oxpig / deepcoy Goto Github PK

Dear author,

I've used your code succesfully already, however now I am trying to use it again but I run into some errors and I cannot figure out what is wrong. In the first run, everything went fine, but I noticed that on my part, the smiles I input, didnt have the stereoisomer/enantiomer informations (@,/,\ signs). Now that I added them, DeepCoy is not able to generate the model anymore.
The error code is below:
IndexError Traceback (most recent call last)
in
1 # Setup model and generate molecules
----> 2 model = DenseGGNNChemModel(args)
3 model.train()
4 # Free up some memory
5 model = ''

/data/projects/discovery.science/applic/DeepCoy/DeepCoy.py in init(self, args)
53 class DenseGGNNChemModel(ChemModel):
54 def init(self, args):
---> 55 super().init(args)
56
57 @classmethod

/data/projects/discovery.science/applic/DeepCoy/GGNN_DeepCoy.py in init(self, args)
66 self.annotation_size = 0
67 self.train_data = self.load_data(params['train_file'], is_training_data=True)
---> 68 self.valid_data = self.load_data(params['valid_file'], is_training_data=False)
69
70 # Build the actual model

/data/projects/discovery.science/applic/DeepCoy/GGNN_DeepCoy.py in load_data(self, file_name, is_training_data)
107 self.annotation_size = max(self.annotation_size, len(data[0]["node_features_in"][0]))
...
---> 13 if neighbor != node_in_focus and color[neighbor] < 2 and
14 not check_adjacent_sparse(adj_mat, node_in_focus, neighbor)[0]:
15 min_valence = min(valences[node_in_focus], valences[neighbor], 3)

IndexError: list index out of range