Use code to extract protein features, code error

[zhouhao-learning]

I have an unexpected error when extracting protein features. My code is as follows:

import deepchem as dc
pdbbind_tasks, pdbbind_datasets, transformers = dc.molnet.load_pdbbind(featurizer="grid", split="r")

But in the middle I got the following error:

RemoteTraceback                           Traceback (most recent call last)
RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/home/zh/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/home/zh/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/site-packages/deepchem/feat/base_classes.py", line 16, in _featurize_complex
    return featurizer._featurize_complex(mol_pdb_file, protein_pdb_file)
  File "/home/zh/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/site-packages/deepchem/feat/rdkit_grid_featurizer.py", line 1243, in _featurize_complex
    protein_pdb_file, calc_charges=True, sanitize=self.sanitize)
  File "/home/zh/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/site-packages/deepchem/utils/rdkit_util.py", line 128, in load_molecule
    my_mol = add_hydrogens_to_mol(my_mol)
  File "/home/zh/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/site-packages/deepchem/utils/rdkit_util.py", line 52, in add_hydrogens_to_mol
    fixer.addMissingHydrogens(7.4)
  File "/home/zh/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/site-packages/pdbfixer/pdbfixer.py", line 1019, in addMissingHydrogens
    modeller.addHydrogens(pH=pH)
  File "/home/zh/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/site-packages/simtk/openmm/app/modeller.py", line 901, in addHydrogens
    LocalEnergyMinimizer.minimize(context, 1.0, 50)
  File "/home/zh/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/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-20-499bae175249> in <module>
----> 1 pdbbind_tasks, pdbbind_datasets, transformers = dc.molnet.load_pdbbind(featurizer="grid", split="r")

~/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/site-packages/deepchem/molnet/load_function/pdbbind_datasets.py in load_pdbbind(featurizer, load_binding_pocket, split, subset, reload)
    276   print("Featurizing Complexes")
    277   features, failures = featurizer.featurize_complexes(ligand_files,
--> 278                                                       protein_files)
    279   # Delete labels for failing elements
    280   labels = np.delete(labels, failures)

~/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/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:

~/sda3/Anaconda3/envs/deep2.0.0/lib/python3.6/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

Is this a problem with your code or a problem with the data you provided? How should I solve this problem? Please give me some guidance, thank you

[peastman]

Does this happen consistently? Or if you rerun it does it work correctly?

Here's what the stack trace shows. After loading one of the molecules, it called PDBFixer to add hydrogens that were missing from the PDB file. It does that by first adding the hydrogens at more or less random positions, then doing an energy minimization to move them into more physically realistic positions. If two hydrogens randomly happened to get put at almost exactly the same position, that might potentially lead the minimization to produce a nan. If so, this should just be a rare, random event. But if it happens consistently, we need to investigate further.

[zhouhao-learning]

@peastman Sorry, I ran again, but I still got this error

[zhouhao-learning]

@peastman Can you solve this problem, can I update the code?

[peastman]

I just tried running this, and everything worked correctly for me. Note that there's an error in your code: split="r" is not a legal option. I assume you meant split="random"? Anyway, it ran for me and successfully loaded and featurized the datasets.

That's with the very most recent code for DeepChem, PDBFixer, and OpenMM. What versions do you have? It's conceivable the problem you're seeing is caused by a bug in one of them that has since been fixed.

[zhouhao-learning]

my Deepchem version is 2.1.1, I don't know why, no matter how many times I execute the code, I always get this error.

[peastman]

And what about PDBFixer and OpenMM?

Try upgrading all of them to the latest versions.

[zhouhao-learning]

@peastman I updated PDBFixer and OpenMM, PDBFixer==1.5, OpenMM==7.3.1, both of which are the latest versions, then I try to run the code again and still get this error.

[rbharath]

If you're still having issues, check out the updated tutorials. I've got an tutorial up with pdbbind and grid features now. I'm going to close this issue, but please re-open if you're still facing issues!