Pseudo Atom

  • 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 Atom

images/download/attachments/1806475/ex_pseudo_ch.png
ex_pseudo_ch

images/download/attachments/1806475/no.png
not available

images/download/attachments/1806475/ex_pseudo_f.png
ex_pseudo_f

images/download/attachments/1806475/ex_pseudo_fdel.png
ex_pseudo_f

Detect Pseudo Atom

images/download/attachments/1806475/ex_pseudo_ch2.png
ex_pseudo_ch

images/download/attachments/1806475/ex_pseudo_fgroup.png
ex_pseudo_f

images/download/attachments/1806475/ex_pseudo_fconv.png
ex_pseudo_f

images/download/attachments/1806475/ex_pseudo_fdel2.png
ex_pseudo_f

Detect Pseudo Atom with excluded list

(pseudoatom:excluded='PG')

images/download/attachments/1806475/pseudo_atom_checker_excluded.png

images/download/attachments/1806475/pseudo_atom_checker_excluded_fix_pseudotogroup.png

images/download/attachments/1806475/pseudo_atom_checker_excluded_fix_converttocarbon.png

images/download/attachments/1806475/pseudo_atom_checker_excluded_fix_removeatom.png

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