Created
December 18, 2018 14:36
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Save bbrighttaer/a31e6084e58cdf859c680612bc64d58e to your computer and use it in GitHub Desktop.
I tried loading the core subset of the pdbbind dataset using deepchem 2.1.1
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| /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 | |
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| TIMING: Loading protein coordinates took 138.730 s | |
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| TIMING: Loading protein coordinates took 145.734 s | |
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| TIMING: Loading protein coordinates took 151.042 s | |
| TIMING: Loading ligand coordinates took 0.228 s | |
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| TIMING: Loading protein coordinates took 58.343 s | |
| TIMING: Loading ligand coordinates took 0.207 s | |
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| TIMING: Loading protein coordinates took 59.712 s | |
| TIMING: Loading ligand coordinates took 0.185 s | |
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| TIMING: Loading protein coordinates took 192.040 s | |
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| TIMING: Loading protein coordinates took 27.169 s | |
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| TIMING: Loading protein coordinates took 74.056 s | |
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| TIMING: Loading protein coordinates took 28.232 s | |
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| TIMING: Loading protein coordinates took 17.990 s | |
| TIMING: Loading ligand coordinates took 0.545 s | |
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| TIMING: Loading protein coordinates took 22.372 s | |
| TIMING: Loading ligand coordinates took 0.306 s | |
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| TIMING: Loading ligand coordinates took 0.261 s | |
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| TIMING: Loading protein coordinates took 146.261 s | |
| TIMING: Loading ligand coordinates took 0.167 s | |
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| TIMING: Loading protein coordinates took 22.697 s | |
| TIMING: Loading ligand coordinates took 0.349 s | |
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| TIMING: Loading ligand coordinates took 0.228 s | |
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| TIMING: Loading protein coordinates took 25.804 s | |
| TIMING: Loading ligand coordinates took 0.098 s | |
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| TIMING: Loading protein coordinates took 13.271 s | |
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| TIMING: Loading ligand coordinates took 0.199 s | |
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| TIMING: Loading ligand coordinates took 0.162 s | |
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| TIMING: Loading protein coordinates took 14.881 s | |
| TIMING: Loading ligand coordinates took 0.175 s | |
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| TIMING: Loading protein coordinates took 13.670 s | |
| TIMING: Loading ligand coordinates took 0.178 s | |
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| TIMING: Loading protein coordinates took 65.861 s | |
| TIMING: Loading ligand coordinates took 0.301 s | |
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| TIMING: Loading protein coordinates took 69.517 s | |
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| TIMING: Loading ligand coordinates took 0.152 s | |
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| TIMING: Loading ligand coordinates took 6.784 s | |
| TIMING: Centroid processing took 0.000 s | |
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| TIMING: Loading ligand coordinates took 0.249 s | |
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| TIMING: Loading protein coordinates took 22.135 s | |
| TIMING: Loading protein coordinates took 12.151 s | |
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| TIMING: Loading protein coordinates took 18.172 s | |
| TIMING: Loading ligand coordinates took 0.111 s | |
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| TIMING: Loading ligand coordinates took 0.344 s | |
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| TIMING: Loading ligand coordinates took 0.433 s | |
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| TIMING: Loading protein coordinates took 23.539 s | |
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| TIMING: Loading ligand coordinates took 1.580 s | |
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| 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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