I found the following error while loading the mp_metallicity dataset.
Exception message: Python argument types in
rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect(dict, int)
did not match C++ signature:
GetMorganFingerprintAsBitVect(RDKit::ROMol mol, int radius, unsigned int nBits=2048, boost::python::api::object invariants=[], boost::python::api::object fromAtoms=[], bool useChirality=False, bool useBondTypes=True, bool useFeatures=False, boost::python::api::object bitInfo=None, bool includeRedundantEnvironments=False)
job exception: need at least one array to concatenate
0%| | 0/16 [27:21<?, ?trial/s, best loss=?]
Traceback (most recent call last):
File "fingerprint.py", line 204, in
val_metrics, test_metrics = bayesian_optimization(args)
File "fingerprint.py", line 137, in bayesian_optimization
max_evals=args['num_trials'])
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 553, in fmin
rval.exhaust()
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 356, in exhaust
self.run(self.max_evals - n_done, block_until_done=self.asynchronous)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 292, in run
self.serial_evaluate()
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 170, in serial_evaluate
result = self.domain.evaluate(spec, ctrl)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/base.py", line 907, in evaluate
rval = self.fn(pyll_rval)
File "fingerprint.py", line 120, in objective
val_metrics, test_metrics = main(save_path, configure, hyperparams)
File "fingerprint.py", line 49, in main
args, tasks, all_dataset, transformers = load_dataset(args)
File "/home/v-yuanqidu/moleculenet/examples/utils.py", line 101, in load_dataset
featurizer=featurizer, splitter=splitter, reload=False)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/molnet/load_function/material_datasets/load_mp_metallicity.py", line 107, in load_mp_metallicity
return loader.load_dataset('mp-metallicity', reload)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/molnet/load_function/molnet_loader.py", line 189, in load_dataset
t.create_transformer(transformer_dataset) for t in self.transformers
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/molnet/load_function/molnet_loader.py", line 189, in
t.create_transformer(transformer_dataset) for t in self.transformers
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/molnet/load_function/molnet_loader.py", line 37, in create_transformer
return self.transformer_class(dataset=dataset, **self.kwargs)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/trans/transformers.py", line 916, in init
w = dataset.w
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/data/datasets.py", line 2476, in w
return np.vstack(ws)
File "<__array_function__ internals>", line 6, in vstack
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/numpy/core/shape_base.py", line 283, in vstack
return _nx.concatenate(arrs, 0)
File "<__array_function__ internals>", line 6, in concatenate
ValueError: need at least one array to concatenate
I found the following error while loading the mp_metallicity dataset.
Exception message: Python argument types in rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect(dict, int) did not match C++ signature: GetMorganFingerprintAsBitVect(RDKit::ROMol mol, int radius, unsigned int nBits=2048, boost::python::api::object invariants=[], boost::python::api::object fromAtoms=[], bool useChirality=False, bool useBondTypes=True, bool useFeatures=False, boost::python::api::object bitInfo=None, bool includeRedundantEnvironments=False)
job exception: need at least one array to concatenate
0%| | 0/16 [27:21<?, ?trial/s, best loss=?] Traceback (most recent call last): File "fingerprint.py", line 204, in
val_metrics, test_metrics = bayesian_optimization(args)
File "fingerprint.py", line 137, in bayesian_optimization
max_evals=args['num_trials'])
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 553, in fmin
rval.exhaust()
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 356, in exhaust
self.run(self.max_evals - n_done, block_until_done=self.asynchronous)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 292, in run
self.serial_evaluate()
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 170, in serial_evaluate
result = self.domain.evaluate(spec, ctrl)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/base.py", line 907, in evaluate
rval = self.fn(pyll_rval)
File "fingerprint.py", line 120, in objective
val_metrics, test_metrics = main(save_path, configure, hyperparams)
File "fingerprint.py", line 49, in main
args, tasks, all_dataset, transformers = load_dataset(args)
File "/home/v-yuanqidu/moleculenet/examples/utils.py", line 101, in load_dataset
featurizer=featurizer, splitter=splitter, reload=False)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/molnet/load_function/material_datasets/load_mp_metallicity.py", line 107, in load_mp_metallicity
return loader.load_dataset('mp-metallicity', reload)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/molnet/load_function/molnet_loader.py", line 189, in load_dataset
t.create_transformer(transformer_dataset) for t in self.transformers
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/molnet/load_function/molnet_loader.py", line 189, in
t.create_transformer(transformer_dataset) for t in self.transformers
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/molnet/load_function/molnet_loader.py", line 37, in create_transformer
return self.transformer_class(dataset=dataset, **self.kwargs)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/trans/transformers.py", line 916, in init
w = dataset.w
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/data/datasets.py", line 2476, in w
return np.vstack(ws)
File "<__array_function__ internals>", line 6, in vstack
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/numpy/core/shape_base.py", line 283, in vstack
return _nx.concatenate(arrs, 0)
File "<__array_function__ internals>", line 6, in concatenate
ValueError: need at least one array to concatenate