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@bbrighttaer
Created December 18, 2018 14:36
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I tried loading the core subset of the pdbbind dataset using deepchem 2.1.1
/home/bbrighttaer/anaconda3/envs/deepchem/lib/python3.5/site-packages/deepchem/feat/rdkit_grid_featurizer.py:1033: UserWarning: sanitize is set to False, pi_stack feature will be ignored
feature_type)
/home/bbrighttaer/anaconda3/envs/deepchem/lib/python3.5/site-packages/deepchem/feat/rdkit_grid_featurizer.py:1033: UserWarning: sanitize is set to False, cation_pi feature will be ignored
feature_type)
Featurizing Complexes
TIMING: Loading protein coordinates took 68.712 s
TIMING: Loading ligand coordinates took 0.226 s
TIMING: Centroid processing took 0.031 s
TIMING: Loading protein coordinates took 56.752 s
TIMING: Loading ligand coordinates took 0.258 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 138.730 s
TIMING: Loading ligand coordinates took 0.351 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 145.734 s
TIMING: Loading ligand coordinates took 0.472 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 151.042 s
TIMING: Loading ligand coordinates took 0.228 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 58.343 s
TIMING: Loading ligand coordinates took 0.207 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 59.712 s
TIMING: Loading ligand coordinates took 0.185 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 32.034 s
TIMING: Loading ligand coordinates took 0.123 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 29.732 s
TIMING: Loading ligand coordinates took 0.200 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 37.535 s
TIMING: Loading ligand coordinates took 0.308 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 38.232 s
TIMING: Loading ligand coordinates took 0.125 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 39.697 s
TIMING: Loading ligand coordinates took 0.293 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 43.844 s
TIMING: Loading ligand coordinates took 0.179 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 192.040 s
TIMING: Loading ligand coordinates took 0.195 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 200.334 s
TIMING: Loading ligand coordinates took 0.152 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 27.169 s
TIMING: Loading ligand coordinates took 0.201 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 71.067 s
TIMING: Loading ligand coordinates took 0.322 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 40.862 s
TIMING: Loading ligand coordinates took 0.203 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 46.853 s
TIMING: Loading ligand coordinates took 0.466 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 74.056 s
TIMING: Loading ligand coordinates took 0.127 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 28.232 s
TIMING: Loading ligand coordinates took 0.152 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 33.671 s
TIMING: Loading ligand coordinates took 0.124 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 48.756 s
TIMING: Loading ligand coordinates took 0.222 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 30.611 s
TIMING: Loading ligand coordinates took 0.187 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 31.885 s
TIMING: Loading ligand coordinates took 0.109 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 33.065 s
TIMING: Loading ligand coordinates took 0.154 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 50.392 s
TIMING: Loading ligand coordinates took 0.153 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 50.330 s
TIMING: Loading ligand coordinates took 0.201 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 113.721 s
TIMING: Loading ligand coordinates took 0.200 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 56.760 s
TIMING: Loading ligand coordinates took 0.173 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 28.073 s
TIMING: Loading ligand coordinates took 0.712 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 27.524 s
TIMING: Loading ligand coordinates took 0.241 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 22.017 s
TIMING: Loading ligand coordinates took 0.181 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 25.697 s
TIMING: Loading ligand coordinates took 0.208 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 23.619 s
TIMING: Loading ligand coordinates took 0.137 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 71.132 s
TIMING: Loading ligand coordinates took 0.200 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 19.380 s
TIMING: Loading ligand coordinates took 0.094 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 18.054 s
TIMING: Loading ligand coordinates took 0.209 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 16.051 s
TIMING: Loading ligand coordinates took 0.192 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 17.914 s
TIMING: Loading ligand coordinates took 0.103 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 20.533 s
TIMING: Loading ligand coordinates took 0.106 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 17.652 s
TIMING: Loading ligand coordinates took 0.095 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 123.923 s
TIMING: Loading ligand coordinates took 0.181 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 345.561 s
TIMING: Loading ligand coordinates took 0.200 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 366.242 s
TIMING: Loading ligand coordinates took 0.377 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 375.235 s
TIMING: Loading ligand coordinates took 0.121 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 18.864 s
TIMING: Loading ligand coordinates took 0.761 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 21.214 s
TIMING: Loading ligand coordinates took 0.147 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 19.958 s
TIMING: Loading ligand coordinates took 0.264 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 19.768 s
TIMING: Loading ligand coordinates took 0.297 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 148.126 s
