Structure Checker : Overlapping Bonds

  • 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 Bonds ex_overlappingbonds_ch ex_overlappingbonds_f


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