Abbreviated Group StrCh

  • 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)

    images/download/attachments/1803798/ex_abbrev_excluded01.png
    excluded list
  • Fixer offers(in order of priority):

    • ungroup abbreviated groups (ungroup);

    • expand abbreviated groups (expandgroup);

    • contract abbreviated groups (contractgroup).

Example :

Abbreviated Group Checker (abbrevgroup)

Warning:

Fix

Ungroup (ungroup)

Expand Group (expandgroup)

Contract Group (contractgroup)

Detect Expanded Groups

images/download/attachments/1803798/ex_abbrev_exp_ch.png
ex_abbrev_exp_ch

images/download/attachments/1803798/ex_abbrev_exp_f.png
ex_abbrev_contr_f

images/download/attachments/1803798/no.png
unavailable

images/download/attachments/1803798/ex_abbrev_exp_fcont.png
ex_abbrev_contr_f

Detect Contracted Groups

images/download/attachments/1803798/ex_abbrev_contr_ch.png
ex_abbrev_contr_f

images/download/attachments/1803798/ex_abbrev_contr_f.png
ex_abbrev_contr_f

images/download/attachments/1803798/ex_abbrev_contr_fex.png
ex_abbrev_contr_f

images/download/attachments/1803798/no.png
unavailable

Detect All Groups

images/download/attachments/1803798/ex_abbrev_both_ch.png
ex_abbrev_both_ch

images/download/attachments/1803798/ex_abbrev_both_f.png
ex_abbrev_both_f

images/download/attachments/1803798/ex_abbrev_both_fex.png
ex_abbrev_both_fex

images/download/attachments/1803798/ex_abbrev_both_fcont.png
ex_abbrev_both_fcontr

Detect Contracted Groups with excluded list

images/download/attachments/1803798/ex_abbrev_excluded02_ex.png
ex_abbrev_exclude_ch

images/download/attachments/1803798/ex_abbrev_excluded02_fung.png
ex_abbrev_exclude_f

images/download/attachments/1803798/ex_abbrev_excluded02_fex.png
ex_abbrev_exclude_f

images/download/attachments/1803798/no.png
ex_abbrev_both_fcontr

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

If attachment point is not connected to any atom, ungrouping removes attachment points of the abbreviated group and adds an implicit hydrogen.