TIMING: Loading ligand coordinates took 0.182 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 75.384 s
TIMING: Loading ligand coordinates took 0.157 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 22.592 s
TIMING: Loading ligand coordinates took 0.133 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 17.990 s
TIMING: Loading ligand coordinates took 0.545 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 22.372 s
TIMING: Loading ligand coordinates took 0.306 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 24.377 s
TIMING: Loading ligand coordinates took 0.261 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 146.261 s
TIMING: Loading ligand coordinates took 0.167 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 22.697 s
TIMING: Loading ligand coordinates took 0.349 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 23.308 s
TIMING: Loading ligand coordinates took 0.228 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 25.804 s
TIMING: Loading ligand coordinates took 0.098 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 13.271 s
TIMING: Loading ligand coordinates took 0.149 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 10.516 s
TIMING: Loading ligand coordinates took 0.199 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 12.922 s
TIMING: Loading ligand coordinates took 0.162 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 14.881 s
TIMING: Loading ligand coordinates took 0.175 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 13.670 s
TIMING: Loading ligand coordinates took 0.178 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 19.556 s
TIMING: Loading ligand coordinates took 0.479 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 65.861 s
TIMING: Loading ligand coordinates took 0.301 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 69.517 s
TIMING: Loading ligand coordinates took 0.111 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 71.032 s
TIMING: Loading ligand coordinates took 0.714 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 18.410 s
TIMING: Loading ligand coordinates took 0.152 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 14.085 s
TIMING: Loading ligand coordinates took 0.334 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 13.138 s
TIMING: Loading ligand coordinates took 0.304 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 15.175 s
TIMING: Loading ligand coordinates took 0.227 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 16.727 s
TIMING: Loading ligand coordinates took 0.262 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 34.385 s
TIMING: Loading ligand coordinates took 0.378 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 17.398 s
TIMING: Loading ligand coordinates took 0.252 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 20.040 s
TIMING: Loading ligand coordinates took 0.240 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 18.156 s
TIMING: Loading ligand coordinates took 0.118 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 15.263 s
TIMING: Loading ligand coordinates took 0.313 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 30.096 s
TIMING: Loading ligand coordinates took 0.230 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 28.747 s
TIMING: Loading ligand coordinates took 0.489 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 26.741 s
TIMING: Loading ligand coordinates took 0.480 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 12.010 s
TIMING: Loading ligand coordinates took 0.125 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 12.925 s
TIMING: Loading ligand coordinates took 0.777 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 18.702 s
TIMING: Loading protein coordinates took 15.788 s
TIMING: Loading ligand coordinates took 6.784 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading ligand coordinates took 2.396 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 12.877 s
TIMING: Loading ligand coordinates took 0.147 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 24.906 s
TIMING: Loading ligand coordinates took 0.119 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 15.538 s
TIMING: Loading protein coordinates took 15.077 s
TIMING: Loading ligand coordinates took 0.249 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading ligand coordinates took 0.502 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 22.135 s
TIMING: Loading protein coordinates took 12.151 s
TIMING: Loading ligand coordinates took 0.134 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 22.731 s
TIMING: Loading protein coordinates took 18.172 s
TIMING: Loading ligand coordinates took 0.111 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading ligand coordinates took 3.675 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading ligand coordinates took 8.742 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 11.032 s
TIMING: Loading ligand coordinates took 0.189 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 14.326 s
TIMING: Loading ligand coordinates took 0.329 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 11.595 s
TIMING: Loading ligand coordinates took 0.192 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 14.169 s
TIMING: Loading ligand coordinates took 0.137 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 13.715 s
TIMING: Loading ligand coordinates took 0.344 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 12.938 s
TIMING: Loading ligand coordinates took 0.128 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 24.076 s
TIMING: Loading ligand coordinates took 0.433 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 15.880 s
TIMING: Loading ligand coordinates took 0.112 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 11.433 s
TIMING: Loading ligand coordinates took 0.279 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 13.614 s
TIMING: Loading ligand coordinates took 0.112 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 14.032 s
TIMING: Loading ligand coordinates took 0.184 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 15.341 s
TIMING: Loading ligand coordinates took 0.128 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 13.817 s
