Explicit Hydrogen

    • Checker searches for explicit hydrogens.

      The following different types of explicit hydrogens can be searched:

      • Lonely : hydrogen atom without connection (:lonely=true)

      • Isotopic : hydrogen isotopes (:isotopic=true)

      • Charged : charged hydrogen atoms (:charged=true)

      • Radical : hydrogen radicals (:radical=true)

      • Mapped : mapped hydrogens (:mapped=true)

      • Wedged : hydrogen connecting with wedged bond (:wedged=true)

      • H Connected : hydrogen connected to a hydrogen atom (:hconnected=true)

      • Polymer End Group : hydrogen connected to a SRU S-group (:polymerendgroup=true)

      • S-group End : hydrogen connected to a Superatom S-group (:sgroupend=true)

      • S-group : hydrogen which is the only atom in an S-group (:sgroup=true)

      • Valence Error : hydrogen connected to an atom which has valence error (:valenceerror=true)

      • Bridgehead : hydrogen connected to a bridgehead atom (:bridgehead=true)

    This picture summarizes the applied categorizations:

    • The corresponding fixer offers removing explicit hydrogens and the selected special atoms (removeexplicith).

      Example :

      Explicit Hydrogen Checker (explicith) Warning: Fix
      Remove Explicit Hydrogen (removeexplicith)
      Detect Explicit Hydrogen images/download/attachments/5313217/ex_explh_ch.png ex_explh_ch images/download/attachments/5313217/ex_explh_f.png ex_explh_f