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bjornwallner / DockQ

DockQ is a single continuous quality measure for protein docked models based on the CAPRI evaluation protocol
MIT License
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np.dot(ligand_atoms_sample, rot) error. #29

Closed luwei0917 closed 1 month ago

luwei0917 commented 1 month ago

Hello, Most of my cases run smoothly, but I tried 'DockQ B.cif A.pdb', this give me error, rotated_sample_atoms = np.dot(ligand_atoms_sample, rot) + tran ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: shapes (0,) and (3,3) not aligned: 0 (dim 0) != 3 (dim 0)

case.zip

Do you know why? Thanks.

clami66 commented 1 month ago

Hi,

At the bottom of A.pdb you have small molecules marked as ATOM records.

ATOM   7396  MG   MG     1      42.919  43.434  79.010  1.00 67.80           M  
ATOM   7397  PG  GTP C   2      42.759  40.202  78.638  1.00 41.72           P  
ATOM   7398  O1G GTP C   2      43.055  38.964  79.589  1.00 41.38           O  
...

Delete those or mark them as HETATM instead, and the issue should be fixed