Remove missing PDBs from ModuleIO

[joaomcteixeira]

Closes #307

Removes missing PDBs from ModuleIO when checking the fauly.

[joaomcteixeira]

@amjjbonvin can you test it to see if the #307 error persists?

[codecov-commenter]

Codecov Report

Merging #313 (2db63e5) into main (a2e471c) will decrease coverage by 0.14%.
The diff coverage is 8.33%.

@@            Coverage Diff             @@
##             main     #313      +/-   ##
==========================================
- Coverage   56.18%   56.04%   -0.15%     
==========================================
  Files          56       56              
  Lines        3540     3551      +11     
==========================================
+ Hits         1989     1990       +1     
- Misses       1551     1561      +10     

Impacted Files	Coverage Δ
src/haddock/libs/libontology.py	41.12% <8.33%> (-3.12%)	⬇️

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