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jivankandel / PUResNet

Predicting protein-ligand binding sites using deep convolutional neural network
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What other steps should be taken ahead now? getting error as could not open whole_trained_model.hdf #12

Closed vishal-farande closed 11 months ago

vishal-farande commented 11 months ago

I had entered code as python predict.py -ftype pdb -m 0 -i /Users/vishalfarande/Downloads/PUResNet-main/coach420/966c/protein.pdb -mpath whole_trained_model1.hdf -otype mol2 -o output -gpu 1

further I got something like 2023-11-27 17:59:12.927852: W tensorflow/core/util/tensor_slice_reader.cc:97] Could not open whole_trained_model1.hdf: DATA_LOSS: not an sstable (bad magic number): perhaps your file is in a different file format and you need to use a different restore operator?

*** Open Babel Warning in PerceiveBondOrders Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is /Users/vishalfarande/Downloads/PUResNet-main/coach420/966c/protein.pdb)

2023-11-27 17:59:13.183370: W tensorflow/tsl/platform/profile_utils/cpu_utils.cc:128] Failed to get CPU frequency: 0 Hz 1/1 [==============================] - 1s 742ms/step /Users/vishalfarande/anaconda3/envs/Puresnet/lib/python3.11/site-packages/openbabel/init.py:14: UserWarning: "import openbabel" is deprecated, instead use "from openbabel import openbabel" warnings.warn('"import openbabel" is deprecated, instead use "from openbabel import openbabel"')

jivankandel commented 11 months ago

Dear bishal-farande, whole_trained_model1.hdf this file is uploded through git-lfs, you need to download file from github. Cloning wont work in this case.