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  • Checker searches for pseudo atoms in the molecule. A list of excluded atom labels can be specified, the checker will not find (and fix) pseudo atoms with labels that are indicated in this list.
  • Fixer offers:
    1. converting to abbreviated group if the name is in the abbreviated group list (e.g., Et for ethyl) * (pseudotogroup);
    2. converting to carbon atom (converttocarbon);
    3. deleting atom (removeatom).


Example :

Pseudo Atom Checker (pseudoatom)Warning:Fix
Convert Pseudo Atom to Group (pseudotogroup)Convert to Carbon (converttocarbon)Delete Atom (removeatom)
Detect Pseudo Atomex_pseudo_chnot availableex_pseudo_fex_pseudo_f
Detect Pseudo Atomex_pseudo_chex_pseudo_fex_pseudo_fex_pseudo_f

Detect Pseudo Atom with excluded list

(pseudoatom:excluded='PG')

* Note User defined abbreviated groups  are also available to be applied as recognizable abbreviated group set.