Structure Checking and Fixing

After the validation and standardization, the compound undergoes structure checker steps, and some of the issues are fixed automatically. The structure checking is performed for both single compounds and multi-component compounds.

Example for structure checkers:

  • Three Dimension Checker:
    Thecker searches for 3D (Z) coordinates. Fixer offers: cleaning the structures by 2D clean and setting the atomic z-coordinates to zero.

  • Rare element checker:
    The checker searches for rare elements in the structures: atoms generally not present in organic compounds (E.g. Ru). No fix is available for this checker.

  • Valence error checker:
    Checker searches for valence errors. Fixer offers removing explicit hydrogens if applicable

If the checker is on, and the structure to be registered is not passing the quality check, the submission can be:

      • either autoregistered (in case if the checker has an autofix)

        Click here for an example

        e.g. structures containing radicals are automatically registered without any radical

      • or not autoregistered, and sent to the Staging area for revision.

        Click here for an example

        e.g. dicyclohexylruthenium will fall to the Staging area with "Registration failed" message because of the rare element checker defined within the quality checks. In order to register it, the Perform Quality Checks Switcher (from Staging, Submission page) should be turned off