 -23130.085938 -14.660761 0.0 0.186307 0.197373 0.134399 0.052072 0.307686 0.232751 0.096045
746 746 -26793.425781 5199.767578 75.535492 160.246704 -486.733154 -494.721985 -267.403290 -68.834160 3.259102 32.107140 5199.768066 5199.767578 5199.767578 5199.768066 -5090.809570 -5090.809570 -2012.660889 -660.787964 -660.787964 -660.787964 -64.517212 -64.517212 -23101.767578 -16.678106 0.0 0.191663 0.196840 0.135039 0.049752 0.311829 0.239296 0.111678
747 747 -27015.636719 5086.201660 70.449234 160.201813 -486.951263 -493.339539 -285.030334 -70.170181 0.497078 30.743246 5086.202148 5086.202148 5086.202148 5086.202148 -5084.793945 -5084.793945 -2043.965332 -671.755310 -671.755310 -671.755310 -50.100403 -50.100403 -23160.011719 -18.202587 0.0 0.190715 0.202526 0.142042 0.056540 0.308763 0.234284 0.094402
748 748 -26648.906250 5183.793945 74.939865 172.749924 -492.901886 -495.294739 -294.297852 -69.959084 3.003781 31.331415 5183.793945 5183.793945 5183.793945 5183.793945 -4971.945312 -4971.945312 -1938.311035 -693.062195 -693.062195 -693.062195 -61.316666 -61.316666 -23086.417969 -11.763299 0.0 0.192506 0.184869 0.123867 0.044213 0.291462 0.214939 0.081206
749 749 -26564.939453 5200.723145 80.046982 159.177444 -499.012085 -494.364563 -281.278656 -62.378822 1.121310 33.269279 5200.723145 5200.722656 5200.723145 5200.723145 -5019.849609 -5019.849609 -1929.020996 -639.507324 -639.507324 -639.507324 -75.359619 -75.359619 -23023.156250 -15.924158 0.0 0.186333 0.193042 0.139059 0.056731 0.284373 0.206734 0.089634

750 rows × 33 columns

not able to fold. also fold around the DNA(which I don't want.)

I need consider run the protein only folding first. (by setting the elect_PD to 0 first)

at the same time, I could double the fm potential strength.


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
0 0 3333.349609 0.044572 -3664.265625 257.364899 448.487030 -320.285950 -346.918549 -63.540119 -18.141821 20.633106 31.115551 16154.539062 16154.540039 16154.540039 16154.540039 -2062.196777 -2062.196777 -1913.081299 -20.996777 -20.996777 -20.996777 -6.997639 -6.997639 -5153.212891 -0.037380 -9.176972 0.011396 0.004344 0.000998 0.049455 0.022624 0.004845
1 1 4573.924805 0.043466 -3456.186035 275.213715 600.825745 -262.539795 -266.550934 -21.598471 -6.922228 23.170530 33.710800 17000.748047 17000.748047 17000.748047 17000.748047 -2102.938721 -2102.938721 -1929.632568 -10.261171 -10.261171 -10.261171 -0.438795 -0.438795 -5289.495117 -1.149980 -12.090732 0.011540 0.005091 0.000601 0.044716 0.023299 0.007402
2 2 3927.585938 0.047009 -3546.894043 184.192001 643.550903 -307.681580 -248.466187 -8.262829 -15.520299 0.465830 33.290462 16682.500000 16682.500000 16682.500000 16682.500000 -2111.381592 -2111.381592 -1967.076172 -16.796186 -16.796186 -16.796186 -0.000022 -0.000022 -5385.308594 -0.153467 -8.945887 0.014930 0.008347 0.003033 0.059800 0.030023 0.006928
3 3 2847.348389 0.048234 -3900.821777 258.141754 745.398682 -243.835571 -217.084274 8.502748 -15.434340 1.406526 34.040352 15771.925781 15771.925781 15771.925781 15771.925781 -2105.030762 -2105.030762 -1935.426270 -29.398438 -29.398438 -29.398438 -0.000000 -0.000000 -5516.948242 -0.009942 -8.142038 0.009144 0.004726 0.001268 0.039800 0.018113 0.005726
4 4 3664.427734 0.046618 -3873.283203 276.414185 494.399597 -327.849426 -214.793625 -88.643852 -21.324875 12.332932 33.309967 16669.523438 16669.523438 16669.525391 16669.525391 -2025.959717 -2025.959717 -1978.667236 -23.655382 -23.655382 -23.655382 -0.000000 -0.000000 -5264.561035 0.000000 -2.868078 0.004636 0.001378 0.000137 0.031072 0.014587 0.002754
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -29629.609375 0.164252 -13890.210938 92.670929 161.004425 -481.356628 -513.171570 -267.478180 -67.744888 0.838159 32.005920 5141.227539 5141.227051 5141.227539 5141.227539 -5073.194336 -5073.194336 -3023.112061 -628.009277 -628.009277 -628.009277 -73.901337 -73.901337 -10837.041016 -21.610207 -180.809433 0.071989 0.034812 0.010080 0.296603 0.206923 0.076718
746 746 -30399.722656 0.164833 -14134.255859 70.241409 180.417374 -481.053741 -506.749359 -256.430664 -68.001938 4.444097 31.865253 5052.570801 5052.570801 5052.570801 5052.570312 -5203.379883 -5203.379883 -3223.440674 -686.092590 -686.092590 -686.092590 -86.287643 -86.287643 -10891.375000 -42.734509 -159.730835 0.065753 0.031945 0.008992 0.276616 0.181362 0.045515
747 747 -30158.404297 0.170718 -14023.467773 76.682755 167.771484 -494.236115 -503.929077 -268.584473 -61.445007 0.760293 31.906912 4996.554688 4996.554688 4996.554688 4996.554688 -5128.601562 -5128.601562 -3163.721436 -588.874634 -588.874634 -588.874634 -73.468544 -73.468544 -10881.718750 -69.959839 -174.360184 0.071927 0.036092 0.009893 0.288104 0.192306 0.055870
748 748 -29949.449219 0.173145 -13916.080078 74.562141 203.066803 -472.787445 -474.417542 -267.469269 -68.739700 4.921869 31.853222 5076.749023 5076.749023 5076.749512 5076.749023 -5136.905273 -5136.905273 -3106.018799 -653.154846 -653.154846 -653.154846 -77.826202 -77.826202 -10949.002930 -35.551918 -182.932312 0.068622 0.033213 0.009095 0.310627 0.217024 0.071396
749 749 -29595.912109 0.168019 -13790.462891 73.007278 177.771561 -494.367493 -521.052551 -278.169861 -66.661964 0.381318 29.333956 5146.752930 5146.752441 5146.752441 5146.752930 -5104.381836 -5104.381836 -2972.761719 -654.618164 -654.618164 -654.618164 -75.286026 -75.286026 -10856.363281 -37.807381 -171.504196 0.068770 0.034246 0.009351 0.320737 0.238736 0.092835

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
0 0 7897.604492 16284.689453 257.364899 448.486938 -320.285950 -346.918488 -63.540100 -18.141823 20.633106 31.115549 16284.690430 16284.689453 16284.689453 16284.689453 -2062.196289 -2062.196289 -1147.848877 -20.996778 -20.996778 -20.996778 -6.997639 -6.997639 -5153.213867 -0.018690 -4.588486 0.044572 0.011396 0.004344 0.000998 0.049455 0.022624 0.004845
1 1 9032.875977 17225.041016 275.213715 600.825745 -262.539795 -266.550964 -21.598467 -6.922232 23.170559 33.710796 17225.041016 17225.039062 17225.041016 17225.041016 -2102.938965 -2102.938965 -1157.779541 -10.261171 -10.261171 -10.261171 -0.438794 -0.438794 -5289.496094 -0.574990 -6.045365 0.043466 0.011540 0.005091 0.000601 0.044716 0.023299 0.007402
2 2 8487.603516 16904.244141 184.191986 643.550781 -307.681519 -248.466156 -8.262804 -15.520295 0.465829 33.290459 16904.242188 16904.242188 16904.244141 16904.244141 -2111.381348 -2111.381348 -1180.245605 -16.796186 -16.796186 -16.796186 -0.000022 -0.000022 -5385.308594 -0.076733 -4.472943 0.047009 0.014930 0.008347 0.003033 0.059800 0.030023 0.006928
3 3 7669.874512 15915.384766 258.141724 745.398682 -243.835571 -217.084229 8.502745 -15.434343 1.406526 34.040348 15915.383789 15915.384766 15915.383789 15915.384766 -2105.030273 -2105.030273 -1161.255737 -29.398438 -29.398438 -29.398438 -0.000000 -0.000000 -5516.948730 -0.004971 -4.071020 0.048234 0.009144 0.004726 0.001268 0.039800 0.018113 0.005726
4 4 8475.857422 16814.769531 276.414154 494.399536 -327.849426 -214.793610 -88.643829 -21.324875 12.332931 33.309963 16814.769531 16814.769531 16814.769531 16814.769531 -2025.959351 -2025.959351 -1187.200317 -23.655382 -23.655382 -23.655382 -0.000000 -0.000000 -5264.561523 0.000000 -1.434039 0.046618 0.004636 0.001378 0.000137 0.031072 0.014587 0.002754
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -14411.169922 5159.003906 92.670937 161.004456 -481.356628 -513.171509 -267.478180 -67.744911 0.838157 32.005920 5159.003906 5159.003906 5159.003906 5159.003906 -5073.193848 -5073.193848 -1813.867310 -628.009277 -628.009277 -628.009277 -73.901337 -73.901337 -10837.041016 -10.805105 -90.404709 0.164252 0.071989 0.034812 0.010080 0.296603 0.206923 0.076718
746 746 -14859.990234 5067.438965 70.241409 180.417343 -481.053741 -506.749298 -256.430664 -68.001945 4.444091 31.865252 5067.439453 5067.438965 5067.439453 5067.439453 -5203.379883 -5203.379883 -1934.064453 -686.092651 -686.092651 -686.092651 -86.287605 -86.287605 -10891.375000 -21.367243 -79.865425 0.164833 0.065753 0.031945 0.008992 0.276616 0.181362 0.045515
747 747 -14725.578125 5018.265625 76.682739 167.771484 -494.236115 -503.929047 -268.584503 -61.445019 0.760293 31.906910 5018.265625 5018.265625 5018.265625 5018.265625 -5128.601562 -5128.601562 -1898.232910 -588.874634 -588.874634 -588.874634 -73.468544 -73.468544 -10881.720703 -34.979919 -87.180084 0.170718 0.071927 0.036092 0.009893 0.288104 0.192306 0.055870
748 748 -14662.036133 5096.433594 74.562141 203.066833 -472.787445 -474.417511 -267.469299 -68.739700 4.921869 31.853218 5096.434082 5096.433594 5096.434082 5096.434082 -5136.905273 -5136.905273 -1863.611328 -653.154785 -653.154785 -653.154785 -77.826202 -77.826202 -10949.004883 -17.775949 -91.466148 0.173145 0.068622 0.033213 0.009095 0.310627 0.217024 0.071396
749 749 -14492.439453 5166.001953 73.007263 177.771561 -494.367523 -521.052551 -278.169769 -66.661964 0.381318 29.333956 5166.001953 5166.001953 5166.001953 5166.001953 -5104.381836 -5104.381836 -1783.657104 -654.618164 -654.618164 -654.618164 -75.286026 -75.286026 -10856.365234 -18.903692 -85.752090 0.168019 0.068770 0.034246 0.009351 0.320737 0.238736 0.092835

750 rows × 33 columns

this is just due to accidentally turning off the exlcude volume term.

