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	ex_explh_ch	ex_explh_f