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gcorso / DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
https://arxiv.org/abs/2210.01776
MIT License
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nan value filled SDF files being produced by DiffDock #208

Open KeaunAmani opened 6 months ago

KeaunAmani commented 6 months ago

For some reason the new DiffDock will randomly produce output SDF files like the one below and not report any errors in the process.

     RDKit          3D

 15 14  0  0  0  0  0  0  0  0999 V2000
       nan       nan       nan N   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan C   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan C   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan N   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan C   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan C   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan C   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan C   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan C   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan C   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan N   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan C   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan N   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan Cl  0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
  6 11  1  0
 11 12  2  0
  2 13  2  0
 12  4  1  0
 10  5  1  0
M  END
$$$$
asarigun commented 6 months ago

I also got something like that which has a confidence score of -1000!