The exclude volume term is extremely large, probably because it penetrates the well.

This one leads to an error (Nan in energy).


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 -3502.797852 216.784088 604.204468 -236.717377 -208.287720 -18.921688 -8.608337 3.130348 32.158432 1.697562e+04 1.697562e+04 1.697562e+04 1.697562e+04 -1936.100708 -1936.100708 -1880.886230 -25.550953 -25.550953 -25.550953 0.000000 0.000000 -5118.104980 -3.051370e-01 -7.352313 0.007726 0.001614 0.000001 0.039910 0.018513 0.006575
1 1 4.839873e+03 0.041714 -3528.088379 325.486755 567.145020 -256.185516 -262.942322 -6.743728 -11.230458 11.402826 29.266075 1.694019e+04 1.694019e+04 1.694019e+04 1.694019e+04 -1941.609741 -1941.609741 -1961.023682 -16.199467 -16.199467 -16.199467 0.000000 0.000000 -5043.357422 -7.768400e-02 -6.203953 0.005758 0.001157 0.000004 0.025384 0.005885 0.000118
2 2 2.617640e+03 0.044255 -4421.237793 298.202240 638.514038 -232.071838 -229.285324 -25.919687 -10.365200 5.298040 29.606083 1.612111e+04 1.612111e+04 1.612111e+04 1.612111e+04 -2039.498779 -2039.498779 -1965.158447 -42.377365 -42.377365 -42.377365 -0.000000 -0.000000 -5504.369141 -3.443670e-01 -4.506615 0.001784 0.000184 0.000000 0.036370 0.019281 0.010063
3 3 4.212543e+03 0.040398 -3809.341064 212.715118 537.349365 -230.112457 -210.232437 -43.502811 -14.042479 1.332218 27.776890 1.700405e+04 1.700405e+04 1.700405e+04 1.700405e+04 -2051.897217 -2051.897217 -1980.648682 -22.178024 -22.178024 -22.178024 0.000000 0.000000 -5201.027344 -1.089341e+00 -6.662883 0.009209 0.002152 0.000001 0.030662 0.012871 0.002352
4 4 3.832761e+03 0.046615 -4239.596680 339.234375 632.278809 -256.294739 -243.661987 -37.535301 -9.274466 1.100596 27.413500 1.709823e+04 1.709823e+04 1.709823e+04 1.709823e+04 -1964.567627 -1964.567627 -1985.949707 -33.350712 -33.350712 -33.350712 -0.005599 -0.005599 -5484.565918 -4.862530e-01 -10.256733 0.003623 0.000374 0.000000 0.026446 0.011846 0.004285
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
1531 1531 1.835904e+11 0.086942 -6593.646484 238.697235 429.649780 -336.064484 -289.720154 -38.561596 -21.541681 5.874960 29.085995 1.165264e+04 1.165264e+04 1.165264e+04 1.165264e+04 -2677.085938 -2677.085938 -2419.899658 -120.412544 -120.412544 -120.412544 -25.282894 -25.282894 -6998.135254 1.835904e+11 -47.383690 0.004216 0.001339 0.000056 0.085576 0.061217 0.021245
1532 1532 8.644709e+11 0.092654 -6567.783203 113.813187 474.533905 -304.016663 -257.389984 -41.711903 -17.600792 4.039763 30.076029 1.185255e+04 1.185255e+04 1.185255e+04 1.185255e+04 -2627.318115 -2627.318115 -2369.522705 -74.331970 -74.331970 -74.331970 -21.423481 -21.423481 -7048.414062 8.644710e+11 -38.585617 0.002663 0.001165 0.000110 0.086274 0.061217 0.019618
1533 1533 2.203505e+08 0.091075 -5610.623535 174.252518 481.888489 -336.541382 -244.248856 -37.538986 -18.069632 14.111604 31.987423 1.181245e+04 1.181244e+04 1.181244e+04 1.181244e+04 -2825.766113 -2825.766113 -2281.926270 -85.322296 -85.322296 -85.322296 -9.331708 -9.331708 -6772.626953 2.203561e+08 -21.012661 0.002164 0.000571 0.000002 0.080959 0.053339 0.015209
1534 1534 1.914049e+08 0.094393 -5626.024414 195.901215 481.837982 -373.744324 -311.745941 -34.930965 -12.812784 8.375858 31.961525 1.160254e+04 1.160254e+04 1.160254e+04 1.160254e+04 -2882.869873 -2882.869873 -2331.750000 -70.554550 -70.554550 -70.554550 -9.107594 -9.107594 -6679.091309 1.914110e+08 -28.575493 0.004760 0.002417 0.000851 0.089953 0.063804 0.021776
1535 1535 NaN 0.000002 -0.000000 inf 187496.406250 0.000000 NaN 0.000000 0.000000 0.000000 0.000000 4.167559e+11 4.167559e+11 4.167559e+11 4.167559e+11 -309.504333 -309.504333 -1034.588135 0.000000 0.000000 0.000000 0.000000 0.000000 -0.215070 0.000000e+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000

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")


this one, the protein fold around the DNA, the shape is not normal.

still a very large elec-PD.(protein-DNA) -274 compared with -170 in native.

so I decide, to run without the elec-PD first, then bring it back after the protein is folded.


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 -591.627197 0.046304 -3750.447754 158.260208 477.781555 -350.364044 -337.554688 -101.299805 -22.383598 5.276686 30.820671 13181.394531 13181.394531 13181.394531 13181.394531 -2394.257324 -2394.257324 -1936.160889 -21.753494 -21.753494 -21.753494 -0.000183 -0.000183 -5518.477539 -0.087921 -12.437844 0.011712 0.005324 0.001517 0.037225 0.015092 0.004646
1 1 -2319.415039 0.049877 -4844.100586 181.922852 484.479065 -287.615997 -309.621948 -50.050198 -16.093178 8.403635 27.858191 12913.630859 12913.630859 12913.629883 12913.629883 -2460.115234 -2460.115234 -1933.147461 -56.040894 -56.040894 -56.040894 0.000000 0.000000 -5965.864258 -0.001348 -13.115669 0.006242 0.001881 0.000205 0.041438 0.013466 0.004934
2 2 -1437.811768 0.050713 -4784.676270 253.881271 534.353149 -265.211029 -286.368439 -31.059809 -17.342331 2.968157 32.293884 13442.193359 13442.193359 13442.193359 13442.193359 -2228.415039 -2228.415039 -1966.096802 -35.908363 -35.908363 -35.908363 0.000000 0.000000 -6071.927734 -0.917946 -15.657110 0.016637 0.009257 0.003092 0.092303 0.049256 0.009863
3 3 -2172.055664 0.053842 -4827.446289 281.847717 426.217407 -314.825897 -190.567047 -25.410385 -18.896715 9.181881 32.520653 13187.001953 13187.000977 13187.000977 13187.000977 -2508.762695 -2508.762695 -2000.892944 -38.393044 -38.393044 -38.393044 -1.041406 -1.041406 -6171.799805 -0.251922 -10.603043 0.007871 0.004028 0.001231 0.061426 0.029663 0.009421
4 4 -1324.769287 0.051825 -4476.101562 283.268646 523.928223 -257.409546 -262.557281 -27.531574 -11.682346 4.000017 30.571556 13380.287109 13380.287109 13380.287109 13380.287109 -2475.623047 -2475.623047 -1927.803101 -45.686489 -45.686489 -45.686489 -0.000022 -0.000022 -6039.446777 -0.849931 -22.195795 0.008174 0.001989 0.000022 0.068775 0.032622 0.006360
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -29707.246094 0.180550 -13539.585938 60.820023 152.966492 -491.024628 -506.458801 -266.521851 -65.257889 3.940273 32.302399 5188.449219 5188.448730 5188.448730 5188.448730 -5095.400391 -5095.400391 -3286.630127 -632.480835 -632.480835 -632.480835 -55.380669 -55.380669 -10791.519531 -150.857056 -264.930695 0.085679 0.044676 0.012644 0.454433 0.327164 0.118687
746 746 -29827.328125 0.185199 -13654.011719 85.772575 171.248138 -502.159271 -491.975555 -283.862793 -68.162506 0.994475 31.327314 5206.958496 5206.958496 5206.958496 5206.958984 -5095.930176 -5095.930176 -3245.968750 -626.758911 -626.758911 -626.758911 -58.461494 -58.461494 -10876.638672 -147.919189 -272.093170 0.078092 0.037935 0.010390 0.470433 0.334132 0.125079
747 747 -30196.355469 0.182041 -13742.802734 50.330521 168.061584 -475.156738 -501.522888 -281.153992 -65.834267 7.296491 31.829210 4983.755859 4983.756348 4983.755859 4983.755859 -5137.102539 -5137.102539 -3206.036621 -601.453796 -601.453796 -601.453796 -58.691032 -58.691032 -10917.906250 -162.098755 -288.192352 0.084880 0.042917 0.013277 0.467917 0.336607 0.132671
748 748 -29392.640625 0.185684 -13396.259766 79.043900 165.770874 -502.630127 -488.151276 -270.985321 -64.453468 0.666489 31.695663 5322.836914 5322.836914 5322.836914 5322.836914 -5061.817383 -5061.817383 -3176.455322 -634.178223 -634.178223 -634.178223 -57.555031 -57.555031 -10889.916016 -165.939667 -284.634003 0.083850 0.041747 0.011902 0.471999 0.337736 0.124996
749 749 -29857.906250 0.188364 -13687.683594 68.289467 205.726151 -487.147217 -506.653015 -282.655518 -61.409477 2.467853 30.636265 5096.162109 5096.162109 5096.162109 5096.162109 -5105.684082 -5105.684082 -3075.633301 -626.519226 -626.519226 -626.519226 -68.336090 -68.336090 -10931.466797 -153.975769 -274.334991 0.076267 0.037295 0.009711 0.466177 0.338351 0.149536

