Alias

  • Checker searches for aliases in the structure.

  • Fixers:

    • converting alias to abbreviated group if the alias value corresponds to a group in the abbreviated group list * (aliastogroup);

    • converting alias to atom if the alias value corresponds to an element (e.g., Ar) (aliastoatom);

    • removing alias (revealing the atom under the alias) ** (removealias);

    • deleting the atom having alias information (removeatom).

Example :

Alias Checker (alias)

Warning:

Fix

Convert Alias to Group (aliastogroup)

Convert to Atom (aliastoatom)

Remove Alias (removealias)

Delete Atom (removeatom)

Detect Alias

images/download/attachments/1803788/ex_alias_ch.png
ex_alias_ch

images/download/attachments/1803788/ex_alias_fcong.png
convert ot group

images/download/attachments/1803788/ex_alias_fcona.png
convert to atom

images/download/attachments/1803788/ex_alias_frem.png
ex_alias_frem

images/download/attachments/1803788/ex_alias_fdel.png
ex_alias_fdel

"OMe" and "CL" were defined as alias. After converting "OMe" to methoxy group, the abbreviated group is linked correctly to the chain, i.e., bond through the oxygen atom.


* User defined abbreviated groups are also available to be applied as recognizable abbreviated group set.
** Alias only covers the atom, and fixer removes this alias from the original atom.

Alias atoms are not supported in the MolV3000 format. With file conversions from MolV2000 into MolV3000 format the alias info will be lost.