Structure Checker : Abbreviated Group

  • Checker searches for abbreviated groups in the structure  * . Options:
    • expanded (:expanded=true);
    • contracted (:contracted=true);
    • both expanded and contracted groups (default).
    You can specify a list of excluded abbreviated groups, i.e., checker will not find (and fix) abbreviated groups that are indicated in this list. Default and custom abbreviations are also possible to set. The excluded list elements are case sensitive and should be separated by commas (,). (:excluded=Ph,Ala,Gly,MyGroup) 
    excluded list
  • Fixer offers - in order of priority -:
    1. ungroup abbreviated groups (ungroup);
    2. expand abbreviated groups (expandgroup);
    3. contract abbreviated groups (contractgroup).


Example :

Abbreviated Group Checker (abbrevgroup) Warning: Fix
Ungroup (ungroup) Expand Group (expandgroup) Contract Group (contractgroup)
Detect Expanded Groups ex_abbrev_exp_ch ex_abbrev_contr_f unavailable ex_abbrev_contr_f
Detect Contracted Groups ex_abbrev_contr_f ex_abbrev_contr_f ex_abbrev_contr_f unavailable
Detect All Groups ex_abbrev_both_ch ex_abbrev_both_f ex_abbrev_both_fex ex_abbrev_both_fcontr
Detect Contracted Groups with excluded list ex_abbrev_exclude_ch ex_abbrev_exclude_f ex_abbrev_exclude_f ex_abbrev_both_fcontr


* Note :  User defined abbreviated groups  are also available to be applied as recognizable abbreviated group set.
Note : If attachment point is not connected to any atom, ungrouping removes attachment points of the abbreviated group and adds an implicit hydrogen.