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  • Checker searches for overlapping bonds: bonds crossing each other or bonds closer to each other than the set minimal value.
  • Fixer offers cleaning the structure by:
    1. 2D clean or (clean);
    2. partial clean (partialclean).


Example :

Overlapping Bonds Checker (overlappingBonds)Warning:Fix
Clean (clean)
Detect Overlapping Bondsex_overlappingbonds_chex_overlappingbonds_f


Note : Bridged polycycles are cleaned as far as their structure allows it, and the overlapping bonds warning will remain.