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:

images/download/attachments/1806488/explicit_H_types.png

  • 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/1806488/ex_explh_ch.png
ex_explh_ch

images/download/attachments/1806488/ex_explh_f.png
ex_explh_f