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 -350.364044 -337.554657 -101.299789 -22.383596 5.276686 30.820669 13280.344727 13280.344727 13280.344727 13280.344727 -2394.257324 -2394.257324 -1161.696533 -21.753496 -21.753496 -21.753496 -0.000183 -0.000183 -5518.478027 -0.131882 -18.656765 0.046304 0.011712 0.005324 0.001517 0.037225 0.015092 0.004646
1 1 3442.242188 13064.487305 181.922791 484.479095 -287.615997 -309.621918 -50.050182 -16.093176 8.403636 27.858189 13064.486328 13064.486328 13064.487305 13064.487305 -2460.115234 -2460.115234 -1159.888428 -56.040890 -56.040890 -56.040890 -0.000000 -0.000000 -5965.865234 -0.002022 -19.673506 0.049877 0.006242 0.001881 0.000205 0.041438 0.013466 0.004934
2 2 4274.123535 13591.301758 253.881256 534.353271 -265.211060 -286.368378 -31.059803 -17.342335 2.968159 32.293880 13591.300781 13591.302734 13591.302734 13591.301758 -2228.415039 -2228.415039 -1179.658081 -35.908363 -35.908363 -35.908363 0.000000 0.000000 -6071.928711 -1.376919 -23.485664 0.050713 0.016637 0.009257 0.003092 0.092303 0.049256 0.009863
3 3 3613.936523 13350.619141 281.847626 426.217529 -314.825897 -190.567062 -25.410397 -18.896715 9.181882 32.520649 13350.619141 13350.619141 13350.619141 13350.619141 -2508.762695 -2508.762695 -1200.535645 -38.393044 -38.393044 -38.393044 -1.041406 -1.041406 -6171.801270 -0.377883 -15.904561 0.053842 0.007871 0.004028 0.001231 0.061426 0.029663 0.009421
4 4 4062.674316 13532.033203 283.268677 523.928223 -257.409515 -262.557251 -27.531567 -11.682342 4.000018 30.571556 13532.033203 13532.032227 13532.033203 13532.033203 -2475.622803 -2475.622803 -1156.681885 -45.686485 -45.686485 -45.686485 -0.000022 -0.000022 -6039.448242 -1.274896 -33.293690 0.051825 0.008174 0.001989 0.000022 0.068775 0.032622 0.006360
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -15033.839844 5215.513184 60.820015 152.966522 -491.024628 -506.458740 -266.521790 -65.257889 3.940270 32.302399 5215.513672 5215.513184 5215.512695 5215.513184 -5095.399414 -5095.399414 -1971.978149 -632.480835 -632.480835 -632.480835 -55.380661 -55.380661 -10791.521484 -226.285583 -397.396027 0.180550 0.085679 0.044676 0.012644 0.454433 0.327164 0.118687
746 746 -15071.269531 5220.625977 85.772568 171.248138 -502.159271 -491.975555 -283.862701 -68.162491 0.994473 31.327316 5220.625977 5220.625977 5220.625977 5220.625977 -5095.929688 -5095.929688 -1947.581299 -626.758850 -626.758850 -626.758850 -58.461498 -58.461498 -10876.640625 -221.878799 -408.139740 0.185199 0.078092 0.037935 0.010390 0.470433 0.334132 0.125079
747 747 -15375.636719 5004.402832 50.330532 168.061630 -475.156738 -501.522827 -281.153992 -65.834267 7.296498 31.829205 5004.403320 5004.402832 5004.402832 5004.403320 -5137.102539 -5137.102539 -1923.621948 -601.453735 -601.453735 -601.453735 -58.691025 -58.691025 -10917.906250 -243.148132 -432.288513 0.182041 0.084880 0.042917 0.013277 0.467917 0.336607 0.132671
748 748 -14928.156250 5345.765625 79.043884 165.770874 -502.630127 -488.151276 -270.985352 -64.453476 0.666489 31.695662 5345.765625 5345.765625 5345.765625 5345.765625 -5061.817383 -5061.817383 -1905.873291 -634.178101 -634.178101 -634.178101 -57.555027 -57.555027 -10889.917969 -248.909485 -426.950989 0.185684 0.083850 0.041747 0.011902 0.471999 0.337736 0.124996
749 749 -15132.220703 5118.064941 68.289459 205.726151 -487.147217 -506.653015 -282.655487 -61.409458 2.467852 30.636261 5118.064941 5118.065430 5118.065430 5118.065430 -5105.683594 -5105.683594 -1845.380005 -626.519165 -626.519165 -626.519165 -68.336090 -68.336090 -10931.468750 -230.963654 -411.502441 0.188364 0.076267 0.037295 0.009711 0.466177 0.338351 0.149536

750 rows × 33 columns

This fold to crowded. too large contact and elctro term

i decrease the electro k to 3, and contact to 0.6


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 -3975.183105 213.720657 446.278412 -342.176544 -340.320770 -87.032585 -29.616756 10.055121 31.307692 12814.176758 12814.176758 12814.176758 12814.175781 -2319.988281 -2319.988281 -2019.848633 -24.214420 -24.214420 -24.214420 -2.606051 -2.606051 -5645.746094 -0.707964 -3.750574 0.014584 0.008042 0.002684 0.055331 0.029833 1.166996e-02
1 1 -1117.047241 0.047039 -4022.068359 233.990997 434.423523 -332.631531 -311.402893 -33.870060 -13.922815 7.842590 29.874681 13223.242188 13223.242188 13223.242188 13223.242188 -2627.866943 -2627.866943 -2032.746460 -26.395811 -26.395811 -26.395811 -2.556224 -2.556224 -5635.454590 -0.265296 -7.296427 0.006082 0.002318 0.000660 0.042173 0.019367 3.153285e-03
2 2 -1255.271729 0.050780 -4633.486816 150.035248 456.900696 -295.273010 -303.788239 -7.998295 -8.315025 21.840111 28.099506 13727.435547 13727.435547 13727.434570 13727.435547 -2340.547363 -2340.547363 -2060.383057 -21.627968 -21.627968 -21.627968 -0.111557 -0.111557 -5955.474609 -2.241368 -10.389204 0.002883 0.000385 0.000000 0.019886 0.003181 8.012001e-09
3 3 -2515.203369 0.053514 -4950.270508 263.255066 549.169434 -299.608765 -295.383667 -15.696991 -7.779157 1.726174 28.249380 12837.708984 12837.709961 12837.709961 12837.709961 -2401.757568 -2401.757568 -2066.503418 -73.142250 -73.142250 -73.142250 -16.312021 -16.312021 -6046.386719 -5.757246 -16.774910 0.005349 0.001520 0.000005 0.042084 0.023925 2.213108e-03
4 4 -2773.610840 0.057187 -5151.971680 277.642273 554.294556 -281.504425 -270.216370 -11.418318 -7.857366 5.273697 28.883514 12986.953125 12986.953125 12986.952148 12986.953125 -2538.182129 -2538.182129 -2156.076660 -63.303425 -63.303425 -63.303425 -9.614212 -9.614212 -6124.580078 -6.036125 -5.956220 0.001625 0.000195 0.000000 0.032677 0.014008 4.615912e-03
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -29647.820312 0.174253 -12966.069336 73.332268 154.937408 -501.866089 -453.833008 -259.537415 -57.208065 3.519470 39.181747 5158.396484 5158.395508 5158.395996 5158.395508 -4869.236816 -4869.236816 -4421.633789 -600.745605 -600.745605 -600.745605 -101.301743 -101.301743 -10100.066406 -277.046570 -469.113708 0.170900 0.096230 0.032073 0.659021 0.491939 2.162995e-01
746 746 -29861.570312 0.172975 -12997.693359 94.608513 163.193542 -502.075806 -445.566895 -274.083344 -63.066883 11.536770 40.124180 5025.058105 5025.058105 5025.057617 5025.058105 -4913.288086 -4913.288086 -4427.550781 -620.641541 -620.641541 -620.641541 -116.028503 -116.028503 -10103.102539 -264.848816 -468.630646 0.178934 0.101045 0.033991 0.669058 0.510056 2.314054e-01
747 747 -29743.214844 0.174273 -13040.927734 77.943298 186.227722 -499.087311 -443.266357 -252.712921 -61.326359 3.869683 41.342808 5125.562012 5125.562500 5125.562012 5125.562012 -4859.956055 -4859.956055 -4376.978027 -636.947876 -636.947876 -636.947876 -107.263344 -107.263344 -10159.412109 -276.683746 -464.064972 0.171362 0.094312 0.027886 0.661617 0.500228 2.252713e-01
748 748 -29611.640625 0.174808 -13095.754883 92.791779 225.841248 -474.238342 -466.915039 -263.965881 -62.675774 4.623479 39.833611 5345.441895 5345.441895 5345.441895 5345.441895 -4969.125488 -4969.125488 -4419.517578 -594.031250 -594.031250 -594.031250 -103.955650 -103.955650 -10146.974609 -271.192627 -452.315765 0.178459 0.101798 0.035575 0.674409 0.505268 2.287832e-01
749 749 -29393.707031 0.171729 -12899.969727 88.008614 156.585587 -483.028259 -454.568420 -246.376831 -61.220921 13.772707 41.063721 5267.428711 5267.428711 5267.428711 5267.428711 -4872.974609 -4872.974609 -4485.937988 -589.827148 -589.827148 -589.827148 -99.626549 -99.626549 -10053.673828 -260.353668 -453.488220 0.175707 0.097865 0.033931 0.669645 0.504811 2.286419e-01

