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DeepRank / iScore

iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines
Apache License 2.0
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error when some pdb files cannot have graph generated #16

Closed LilySnow closed 4 years ago

LilySnow commented 4 years ago

When some pdb files cannot have graph generated, we will have the error message below. In this situation, all the pdb files have haddock energy (Energy.dat) and some models are missing from graphrank file (GraphRank.dat).

Traceback (most recent call last): File "/home/lixue/tools/iScore/bin/iScore.predict", line 63, i iscore() File "/home/lixue/tools/iScore/iScore/function/score.py", line self.read_graphrank() File "/home/lixue/tools/iScore/iScore/function/score.py", line data.append(self.features[m]['grank']) KeyError: 'grank'

This bug can be fixed by switching the order of the following two lines (quick and dirty):

From 

          self.read_graphrank()
         self.read_energy()

to 

          self.read_energy()
          self.read_graphrank()
CunliangGeng commented 4 years ago

if some models did not generate graphs, there should be a warning like Warning : Graph ** not exported (num_nodes = 0)' **). Did you see the warning ?

LilySnow commented 4 years ago

Yes. The warnings are there.

CunliangGeng commented 4 years ago

I have fixed the bug, please review PR #17.