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devalab / DeepPocket

Ligand Binding Site detection using Deep Learning
MIT License
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IndexError: list index out of range in output_pocket_pdb (segment_pockets.py) #3

Closed pjmartel closed 3 years ago

pjmartel commented 3 years ago

Hello,

I'm trying to run the the Predicting Binding Site section example:

python predict.py -p protein.pdb -c first_model_fold1_best_test_auc_85001.pth.tar -s seg0_best_test_IOU_91.pth.tar -r 3

But it crashes with the following errors:

***** POCKET HUNTING BEGINS ***** ***** POCKET HUNTING ENDS ***** /usr/local/lib/python3.7/dist-packages/Bio/PDB/StructureBuilder.py:92: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 1951. PDBConstructionWarning, /usr/local/lib/python3.7/dist-packages/Bio/PDB/StructureBuilder.py:92: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 2008. PDBConstructionWarning, /content/DeepPocket/rank_pockets.py:87: UserWarning: Implicit dimension choice for softmax has been deprecated. Change the call to include dim=X as an argument. all_probs.append(F.softmax(output).detach().cpu()) @> 1674 atoms and 1 coordinate set(s) were parsed in 0.01s. Traceback (most recent call last): File "predict.py", line 116, in <module> test(seg_model, seg_eptest, seg_gmaker,device,dx_name, args) File "/content/DeepPocket/segment_pockets.py", line 142, in test output_pocket_pdb(dx_name+'_pocket'+str(count)+'.pdb',prot_prody,pred_aa) File "/content/DeepPocket/segment_pockets.py", line 82, in output_pocket_pdb pocket=prot_prody.select(sel_str) File "/usr/local/lib/python3.7/dist-packages/prody/atomic/atomic.py", line 232, in select return SELECT.select(self, selstr, **kwargs) File "/usr/local/lib/python3.7/dist-packages/prody/atomic/select.py", line 885, in select indices = self.getIndices(atoms, selstr, **kwargs) File "/usr/local/lib/python3.7/dist-packages/prody/atomic/select.py", line 943, in getIndices torf = self.getBoolArray(atoms, selstr, **kwargs) File "/usr/local/lib/python3.7/dist-packages/prody/atomic/select.py", line 995, in getBoolArray tokens = parser(selstr, parseAll=True) File "/usr/local/lib/python3.7/dist-packages/prody/atomic/select.py", line 1100, in _noParser return [self._default(selstr, 0, selstr.split())] File "/usr/local/lib/python3.7/dist-packages/prody/atomic/select.py", line 1118, in _default torf, err = self._and2(sel, loc, tokens) File "/usr/local/lib/python3.7/dist-packages/prody/atomic/select.py", line 1319, in _and2 firsttoken = tokens[0] if not isinstance(tokens[0], Iterable) else list(tokens[0]) IndexError: list index out of range

Ubuntu 18.04 on Google Colab (pytorch 1.9+cuda 10.2) with prody version 2.0.

RishalAggarwal commented 3 years ago

Hi, could you also share the pdb file to reproduce the error

pjmartel commented 3 years ago

My apologies. The pdb file is 1k2c.pdb - in fact I used the following command line:

python predict.py -p 1k2c.pdb -c first_model_fold1_best_test_auc_85001.pth.tar -s seg0_best_test_IOU_91.pth.tar -r 3.

RishalAggarwal commented 3 years ago

Thank you for bringing this to my attention, the script could not handle cases where no binding site residues are predicted (which unfortunately can be the case sometimes with Deep Learning models). Fixed the issue it should work now. Also, now I've made sure that the script doesn't run if the model weights are not specified, hopefully that addresses the other problem you had. Closing the issue now, do reopen if you have any more issues.