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 -2319.988281 -2319.988281 -2019.848633 -24.214420 -24.214420 -24.214420 -2.606051 -2.606051 -5645.747070 -1.769911 -9.376433 0.044242 0.014584 0.008042 0.002684 0.055331 0.029833 1.166996e-02
1 1 2977.150391 13306.714844 233.990997 434.423584 -332.631470 -311.402832 -33.870079 -13.922819 7.842584 29.874681 13306.713867 13306.714844 13306.713867 13306.714844 -2627.866699 -2627.866699 -2032.746338 -26.395809 -26.395809 -26.395809 -2.556221 -2.556221 -5635.454590 -0.663241 -18.241068 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 -295.272980 -303.788239 -7.998293 -8.315023 21.840113 28.099504 13938.670898 13938.670898 13938.669922 13938.669922 -2340.547363 -2340.547363 -2060.383057 -21.627968 -21.627968 -21.627968 -0.111558 -0.111558 -5955.475098 -5.603431 -25.973005 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 -299.608704 -295.383636 -15.696985 -7.779157 1.726175 28.249378 12937.806641 12937.806641 12937.806641 12937.806641 -2401.757568 -2401.757568 -2066.503418 -73.142242 -73.142242 -73.142242 -16.312021 -16.312021 -6046.387207 -14.393115 -41.937271 0.053514 0.005349 0.001520 0.000005 0.042084 0.023925 2.213108e-03
4 4 2531.562988 13158.144531 277.642212 554.294556 -281.504333 -270.216339 -11.418300 -7.857361 5.273691 28.883511 13158.144531 13158.144531 13158.144531 13158.144531 -2538.181885 -2538.181885 -2156.077148 -63.303421 -63.303421 -63.303421 -9.614212 -9.614212 -6124.581055 -15.090312 -14.890550 0.057187 0.001625 0.000195 0.000000 0.032677 0.014008 4.615912e-03
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -17743.507812 5215.877441 73.332260 154.937393 -501.866119 -453.833008 -259.537415 -57.208065 3.519470 39.181747 5215.877930 5215.877930 5215.877441 5215.877441 -4869.236328 -4869.236328 -4421.633789 -600.745605 -600.745605 -600.745605 -101.301743 -101.301743 -10100.067383 -692.616333 -1172.784302 0.174253 0.170900 0.096230 0.032073 0.659021 0.491939 2.162995e-01
746 746 -17915.023438 5074.129883 94.608505 163.193542 -502.075806 -445.566833 -274.083374 -63.066891 11.536770 40.124176 5074.129883 5074.130371 5074.129883 5074.130371 -4913.288086 -4913.288086 -4427.550781 -620.641479 -620.641479 -620.641479 -116.028511 -116.028511 -10103.103516 -662.122070 -1171.576416 0.172975 0.178934 0.101045 0.033991 0.669058 0.510056 2.314054e-01
747 747 -17752.500000 5186.471191 77.943291 186.227692 -499.087250 -443.266357 -252.712921 -61.326370 3.869683 41.342804 5186.471680 5186.471191 5186.471191 5186.471680 -4859.955078 -4859.955078 -4376.978027 -636.947876 -636.947876 -636.947876 -107.263344 -107.263344 -10159.414062 -691.709351 -1160.162354 0.174273 0.171362 0.094312 0.027886 0.661617 0.500228 2.252713e-01
748 748 -17549.781250 5396.810059 92.791763 225.841217 -474.238281 -466.915009 -263.965851 -62.675781 4.623479 39.833614 5396.810547 5396.810547 5396.810547 5396.810547 -4969.125000 -4969.125000 -4419.517578 -594.031189 -594.031189 -594.031189 -103.955620 -103.955620 -10146.976562 -677.981567 -1130.789429 0.174808 0.178459 0.101798 0.035575 0.674409 0.505268 2.287832e-01
749 749 -17510.771484 5321.157227 88.008652 156.585602 -483.028259 -454.568390 -246.376846 -61.220936 13.772704 41.063721 5321.157227 5321.157227 5321.157227 5321.157227 -4872.973633 -4872.973633 -4485.938477 -589.827148 -589.827148 -589.827148 -99.626518 -99.626518 -10053.673828 -650.884216 -1133.720459 0.171729 0.175707 0.097865 0.033931 0.669645 0.504811 2.286419e-01

750 rows × 33 columns

there is a mirror image, probably due to the annealing is too fast.

also, maybe the current potential is too large. so it stuck at some local minimum.

I will try to increase the temperature, and drop the amh-go term.

currently, the protein fold at around 600K.


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 -2752.714844 -2752.714844 -2403.342285 -205.898102 -205.898102 -205.898102 -26.384335 -26.384335 -8880.485352 -0.008041 -7.999700 0.004094 0.000623 0.000000 0.034682 0.011836 0.002413
1 1 -15817.218750 0.112425 -13717.338867 228.072342 417.927734 -313.610962 -276.851471 -45.610928 -13.101348 2.812229 30.374706 13517.341797 13517.341797 13517.341797 13517.341797 -3218.535889 -3218.535889 -2565.927734 -376.312805 -376.312805 -376.312805 -70.006729 -70.006729 -9411.076172 -0.044598 -5.457299 0.010677 0.003660 0.000615 0.053712 0.021517 0.004012
2 2 -16640.150391 0.132516 -14857.622070 186.258850 426.691223 -311.815521 -309.777832 5.608495 -15.508778 4.318938 30.590771 13906.835938 13906.834961 13906.835938 13906.835938 -3024.222900 -3024.222900 -2513.442871 -397.080139 -397.080139 -397.080139 -68.955940 -68.955940 -9694.790039 -0.113174 -7.280909 0.015267 0.006940 0.000983 0.053068 0.030309 0.010282
3 3 -19121.332031 0.195720 -16053.638672 163.782227 472.322388 -287.218658 -319.453552 -15.821905 -9.537273 1.192322 27.967075 13418.086914 13418.087891 13418.086914 13418.087891 -3283.142334 -3283.142334 -2657.123291 -380.883972 -380.883972 -380.883972 -74.734650 -74.734650 -10117.589844 -1.196963 -4.554054 0.010680 0.003587 0.000918 0.055361 0.023310 0.005872
4 4 -20265.617188 0.238421 -16940.810547 233.142395 541.981812 -272.532715 -292.790649 -37.592258 -16.264042 0.465356 30.907730 13298.978516 13298.978516 13298.978516 13298.978516 -3494.699951 -3494.699951 -2813.550781 -425.137512 -425.137512 -425.137512 -69.351929 -69.351929 -9984.282227 -4.198914 -20.143860 0.016455 0.006716 0.001608 0.069481 0.038396 0.014067
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -38422.332031 0.524700 -21104.023438 41.598854 103.465637 -507.283752 -440.298645 -294.400391 -66.015854 1.136151 37.929596 3827.874023 3827.874023 3827.874023 3827.874023 -4664.638672 -4664.638672 -3202.687500 -760.219971 -760.219971 -760.219971 -130.057251 -130.057251 -10998.607422 -114.297165 -152.451401 0.076633 0.033880 0.008898 0.634532 0.443723 0.146425
746 746 -37996.253906 0.524586 -21114.894531 56.193478 127.726250 -514.384827 -445.876373 -285.449005 -66.659737 2.700405 37.998619 4187.053711 4187.053711 4187.053711 4187.053711 -4627.801758 -4627.801758 -3182.206543 -776.521484 -776.521484 -776.521484 -132.857101 -132.857101 -10983.435547 -128.548676 -149.943253 0.082289 0.037888 0.008515 0.643083 0.454308 0.151068
747 747 -38202.527344 0.518202 -21113.101562 45.844772 131.175369 -504.280884 -441.355927 -289.696289 -65.251602 1.604773 37.929401 4053.935547 4053.935547 4053.935547 4053.935547 -4676.686523 -4676.686523 -3225.516602 -783.119751 -783.119751 -783.119751 -130.698318 -130.698318 -10968.054688 -125.334274 -150.558868 0.076874 0.034742 0.008071 0.633326 0.442434 0.139372
748 748 -38249.167969 0.513549 -21096.587891 53.846836 131.354858 -503.173584 -442.483643 -288.690948 -68.287811 0.955609 38.580032 3939.638184 3939.638184 3939.638184 3939.637939 -4638.767578 -4638.767578 -3189.104004 -771.075623 -771.075623 -771.075623 -136.379486 -136.379486 -11024.023438 -111.900162 -143.708740 0.079758 0.037335 0.010537 0.631968 0.443605 0.144297
749 749 -38157.593750 0.520546 -21051.214844 72.694794 130.819962 -497.553711 -455.650604 -283.759216 -62.429966 1.340667 37.391083 4005.538086 4005.538086 4005.538330 4005.538086 -4622.647461 -4622.647461 -3243.033203 -786.723083 -786.723083 -786.723083 -130.643204 -130.643204 -10986.787109 -130.619141 -154.973145 0.081971 0.038384 0.009942 0.640993 0.448265 0.152871