TIMING: Loading ligand coordinates took 0.160 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 16.289 s
TIMING: Loading ligand coordinates took 0.134 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 11.999 s
TIMING: Loading ligand coordinates took 0.457 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 8.293 s
TIMING: Loading ligand coordinates took 0.274 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 11.667 s
TIMING: Loading ligand coordinates took 0.157 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 23.583 s
TIMING: Loading ligand coordinates took 0.190 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 9.789 s
TIMING: Loading ligand coordinates took 0.153 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 10.549 s
TIMING: Loading ligand coordinates took 0.211 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 59.172 s
TIMING: Loading ligand coordinates took 0.167 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 12.169 s
TIMING: Loading ligand coordinates took 0.257 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 10.238 s
TIMING: Loading ligand coordinates took 0.150 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 57.103 s
TIMING: Loading ligand coordinates took 0.955 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 13.453 s
TIMING: Loading ligand coordinates took 0.387 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 23.539 s
TIMING: Loading ligand coordinates took 0.108 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 15.320 s
TIMING: Loading ligand coordinates took 1.580 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 11.295 s
TIMING: Loading ligand coordinates took 0.518 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 19.396 s
TIMING: Loading ligand coordinates took 0.155 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 17.461 s
TIMING: Loading ligand coordinates took 0.182 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 19.456 s
TIMING: Loading ligand coordinates took 0.330 s
TIMING: Centroid processing took 0.003 s
TIMING: Loading protein coordinates took 7.509 s
TIMING: Loading ligand coordinates took 0.550 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 38.651 s
TIMING: Loading ligand coordinates took 0.133 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 9.310 s
TIMING: Loading ligand coordinates took 0.204 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 8.173 s
TIMING: Loading protein coordinates took 7.619 s
TIMING: Loading ligand coordinates took 0.125 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading ligand coordinates took 0.150 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 9.802 s
TIMING: Loading ligand coordinates took 0.156 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 6.746 s
TIMING: Loading ligand coordinates took 0.189 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 15.488 s
TIMING: Loading ligand coordinates took 0.114 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 18.546 s
TIMING: Loading ligand coordinates took 0.214 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 57.718 s
TIMING: Loading ligand coordinates took 0.289 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 15.249 s
TIMING: Loading ligand coordinates took 0.164 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 9.919 s
TIMING: Loading ligand coordinates took 0.211 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 9.767 s
TIMING: Loading ligand coordinates took 0.189 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 74.540 s
TIMING: Loading ligand coordinates took 0.253 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 8.837 s
TIMING: Loading ligand coordinates took 0.232 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 14.539 s
TIMING: Loading ligand coordinates took 0.354 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 20.324 s
TIMING: Loading ligand coordinates took 0.300 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 15.380 s
TIMING: Loading ligand coordinates took 0.099 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 14.199 s
TIMING: Loading ligand coordinates took 0.288 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 14.002 s
TIMING: Loading ligand coordinates took 0.116 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 47.555 s
TIMING: Loading ligand coordinates took 0.536 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 17.081 s
TIMING: Loading ligand coordinates took 0.281 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 14.119 s
TIMING: Loading ligand coordinates took 0.232 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 23.666 s
TIMING: Loading ligand coordinates took 0.369 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 197.293 s
TIMING: Loading ligand coordinates took 0.116 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 13.116 s
TIMING: Loading ligand coordinates took 0.128 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 13.518 s
TIMING: Loading ligand coordinates took 0.268 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 13.743 s
TIMING: Loading ligand coordinates took 0.331 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 5.172 s
TIMING: Loading ligand coordinates took 0.084 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 9.810 s
TIMING: Loading ligand coordinates took 0.092 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 10.328 s
TIMING: Loading ligand coordinates took 1.338 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 7.030 s
TIMING: Loading ligand coordinates took 0.085 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 6.804 s
TIMING: Loading ligand coordinates took 0.090 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 7.626 s
TIMING: Loading ligand coordinates took 0.093 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 29.528 s
TIMING: Loading ligand coordinates took 0.091 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 29.934 s
TIMING: Loading ligand coordinates took 0.336 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 27.520 s
TIMING: Loading ligand coordinates took 0.119 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 5.993 s
TIMING: Loading ligand coordinates took 0.184 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 4.592 s
