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  • 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 Hydrogenex_explh_chex_explh_f