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 -18.530704 0.609951 30.964396 13776.740234 13776.740234 13776.740234 13776.740234 -2752.714600 -2752.714600 -2403.342041 -205.898087 -205.898087 -205.898087 -26.384338 -26.384338 -8880.487305 -0.020102 -19.999249 0.004094 0.000623 0.000000 0.034682 0.011836 0.002413
1 1 -46726.242188 -44761.757812 13661.101562 228.072327 417.927673 -313.610962 -276.851471 -45.610909 -13.101356 2.812228 30.374704 13661.101562 13661.101562 13661.101562 13661.101562 -3218.535645 -3218.535645 -2565.927734 -376.312775 -376.312775 -376.312775 -70.006737 -70.006737 -9411.077148 -0.111495 -13.643248 0.010677 0.003660 0.000615 0.053712 0.021517 0.004012
2 2 -52470.546875 -50902.460938 14132.503906 186.258789 426.691223 -311.815491 -309.777802 5.608494 -15.508768 4.318938 30.590771 14132.502930 14132.503906 14132.502930 14132.503906 -3024.222412 -3024.222412 -2513.442871 -397.080139 -397.080139 -397.080139 -68.955940 -68.955940 -9694.791016 -0.282934 -18.202272 0.015267 0.006940 0.000983 0.053068 0.030309 0.010282
3 3 -60475.433594 -57563.722656 13582.892578 163.782181 472.322449 -287.218658 -319.453552 -15.821922 -9.537271 1.192320 27.967072 13582.892578 13582.893555 13582.893555 13582.893555 -3283.142090 -3283.142090 -2657.123291 -380.883972 -380.883972 -380.883972 -74.734650 -74.734650 -10117.588867 -2.992409 -11.385138 0.010680 0.003587 0.000918 0.055361 0.023310 0.005872
4 4 -67496.343750 -64251.734375 13415.923828 233.142365 541.981812 -272.532684 -292.790619 -37.592285 -16.264044 0.465354 30.907730 13415.923828 13415.923828 13415.923828 13415.923828 -3494.699707 -3494.699707 -2813.550781 -425.137482 -425.137482 -425.137482 -69.351929 -69.351929 -9984.283203 -10.497284 -50.359650 0.016455 0.006716 0.001608 0.069481 0.038396 0.014067
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -100683.921875 -83015.343750 3878.244629 41.598839 103.465591 -507.283752 -440.298645 -294.400360 -66.015846 1.136153 37.929596 3878.244629 3878.244629 3878.244629 3878.244629 -4664.638672 -4664.638672 -3202.687500 -760.219971 -760.219971 -760.219971 -130.057251 -130.057251 -10998.608398 -285.742920 -381.128479 0.076633 0.033880 0.008898 0.634532 0.443723 0.146425
746 746 -100322.437500 -83063.031250 4227.273926 56.193466 127.726288 -514.384888 -445.876343 -285.449005 -66.659752 2.700405 37.998615 4227.273438 4227.273438 4227.273926 4227.273926 -4627.801758 -4627.801758 -3182.206543 -776.521423 -776.521423 -776.521423 -132.857117 -132.857117 -10983.435547 -321.371704 -374.858124 0.082289 0.037888 0.008515 0.643083 0.454308 0.151068
747 747 -100408.828125 -82946.453125 4095.352783 45.844772 131.175354 -504.280853 -441.355927 -289.696289 -65.251602 1.604773 37.929398 4095.352539 4095.352539 4095.352539 4095.352539 -4676.686523 -4676.686523 -3225.516602 -783.119690 -783.119690 -783.119690 -130.698318 -130.698318 -10968.055664 -313.335693 -376.397156 0.076874 0.034742 0.008071 0.633326 0.442434 0.139372
748 748 -100548.296875 -83051.609375 3979.464355 53.846851 131.354889 -503.173584 -442.483612 -288.690979 -68.287827 0.955607 38.580029 3979.464355 3979.464600 3979.464844 3979.464600 -4638.767578 -4638.767578 -3189.104004 -771.075562 -771.075562 -771.075562 -136.379486 -136.379486 -11024.025391 -279.750427 -359.271820 0.079758 0.037335 0.010537 0.631968 0.443605 0.144297
749 749 -100435.648438 -82949.820312 4055.005127 72.694817 130.819962 -497.553680 -455.650604 -283.759155 -62.429962 1.340666 37.391083 4055.005371 4055.005127 4055.005371 4055.005127 -4622.646973 -4622.646973 -3243.033203 -786.723022 -786.723022 -786.723022 -130.643204 -130.643204 -10986.789062 -326.547882 -387.432831 0.081970 0.038384 0.009942 0.640993 0.448265 0.152871

750 rows × 33 columns

increase the cutoff of AMH-GO term, improved the Q_protein.

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 -17128.343750 0.116952 -14603.701172 146.953308 489.531677 -299.672058 -255.312149 -49.175858 -14.365455 5.225780 33.911648 13719.543945 13719.543945 13719.543945 13719.544922 -3216.645996 -3216.645996 -2501.313965 -384.308746 -384.308746 -384.308746 -55.200417 -55.200417 -10143.280273 -0.206447 -0.458015 0.007040 0.003918 0.001824 0.045428 0.023850 0.006152
1 1 -19392.123047 0.177122 -16584.847656 227.527847 527.590149 -325.255798 -249.528748 -22.831799 -17.290840 10.705187 34.084347 13990.775391 13990.775391 13990.775391 13990.775391 -3446.583008 -3446.583008 -2642.278076 -415.942841 -415.942841 -415.942841 -60.242958 -60.242958 -10429.062500 4.251391 6.619689 0.007123 0.002917 0.000983 0.044489 0.025576 0.008882
2 2 -21480.886719 0.264335 -18751.417969 176.604767 494.746124 -312.765045 -304.191956 -69.215302 -20.777632 3.038112 32.298748 14464.813477 14464.813477 14464.813477 14464.813477 -3291.305664 -3291.305664 -2838.295166 -476.329407 -476.329407 -476.329407 -108.248222 -108.248222 -10463.205078 -0.155727 -16.755453 0.008376 0.002208 0.000299 0.066305 0.028155 0.007554
3 3 -24360.800781 0.368844 -20440.398438 240.809555 403.346558 -325.337769 -267.300110 -43.077816 -18.757130 2.351897 33.191490 14274.659180 14274.659180 14274.659180 14274.659180 -3800.162109 -3800.162109 -2917.007568 -561.603149 -561.603149 -561.603149 -133.319412 -133.319412 -10777.850586 -5.285232 -25.462124 0.021175 0.008526 0.001697 0.128154 0.051429 0.016848
4 4 -24577.890625 0.381158 -20552.609375 173.109344 480.086853 -351.632996 -310.278687 -38.378777 -7.215595 1.496390 32.398083 13985.944336 13985.944336 13985.945312 13985.943359 -3482.352539 -3482.352539 -2869.675293 -613.383057 -613.383057 -613.383057 -127.662384 -127.662384 -10858.716797 -6.991767 -32.464993 0.034566 0.015261 0.003510 0.209081 0.093025 0.017609
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -38144.640625 0.692829 -21755.726562 39.873760 126.750160 -505.605469 -526.474182 -298.282532 -69.617584 0.816472 31.011040 4759.320312 4759.320312 4759.320312 4759.320312 -4607.873047 -4607.873047 -3054.125000 -782.166260 -782.166260 -782.166260 -101.221481 -101.221481 -11218.453125 -60.183132 -123.639565 0.151031 0.085644 0.026543 0.560658 0.372555 0.120982
746 746 -37998.812500 0.693175 -21735.675781 46.600971 114.086853 -507.295715 -515.546997 -304.073334 -70.855804 2.688676 30.718037 4831.432617 4831.432617 4831.432617 4831.432617 -4637.567383 -4637.567383 -3030.179688 -724.079224 -724.079224 -724.079224 -99.123505 -99.123505 -11209.185547 -66.250542 -125.463928 0.151405 0.085875 0.025683 0.566575 0.376318 0.108822
747 747 -38111.281250 0.691325 -21738.675781 37.133106 106.935028 -488.953461 -515.929321 -311.949738 -70.660736 0.959485 29.900311 4814.083008 4814.083008 4814.083008 4814.083008 -4630.423828 -4630.423828 -3069.170410 -746.102173 -746.102173 -746.102173 -102.975235 -102.975235 -11228.294922 -68.128761 -129.983276 0.154134 0.087641 0.026912 0.586933 0.396252 0.132081
748 748 -38121.042969 0.691387 -21767.707031 57.228374 151.500854 -526.246948 -517.678406 -293.462280 -71.246544 2.887837 30.156889 4797.367676 4797.367676 4797.368164 4797.367676 -4657.717773 -4657.717773 -3083.202637 -739.666504 -739.666504 -739.666504 -96.129868 -96.129868 -11208.927734 -68.311913 -130.845093 0.151612 0.086383 0.026542 0.597275 0.412250 0.133921
749 749 -38158.750000 0.692693 -21777.593750 51.980255 105.414421 -507.669037 -513.667419 -304.206665 -68.411415 2.937351 30.635065 4873.005859 4873.005859 4873.005859 4873.006348 -4660.175781 -4660.175781 -3086.310303 -781.732971 -781.732971 -781.732971 -99.466385 -99.466385 -11229.476562 -66.399506 -128.577911 0.153225 0.086978 0.028363 0.580340 0.392811 0.129013

750 rows × 33 columns

a stronger AMH-GO term. somehow doesn't further guide the folding.

the minimum is ~24000, but it only reaches ~20000.

might be because it was stuck somewhere.

the protein - DNA interaction is weak. should be increased.

why I cannot fold the protein?