TIMING: Loading ligand coordinates took 0.109 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 3.728 s
TIMING: Loading ligand coordinates took 0.134 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 9.151 s
TIMING: Loading ligand coordinates took 0.140 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 6.513 s
TIMING: Loading ligand coordinates took 0.586 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 10.200 s
TIMING: Loading ligand coordinates took 0.463 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 291.789 s
TIMING: Loading ligand coordinates took 0.211 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 11.282 s
TIMING: Loading ligand coordinates took 0.222 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 10.911 s
TIMING: Loading ligand coordinates took 0.270 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 343.876 s
TIMING: Loading ligand coordinates took 0.091 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 9.745 s
TIMING: Loading ligand coordinates took 0.161 s
TIMING: Centroid processing took 0.005 s
TIMING: Loading protein coordinates took 362.334 s
TIMING: Loading ligand coordinates took 0.302 s
TIMING: Centroid processing took 0.001 s
WARNING:root:Unable to add hydrogens math domain error
WARNING:root:Some molecules cannot be loaded by Rdkit. Skipping
TIMING: Loading protein coordinates took 49.391 s
TIMING: Loading ligand coordinates took 0.103 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 61.128 s
TIMING: Loading ligand coordinates took 0.227 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 56.799 s
TIMING: Loading ligand coordinates took 0.141 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 145.235 s
TIMING: Loading ligand coordinates took 0.379 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 139.361 s
TIMING: Loading ligand coordinates took 0.296 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 11.756 s
TIMING: Loading ligand coordinates took 0.198 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 10.075 s
TIMING: Loading ligand coordinates took 0.194 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 10.108 s
TIMING: Loading ligand coordinates took 0.102 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 10.616 s
TIMING: Loading ligand coordinates took 0.135 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 10.900 s
TIMING: Loading ligand coordinates took 0.128 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 11.485 s
TIMING: Loading ligand coordinates took 0.200 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 7.925 s
TIMING: Loading ligand coordinates took 0.254 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 7.115 s
TIMING: Loading ligand coordinates took 0.211 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 142.527 s
TIMING: Loading ligand coordinates took 0.250 s
TIMING: Centroid processing took 0.001 s
TIMING: Loading protein coordinates took 21.305 s
TIMING: Loading ligand coordinates took 0.283 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 12.979 s
TIMING: Loading ligand coordinates took 0.258 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 14.379 s
TIMING: Loading ligand coordinates took 0.090 s
TIMING: Centroid processing took 0.000 s
TIMING: Loading protein coordinates took 11.495 s
TIMING: Loading ligand coordinates took 0.075 s
TIMING: Centroid processing took 0.000 s
---------------------------------------------------------------------------
RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/bbrighttaer/anaconda3/envs/deepchem/lib/python3.5/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/home/bbrighttaer/anaconda3/envs/deepchem/lib/python3.5/site-packages/deepchem/feat/base_classes.py", line 16, in _featurize_complex
return featurizer._featurize_complex(mol_pdb_file, protein_pdb_file)
File "/home/bbrighttaer/anaconda3/envs/deepchem/lib/python3.5/site-packages/deepchem/feat/rdkit_grid_featurizer.py", line 1243, in _featurize_complex
protein_pdb_file, calc_charges=True, sanitize=self.sanitize)
File "/home/bbrighttaer/anaconda3/envs/deepchem/lib/python3.5/site-packages/deepchem/utils/rdkit_util.py", line 128, in load_molecule
my_mol = add_hydrogens_to_mol(my_mol)
File "/home/bbrighttaer/anaconda3/envs/deepchem/lib/python3.5/site-packages/deepchem/utils/rdkit_util.py", line 52, in add_hydrogens_to_mol
fixer.addMissingHydrogens(7.4)
File "/home/bbrighttaer/anaconda3/envs/deepchem/lib/python3.5/site-packages/pdbfixer/pdbfixer.py", line 1019, in addMissingHydrogens
modeller.addHydrogens(pH=pH)
File "/home/bbrighttaer/anaconda3/envs/deepchem/lib/python3.5/site-packages/simtk/openmm/app/modeller.py", line 901, in addHydrogens
LocalEnergyMinimizer.minimize(context, 1.0, 50)
File "/home/bbrighttaer/anaconda3/envs/deepchem/lib/python3.5/site-packages/simtk/openmm/openmm.py", line 2631, in minimize
return _openmm.LocalEnergyMinimizer_minimize(context, tolerance, maxIterations)
Exception: Particle coordinate is nan
"""
The above exception was the direct cause of the following exception:
Exception Traceback (most recent call last)
<ipython-input-7-13013ef4197c> in <module>()
----> 1 pdbbind_tasks, pdbbind_datasets, transformers = dc.molnet.load_pdbbind(featurizer="grid", split="random", subset="core")
2 train_dataset, valid_dataset, test_dataset = pdbbind_datasets
~/anaconda3/envs/deepchem/lib/python3.5/site-packages/deepchem/molnet/load_function/pdbbind_datasets.py in load_pdbbind(featurizer, split, subset, reload)
238 print("Featurizing Complexes")
239 features, failures = featurizer.featurize_complexes(ligand_files,
--> 240 protein_files)
241 # Delete labels for failing elements
242 labels = np.delete(labels, failures)
~/anaconda3/envs/deepchem/lib/python3.5/site-packages/deepchem/feat/base_classes.py in featurize_complexes(self, mol_files, protein_pdbs)
51 failures = []
52 for ind, result in enumerate(results):
---> 53 new_features = result.get()
54 # Handle loading failures which return None
55 if new_features is not None:
~/anaconda3/envs/deepchem/lib/python3.5/multiprocessing/pool.py in get(self, timeout)
642 return self._value
643 else:
--> 644 raise self._value
645
646 def _set(self, i, obj):
Exception: Particle coordinate is nan
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