update key deletion logic in topoaa

[VGPReys]

Solve the dictionary changed size during iteration error in topoaa when

Previous bug:

[2023-12-21 17:24:42,019 libutil ERROR] dictionary changed size during iteration
Traceback (most recent call last):
  File "/trinity/login/vreys/benchmarking/haddock3/src/haddock/libs/libutil.py", line 335, in log_error_and_exit
    yield
  File "/trinity/login/vreys/benchmarking/haddock3/src/haddock/clis/cli.py", line 185, in main
    workflow.run()
  File "/trinity/login/vreys/benchmarking/haddock3/src/haddock/libs/libworkflow.py", line 43, in run
    step.execute()
  File "/trinity/login/vreys/benchmarking/haddock3/src/haddock/libs/libworkflow.py", line 155, in execute
    self.module.run()  # type: ignore
  File "/trinity/login/vreys/benchmarking/haddock3/src/haddock/modules/base_cns_module.py", line 61, in run
    self._run()
  File "/trinity/login/vreys/benchmarking/haddock3/src/haddock/modules/topology/topoaa/__init__.py", line 247, in _run
    self.export_io_models(faulty_tolerance=self.params["tolerance"])
  File "/trinity/login/vreys/benchmarking/haddock3/src/haddock/modules/__init__.py", line 285, in export_io_models
    faulty = io.check_faulty()
  File "/trinity/login/vreys/benchmarking/haddock3/src/haddock/libs/libontology.py", line 214, in check_faulty
    self.remove_missing()
  File "/trinity/login/vreys/benchmarking/haddock3/src/haddock/libs/libontology.py", line 224, in remove_missing
    for key2 in element:
RuntimeError: dictionary changed size during iteration
[2023-12-21 17:24:42,030 libutil ERROR] dictionary changed size during iteration

This bug could appear when input molecules are not PDB compliant.
Now the error is managed and if one of the molecule failed, the tolerance parameter will either accept or terminate the run peroperly.

Closes #759

[codecov]

Codecov Report

Attention: 4 lines in your changes are missing coverage. Please review.

Comparison is base (00c8ac4) 72.54% compared to head (66656a6) 72.51%.
Report is 1 commits behind head on main.

Files	Patch %	Lines
src/haddock/libs/libontology.py	0.00%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #766      +/-   ##
==========================================
- Coverage   72.54%   72.51%   -0.03%     
==========================================
  Files          80       80              
  Lines        7566     7569       +3     
==========================================
  Hits         5489     5489              
- Misses       2077     2080       +3     

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[mgiulini]

it worked on an example!