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 -11349.651367 0.068178 -10437.296875 229.184723 524.388794 -308.894257 -320.585846 -77.693710 -17.556198 7.299036 30.974798 13191.244141 13191.244141 13191.244141 13191.244141 -2839.753662 -2839.753662 -2063.025879 -240.442749 -240.442749 -240.442749 -4.332776 -4.332776 -9018.482422 -0.017040 -4.732169 0.001625 0.000052 0.000000 0.026089 0.013131 0.007268
1 1 -14084.978516 0.084096 -12013.707031 176.230942 459.207275 -280.465149 -336.121185 -21.834370 -15.261388 4.649366 28.876444 13429.396484 13429.396484 13429.396484 13429.396484 -3083.194824 -3083.194824 -2222.266113 -324.775696 -324.775696 -324.775696 -28.613426 -28.613426 -9854.440430 -1.987315 -0.784427 0.018211 0.007941 0.003059 0.040210 0.017146 0.005180
2 2 -17059.992188 0.101687 -13908.556641 214.218445 389.616669 -335.475525 -355.794220 -105.173904 -25.313942 3.374076 32.034401 12884.892578 12884.891602 12884.891602 12884.892578 -3346.017578 -3346.017578 -2239.096191 -376.672058 -376.672058 -376.672058 -37.955879 -37.955879 -9849.548828 -0.507133 -4.144104 0.017030 0.007536 0.001813 0.050590 0.026671 0.010551
3 3 -16731.947266 0.106183 -14512.938477 229.765549 515.253052 -323.237915 -276.040558 -23.327225 -15.916163 20.737286 34.048325 13660.233398 13660.234375 13660.234375 13660.234375 -3155.703857 -3155.703857 -2401.351562 -369.741272 -369.741272 -369.741272 -51.217651 -51.217651 -10046.423828 -3.965032 -12.284704 0.033557 0.019071 0.005181 0.076670 0.048978 0.015251
4 4 -18375.710938 0.110928 -15078.777344 189.639374 442.696381 -243.429733 -301.115112 -33.101917 -18.181795 3.875393 30.610514 13234.298828 13234.298828 13234.299805 13234.299805 -3418.221680 -3418.221680 -2449.976074 -405.144470 -405.144470 -405.144470 -51.973503 -51.973503 -10257.574219 -7.673388 -11.840055 0.037932 0.023234 0.006917 0.090435 0.052514 0.009238
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
745 745 -38212.691406 0.283995 -20336.820312 58.009045 123.575005 -511.079803 -494.487854 -304.937836 -75.029045 2.687514 32.131157 3956.689209 3956.689209 3956.689209 3956.689209 -4720.538574 -4720.538574 -3660.722168 -760.785645 -760.785645 -760.785645 -115.213715 -115.213715 -11290.381836 -41.111095 -75.206398 0.138015 0.082228 0.026912 0.256809 0.178922 0.063281
746 746 -38280.851562 0.285329 -20318.714844 38.719402 118.692078 -513.610901 -513.120605 -312.903687 -73.642670 0.687082 30.368240 3926.859375 3926.859619 3926.859619 3926.859619 -4765.365234 -4765.365234 -3619.219727 -760.554993 -760.554993 -760.554993 -109.761879 -109.761879 -11303.708984 -33.348305 -72.747734 0.132189 0.078057 0.027127 0.248193 0.171748 0.065281
747 747 -38079.382812 0.291415 -20329.679688 60.986191 119.370621 -513.069214 -492.840881 -293.534943 -68.005554 0.812024 32.676510 4105.003906 4105.003906 4105.003906 4105.003418 -4771.679688 -4771.679688 -3638.356445 -764.999023 -764.999023 -764.999023 -103.635193 -103.635193 -11303.781250 -40.172920 -79.017365 0.139154 0.083640 0.027684 0.255260 0.175519 0.053913
748 748 -38259.046875 0.287246 -20341.089844 47.043564 127.358841 -499.029938 -497.525024 -294.895660 -67.680504 0.535318 31.628651 3932.154541 3932.154297 3932.154541 3932.154541 -4777.693359 -4777.693359 -3654.947754 -769.493286 -769.493286 -769.493286 -103.545235 -103.545235 -11271.665039 -43.244003 -77.514091 0.146075 0.091560 0.029992 0.258184 0.180641 0.061601
749 749 -38396.617188 0.285596 -20352.402344 49.127647 136.112961 -512.312622 -501.881561 -296.989075 -75.481476 0.353090 33.288712 3828.843506 3828.843750 3828.843750 3828.843506 -4778.930664 -4778.930664 -3628.745361 -755.908569 -755.908569 -755.908569 -114.017532 -114.017532 -11302.990234 -46.803482 -78.430397 0.146234 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 -41761.898438 0.910350 -24148.511719 72.628693 174.160477 -492.280762 -496.281281 -299.294342 -65.298683 1.116977 32.101761 4982.414062 4982.413574 4982.414062 4982.413574 -5116.578125 -5116.578125 -3372.669434 -788.578857 -788.578857 -788.578857 -87.048683 -87.048683 -11913.384766 -74.894501 -172.878815 0.967220 0.916209 0.598239 0.972316 0.928374 0.626994
1 1 -41800.851562 0.925077 -24174.560547 72.544197 165.041199 -480.148041 -500.106628 -274.647064 -63.609055 0.172277 30.470150 4873.564453 4873.563965 4873.564453 4873.564453 -5086.610840 -5086.610840 -3325.110840 -782.810059 -782.810059 -782.810059 -82.263390 -82.263390 -11943.054688 -62.340652 -170.711533 0.961359 0.901237 0.553961 0.959051 0.895604 0.541304
2 2 -41745.632812 0.851793 -24189.828125 91.083344 172.127487 -461.366455 -494.880646 -291.325989 -64.341721 0.568332 31.616669 5072.878906 5072.878906 5072.878906 5072.878906 -5138.804688 -5138.804688 -3395.028320 -788.807373 -788.807373 -788.807373 -79.207420 -79.207420 -11924.847656 -110.780952 -177.901993 0.956154 0.888922 0.523362 0.959400 0.896102 0.538825
3 3 -41892.742188 0.886018 -24129.302734 51.578461 184.347809 -506.004578 -479.178986 -276.171234 -59.279732 1.358014 31.211781 4813.846680 4813.846680 4813.846680 4813.846680 -5095.519531 -5095.519531 -3352.770020 -804.503418 -804.503418 -804.503418 -84.143646 -84.143646 -11909.226562 -111.979210 -170.268646 0.958449 0.894621 0.536966 0.965112 0.908757 0.528775
4 4 -41876.664062 0.916250 -24161.134766 88.812004 172.881195 -492.063080 -504.710785 -276.787720 -68.570572 2.135250 31.823505 4870.122070 4870.122070 4870.122070 4870.121582 -5147.251953 -5147.251953 -3358.418945 -787.141235 -787.141235 -787.141235 -80.618805 -80.618805 -11920.861328 -82.409134 -165.794693 0.961920 0.902782 0.556735 0.964789 0.908582 0.554520
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
245 245 -44218.445312 0.910282 -24328.419922 53.136841 105.146851 -508.894928 -512.151855 -310.310913 -76.330750 1.095423 32.260189 3308.041260 3308.041016 3308.041016 3308.041260 -5325.213867 -5325.213867 -3454.216309 -854.620117 -854.620117 -854.620117 -80.490845 -80.490845 -11994.501953 -103.738083 -171.799683 0.811682 0.621376 0.232360 0.960487 0.898759 0.543176
246 246 -44081.304688 0.869112 -24308.099609 58.100685 124.604019 -516.636841 -512.087708 -298.018494 -66.826683 0.774467 31.588593 3324.935547 3324.935547 3324.935303 3324.935547 -5292.588867 -5292.588867 -3438.642822 -846.340088 -846.340088 -846.340088 -80.363419 -80.363419 -11994.630859 -101.965279 -167.570999 0.791153 0.591524 0.220003 0.954601 0.887171 0.539565
247 247 -43920.828125 0.884810 -24328.154297 56.388245 144.464966 -480.523895 -513.313965 -315.142426 -69.884544 0.503394 31.224329 3461.500488 3461.500732 3461.500488 3461.500488 -5305.854004 -5305.854004 -3445.930420 -833.889404 -833.889404 -833.889404 -89.813217 -89.813217 -11970.527344 -95.103828 -169.201202 0.787529 0.580062 0.186515 0.943319 0.861994 0.483121
248 248 -44173.488281 0.905386 -24323.910156 47.034550 116.440445 -496.897888 -512.915588 -299.912720 -70.170296 0.917068 32.955006 3295.433594 3295.433350 3295.433350 3295.433594 -5339.147949 -5339.147949 -3465.430420 -837.304932 -837.304932 -837.304932 -79.374741 -79.374741 -11985.265625 -90.838982 -167.697739 0.819279 0.636080 0.250024 0.955081 0.885529 0.497608
249 249 -44217.929688 0.881131 -24323.048828 57.388577 98.314499 -520.283386 -528.126709 -308.141663 -77.708755 0.809490 32.398632 3235.748535 3235.749023 3235.748779 3235.749023 -5325.193848 -5325.193848 -3415.360840 -816.455688 -816.455688 -816.455688 -80.864258 -80.864258 -11989.242188 -102.605324 -158.091797 0.811218 0.621944 0.227924 0.944277 0.866626 0.491240

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 -9678.261719 149.426193 517.377930 -319.720062 -275.121674 -104.039024 -24.935095 13.402123 34.191772 13019.257812 13019.257812 13019.257812 13019.257812 -2925.430420 -2925.430420 -2049.059082 -240.644409 -240.644409 -240.644409 -15.202121 -15.202121 -8845.755859 -0.032407 -6.474565 0.008932 0.002523 0.000065 0.045451 0.021238 0.007407
1 1 -13297.464844 0.075604 -11053.300781 213.087036 501.993713 -338.494598 -313.467285 -33.131500 -26.611055 3.097094 28.511181 12592.583984 12592.583984 12592.583984 12592.583984 -3026.788574 -3026.788574 -2087.078369 -284.897614 -284.897614 -284.897614 -24.010159 -24.010159 -9439.740234 -0.583866 -8.723352 0.008905 0.004141 0.002208 0.045573 0.023506 0.007652
2 2 -14902.109375 0.083236 -12035.213867 181.505737 466.779846 -292.776245 -346.465729 -33.652851 -12.882930 12.337412 29.659906 12704.085938 12704.085938 12704.085938 12704.085938 -3162.030762 -3162.030762 -2219.551758 -326.753876 -326.753876 -326.753876 -42.867634 -42.867634 -9815.275391 -1.333590 -7.771951 0.009193 0.004356 0.001086 0.044340 0.022768 0.009180
3 3 -15947.250000 0.088237 -12537.917969 247.747009 517.660400 -308.050293 -278.021027 -42.643871 -15.114118 4.471396 29.861839 12395.682617 12395.683594 12395.682617 12395.682617 -3292.691406 -3292.691406 -2303.702637 -376.941223 -376.941223 -376.941223 -49.230354 -49.230354 -9931.307617 -0.695494 -6.456980 0.008273 0.003059 0.001282 0.048153 0.024711 0.008717
4 4 -15843.654297 0.093418 -12806.130859 153.598907 528.759277 -352.527618 -260.748627 -42.027218 -24.561172 0.508689 26.447130 12933.581055 12933.582031 12933.581055 12933.582031 -3276.439453 -3276.439453 -2357.783691 -345.748291 -345.748291 -345.748291 -48.900566 -48.900566 -9969.236328 -0.001859 -2.540337 0.002814 0.000520 0.000000 0.030861 0.014815 0.005132
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
245 245 -39596.703125 0.314597 -20387.183594 55.472801 138.631836 -496.102478 -517.640259 -301.709351 -73.817024 1.231170 30.545010 3564.943359 3564.943359 3564.943359 3564.943359 -5073.248535 -5073.248535 -3817.854248 -884.813660 -884.813660 -884.813660 -98.950142 -98.950142 -11652.811523 -37.167469 -46.569012 0.018206 0.004971 0.000094 0.366046 0.245616 0.093013
246 246 -39606.546875 0.310633 -20429.335938 70.273003 130.749512 -510.427429 -511.141541 -303.869232 -74.540977 0.828926 31.340694 3511.935059 3511.935059 3511.935059 3511.934814 -5075.781738 -5075.781738 -3757.188965 -848.139526 -848.139526 -848.139526 -101.281425 -101.281425 -11663.464844 -29.187309 -47.645374 0.014301 0.003171 0.000015 0.340545 0.222283 0.084025
247 247 -39578.765625 0.309249 -20390.837891 59.400360 96.042801 -516.172241 -510.332550 -310.443481 -71.254417 2.212485 30.084549 3513.275879 3513.275879 3513.275879 3513.275879 -5048.608887 -5048.608887 -3727.603027 -849.633484 -849.633484 -849.633484 -103.713051 -103.713051 -11674.329102 -33.957264 -43.225075 0.018221 0.004995 0.000139 0.340143 0.218399 0.073112
248 248 -39468.675781 0.306236 -20398.111328 60.345993 127.284348 -493.340912 -523.022644 -308.064453 -72.393158 1.028468 30.895117 3640.344238 3640.344238 3640.344238 3640.344238 -5077.127930 -5077.127930 -3785.028320 -852.375305 -852.375305 -852.375305 -105.115555 -105.115555 -11628.417969 -40.147713 -45.759357 0.019302 0.005423 0.000171 0.353723 0.230047 0.072046
249 249 -39478.097656 0.306462 -20409.382812 43.699539 128.529327 -499.468048 -516.597412 -300.053864 -67.303329 1.255454 30.709763 3644.728027 3644.727783 3644.728027 3644.728027 -5070.782227 -5070.782227 -3763.679199 -857.035278 -857.035278 -857.035278 -106.536072 -106.536072 -11641.979492 -46.016319 -48.530964 0.027034 0.009588 0.001276 0.386297 0.258224 0.090736

