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 (clean) or;

      2. partial clean (partialclean).

      Example :

      Overlapping Bonds Checker (overlappingBonds) Warning: Fix
      Clean (clean)
      Detect Overlapping Bonds overlapping bonds checked overlapping bonds fixed

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