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 -21279.523438 75.343140 276.041138 -404.931763 -447.719666 -191.299591 -40.055309 1.675032 33.851437 5306.451172 5306.451172 5306.451172 5306.451172 -5018.418945 -5018.418945 -3669.246338 -700.023132 -700.023132 -700.023132 -92.312614 -92.312614 -11098.678711 -96.125244 -162.978729 0.936808 0.849419 0.462407 0.943508 0.861644 0.477094
1 1 -37955.546875 0.762591 -21053.363281 78.837845 202.295853 -463.306152 -500.029388 -240.514221 -61.044048 4.596742 31.475452 5053.401855 5053.401855 5053.401855 5053.401855 -5036.673828 -5036.673828 -3837.937500 -722.758911 -722.758911 -722.758911 -98.811935 -98.811935 -11066.539062 -72.813553 -175.399582 0.939737 0.855479 0.478177 0.944268 0.864043 0.497012
2 2 -38121.593750 0.726033 -20720.347656 45.343384 182.227203 -466.012146 -497.576752 -246.141342 -58.878990 3.851925 30.994719 4868.972656 4868.972656 4868.972656 4868.972656 -5122.433594 -5122.433594 -3992.948730 -731.085510 -731.085510 -731.085510 -98.652359 -98.652359 -11059.134766 -97.045013 -165.617493 0.921879 0.819948 0.426885 0.927760 0.827538 0.417590
3 3 -37943.062500 0.707940 -20568.064453 64.157227 163.367310 -460.815002 -489.121063 -270.730865 -62.089294 0.573608 29.920189 4948.175781 4948.174805 4948.175293 4948.175293 -5069.142578 -5069.142578 -3956.500000 -741.189331 -741.189331 -741.189331 -92.324829 -92.324829 -11163.899414 -98.695709 -179.610443 0.923301 0.827752 0.466873 0.937775 0.851382 0.478145
4 4 -37851.929688 0.718896 -20688.535156 63.687714 146.258972 -476.539734 -496.871429 -256.511627 -65.100105 1.010401 29.678308 5107.648438 5107.648438 5107.648438 5107.648438 -5062.105469 -5062.105469 -3953.353516 -687.670166 -687.670166 -687.670166 -99.194931 -99.194931 -11149.169922 -89.037231 -179.094177 0.926199 0.834396 0.488929 0.944327 0.866481 0.520145
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
1354 1354 -36506.070312 0.430025 -19029.640625 90.647491 192.593079 -469.639801 -468.173981 -270.791748 -71.202927 0.528190 30.002695 5095.862793 5095.862793 5095.862793 5095.862793 -5181.653320 -5181.653320 -4373.848145 -766.270508 -766.270508 -766.270508 -109.655212 -109.655212 -10910.877930 -102.723877 -162.677963 0.544092 0.363078 0.115236 0.824331 0.681142 0.361538
1355 1355 -36861.421875 0.424452 -19395.335938 67.424347 174.690506 -477.919586 -487.781250 -266.450928 -60.205299 4.617456 31.505207 5152.247070 5152.247070 5152.247070 5152.247070 -5129.292969 -5129.292969 -4346.389648 -752.145691 -752.145691 -752.145691 -105.230370 -105.230370 -11011.666992 -101.783218 -159.132965 0.534918 0.355067 0.115245 0.811602 0.660185 0.323518
1356 1356 -36988.414062 0.412031 -19329.656250 76.937561 191.284973 -473.358185 -480.496857 -254.787170 -66.500061 0.077047 30.118217 4912.732910 4912.732910 4912.733398 4912.732910 -5098.809082 -5098.809082 -4420.116211 -716.462769 -716.462769 -716.462769 -108.879242 -108.879242 -10971.794922 -120.431839 -159.718750 0.539219 0.369290 0.128632 0.830618 0.690483 0.354045
1357 1357 -37012.460938 0.416456 -19312.449219 76.072525 159.028076 -466.892578 -502.093353 -242.101013 -59.811340 0.785941 30.083233 4942.964355 4942.964355 4942.963867 4942.963867 -5079.197754 -5079.197754 -4377.551270 -759.709412 -759.709412 -759.709412 -101.870842 -101.870842 -11024.326172 -131.442886 -165.441696 0.553682 0.383390 0.138519 0.839096 0.704828 0.350625
1358 1358 -36703.621094 0.422809 -19191.089844 85.468567 158.939087 -484.828491 -508.127014 -278.751129 -57.349087 1.047828 30.279930 5236.811523 5236.811523 5236.811523 5236.811523 -5098.156738 -5098.156738 -4395.380859 -793.282471 -793.282471 -793.282471 -104.880661 -104.880661 -11016.498047 -121.260918 -168.081085 0.566000 0.391892 0.139611 0.839462 0.706048 0.381064

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 -6479.621094 193.614624 389.494141 -337.716522 -332.910492 -36.121056 -22.702259 0.020081 31.347294 13908.466797 13908.466797 13908.466797 13908.466797 -2489.110107 -2489.110107 -2115.102051 -86.351395 -86.351395 -86.351395 -9.196173 -9.196173 -7569.404297 -0.329790 -7.603122 0.006733 0.002764 0.000563 4.585004e-02 1.445732e-02 0.000562
1 1 -7802.266113 0.058871 -7683.869629 207.127121 519.555725 -325.887848 -206.008972 -4.853895 -5.854814 7.975885 30.976982 12999.916016 12999.916016 12999.915039 12999.915039 -2809.565430 -2809.565430 -2095.776123 -120.844002 -120.844002 -120.844002 -0.000497 -0.000497 -8312.000000 0.000000 -3.222071 0.005638 0.002179 0.000444 3.636368e-02 1.135518e-02 0.000390
2 2 -9053.828125 0.068091 -8166.125977 307.757141 478.538879 -362.240845 -349.713165 -32.963295 -14.374836 0.852112 27.070225 12746.144531 12746.143555 12746.142578 12746.144531 -2711.636719 -2711.636719 -2032.897461 -141.450775 -141.450775 -141.450775 -1.757518 -1.757518 -8788.251953 -0.048225 -12.809216 0.007530 0.004084 0.001917 5.672172e-02 2.550467e-02 0.006587
3 3 -9764.839844 0.072248 -8775.859375 181.355347 514.997986 -327.461060 -301.684448 -78.616936 -15.030621 1.428239 29.101568 13285.304688 13285.304688 13285.303711 13285.304688 -2995.083984 -2995.083984 -2119.717773 -200.412613 -200.412613 -200.412613 -0.000001 -0.000001 -8949.250977 -0.246529 -13.742972 0.005916 0.002121 0.000272 6.036279e-02 2.686299e-02 0.005769
4 4 -10567.179688 0.082018 -9535.031250 217.547180 591.753052 -370.520905 -261.485016 -26.641947 -13.509037 0.000000 30.445271 13473.679688 13473.679688 13473.679688 13473.679688 -3035.397461 -3035.397461 -2208.354004 -184.876251 -184.876251 -184.876251 -0.000345 -0.000345 -9212.654297 -4.897475 -27.331352 0.008621 0.003056 0.000858 6.992062e-02 4.013824e-02 0.019951
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
2495 2495 -36563.640625 0.242864 -16216.877930 41.515511 106.215195 -508.794769 -502.782135 -303.192627 -71.480873 0.203188 29.868338 3382.899658 3382.899658 3382.899902 3382.899658 -5261.002441 -5261.002441 -4907.549805 -725.551636 -725.551636 -725.551636 -76.920341 -76.920341 -11550.431641 0.000000 0.000000 0.000000 0.000000 0.000000 1.094924e-27 4.828834e-71 0.000000
2496 2496 -36352.265625 0.237273 -16116.456055 56.799339 146.473862 -515.979736 -524.444519 -312.506287 -75.415520 0.854753 30.287872 3462.850098 3462.850098 3462.849854 3462.850098 -5263.055664 -5263.055664 -4828.315918 -750.683228 -750.683228 -750.683228 -76.535454 -76.535454 -11586.374023 0.000000 0.000000 0.000000 0.000000 0.000000 2.743599e-27 6.183768e-70 0.000000
2497 2497 -36430.898438 0.240580 -16319.963867 48.113899 84.582481 -519.115356 -514.517883 -305.784332 -72.026321 0.400839 30.814110 3461.850098 3461.850098 3461.850098 3461.850098 -5211.725586 -5211.725586 -4759.703125 -723.094971 -723.094971 -723.094971 -77.237404 -77.237404 -11553.726562 0.000000 0.000000 0.000000 0.000000 0.000000 3.428768e-28 1.894132e-72 0.000000
2498 2498 -36592.046875 0.238279 -16310.494141 50.091408 120.050140 -523.828125 -522.137390 -305.585388 -76.846069 1.107746 31.206524 3345.335449 3345.335205 3345.335449 3345.335449 -5216.617676 -5216.617676 -4860.385742 -705.467285 -705.467285 -705.467285 -77.962280 -77.962280 -11540.755859 0.000000 0.000000 0.000000 0.000000 0.000000 9.521503e-30 9.106016e-77 0.000000
2499 2499 -36301.097656 0.240433 -16182.482422 55.518173 116.415909 -505.374084 -510.044006 -306.866028 -73.560120 0.091450 30.793739 3463.173340 3463.173340 3463.173340 3463.173340 -5209.402344 -5209.402344 -4815.437500 -717.541260 -717.541260 -717.541260 -70.136185 -70.136185 -11576.488281 0.000000 0.000000 0.000000 0.000000 0.000000 9.465677e-29 5.377658e-74 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 -337.716522 -332.910492 -36.121056 -22.702259 0.020081 31.347294 0.054905 13908.466797 13908.466797 13908.466797 13908.466797 -2489.110107 -2489.110107 -2115.102295 -86.351395 -86.351395 -86.351395 -9.196173 -9.196173 -7569.404297 -0.329790 -7.603123 0.006733 0.002764 0.000563 4.585004e-02 1.445732e-02 0.000562
1 1 -118.396622 207.127121 519.555725 -325.887848 -206.008972 -4.853895 -5.854814 7.975885 30.976984 0.058871 12999.915039 12999.915039 12999.915039 12999.916016 -2809.565430 -2809.565430 -2095.776123 -120.844002 -120.844002 -120.844002 -0.000497 -0.000497 -8312.000000 0.000000 -3.222071 0.005638 0.002179 0.000444 3.636368e-02 1.135518e-02 0.000390
2 2 -887.701416 307.757141 478.538879 -362.240845 -349.713165 -32.963295 -14.374836 0.852112 27.070225 0.068091 12746.143555 12746.143555 12746.143555 12746.143555 -2711.636719 -2711.636719 -2032.897461 -141.450775 -141.450775 -141.450775 -1.757518 -1.757518 -8788.251953 -0.048225 -12.809216 0.007530 0.004084 0.001917 5.672172e-02 2.550467e-02 0.006587
3 3 -988.980469 181.355347 514.997986 -327.461060 -301.684448 -78.616936 -15.030621 1.428239 29.101566 0.072248 13285.304688 13285.303711 13285.303711 13285.304688 -2995.083984 -2995.083984 -2119.718018 -200.412613 -200.412613 -200.412613 -0.000001 -0.000001 -8949.250977 -0.246529 -13.742972 0.005916 0.002121 0.000272 6.036279e-02 2.686299e-02 0.005769
4 4 -1032.149292 217.547180 591.753052 -370.520905 -261.485016 -26.641947 -13.509037 0.000000 30.445271 0.082018 13473.679688 13473.679688 13473.679688 13473.679688 -3035.397461 -3035.397461 -2208.354004 -184.876251 -184.876251 -184.876251 -0.000345 -0.000345 -9212.654297 -4.897475 -27.331352 0.008621 0.003056 0.000858 6.992062e-02 4.013824e-02 0.019951
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
2495 2495 -20346.761719 41.515511 106.215195 -508.794769 -502.782135 -303.192627 -71.480873 0.203188 29.868340 0.242864 3382.899902 3382.899902 3382.899658 3382.899658 -5261.002441 -5261.002441 -4907.549805 -725.551636 -725.551636 -725.551636 -76.920341 -76.920341 -11550.431641 0.000000 0.000000 0.000000 0.000000 0.000000 1.094924e-27 4.828834e-71 0.000000
2496 2496 -20235.808594 56.799339 146.473862 -515.979736 -524.444519 -312.506287 -75.415520 0.854753 30.287872 0.237273 3462.850098 3462.850098 3462.850098 3462.850098 -5263.055664 -5263.055664 -4828.316406 -750.683228 -750.683228 -750.683228 -76.535454 -76.535454 -11586.374023 0.000000 0.000000 0.000000 0.000000 0.000000 2.743599e-27 6.183768e-70 0.000000
2497 2497 -20110.933594 48.113899 84.582481 -519.115356 -514.517883 -305.784332 -72.026321 0.400839 30.814110 0.240580 3461.850098 3461.850098 3461.850098 3461.850098 -5211.725586 -5211.725586 -4759.703613 -723.094971 -723.094971 -723.094971 -77.237404 -77.237404 -11553.726562 0.000000 0.000000 0.000000 0.000000 0.000000 3.428768e-28 1.894132e-72 0.000000
2498 2498 -20281.556641 50.091408 120.050140 -523.828125 -522.137390 -305.585388 -76.846069 1.107746 31.206522 0.238279 3345.335205 3345.335205 3345.335205 3345.335449 -5216.617676 -5216.617676 -4860.386230 -705.467285 -705.467285 -705.467285 -77.962280 -77.962280 -11540.755859 0.000000 0.000000 0.000000 0.000000 0.000000 9.521503e-30 9.106016e-77 0.000000
2499 2499 -20118.617188 55.518173 116.415909 -505.374084 -510.044006 -306.866028 -73.560120 0.091450 30.793739 0.240433 3463.173340 3463.173584 3463.173340 3463.173340 -5209.402344 -5209.402344 -4815.437988 -717.541260 -717.541260 -717.541260 -70.136185 -70.136185 -11576.488281 0.000000 0.000000 0.000000 0.000000 0.000000 9.465677e-29 5.377658e-74 0.000000

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 0 1516.404297 193.614624 389.494202 -337.716492 -332.910553 -36.121040 -22.702257 0.020081 31.347292 13908.466797 13908.465820 13908.466797 13908.466797 -2489.109863 -2489.109863 -2115.102295 -86.351395 -86.351395 -86.351395 -9.196173 -9.196173 -7569.405273 -0.329790 -7.603124 0.006733 0.002764 0.000563 4.585004e-02 1.445732e-02 0.000562
1 1 -118.456543 207.127090 519.555725 -325.887756 -206.008972 -4.853899 -5.854815 7.975883 30.976980 12999.914062 12999.914062 12999.915039 12999.915039 -2809.565186 -2809.565186 -2095.775879 -120.844009 -120.844009 -120.844009 -0.000497 -0.000497 -8312.001953 0.000000 -3.222070 0.005638 0.002179 0.000444 3.636368e-02 1.135518e-02 0.000390
2 2 -887.770996 307.757172 478.538757 -362.240906 -349.713165 -32.963310 -14.374836 0.852110 27.070225 12746.142578 12746.142578 12746.142578 12746.142578 -2711.636719 -2711.636719 -2032.897339 -141.450775 -141.450775 -141.450775 -1.757518 -1.757518 -8788.253906 -0.048225 -12.809214 0.007530 0.004084 0.001917 5.672172e-02 2.550467e-02 0.006587
3 3 -989.054382 181.355347 514.997925 -327.461060 -301.684418 -78.616936 -15.030622 1.428239 29.101564 13285.302734 13285.302734 13285.302734 13285.303711 -2995.083740 -2995.083740 -2119.718018 -200.412598 -200.412598 -200.412598 -0.000001 -0.000001 -8949.251953 -0.246529 -13.742972 0.005916 0.002121 0.000272 6.036279e-02 2.686299e-02 0.005769
4 4 -1032.233154 217.547089 591.753052 -370.520905 -261.484955 -26.641958 -13.509039 0.000000 30.445271 13473.678711 13473.679688 13473.678711 13473.678711 -3035.397461 -3035.397461 -2208.354004 -184.876221 -184.876221 -184.876221 -0.000345 -0.000345 -9212.656250 -4.897471 -27.331348 0.008621 0.003056 0.000858 6.992062e-02 4.013824e-02 0.019951
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
2495 2495 -20347.007812 41.515511 106.215256 -508.794739 -502.782074 -303.192657 -71.480865 0.203189 29.868338 3382.899170 3382.899170 3382.899170 3382.899170 -5261.001953 -5261.001953 -4907.549805 -725.551636 -725.551636 -725.551636 -76.920334 -76.920334 -11550.434570 0.000000 0.000000 0.000000 0.000000 0.000000 1.094924e-27 4.828834e-71 0.000000
2496 2496 -20236.046875 56.799328 146.473892 -515.979736 -524.444458 -312.506256 -75.415527 0.854753 30.287868 3462.849609 3462.849609 3462.849609 3462.849609 -5263.055664 -5263.055664 -4828.315918 -750.683167 -750.683167 -750.683167 -76.535439 -76.535439 -11586.375000 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 -519.115356 -514.517883 -305.784302 -72.026321 0.400839 30.814110 3461.849854 3461.849854 3461.850098 3461.849854 -5211.725586 -5211.725586 -4759.703125 -723.094971 -723.094971 -723.094971 -77.237404 -77.237404 -11553.729492 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 -522.137329 -305.585358 -76.846062 1.107744 31.206522 3345.334473 3345.334717 3345.334961 3345.334961 -5216.617188 -5216.617188 -4860.386230 -705.467285 -705.467285 -705.467285 -77.962288 -77.962288 -11540.756836 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 -510.043976 -306.866058 -73.560104 0.091450 30.793739 3463.173340 3463.173340 3463.173340 3463.173340 -5209.401855 -5209.401855 -4815.437500 -717.541260 -717.541260 -717.541260 -70.136185 -70.136185 -11576.489258 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 [ ]: