changes in abbreviation groups

User 870ab5b546

11-09-2014 14:43:39

The Marvin History of Changes page says that for version 14.9.1.0, "Abbreviation groups have been revisited and formatted according to the IUPAC recommendation." Do you have a page with information about exactly what has changed? If not, can you share that information here?

ChemAxon 7936325a45

11-09-2014 15:32:30

Dear Bob,


In 14.9.1 the only change for the abbrviated groups was that the indexes and charges are subscripted and superscripted again.


The attached file contains a list of the changed abbreviated groups. These groups are having a formatted name since 14.9.8, for example the iBu abbreviation is displayed as iBu.


Regards,
István 

User 870ab5b546

11-09-2014 15:57:44

Interesting. I like the italicization. I don't much care for the superscripting -- it seems archaic, and one doesn't see it much in journals anymore.


Where is the default.abbrevgroups file now located? I looked in jchem14.9.8.0/marvin/chemaxon/marvin/templates/, where it used to be, and it is no longer there. I can't find it anywhere inside jchem14.9.8.0/marvin/. 


Unfortunately, your charge superscripting is buggy when used with our abbrevgroups file. See picture. What do you suggest we do?

ChemAxon 7936325a45

15-09-2014 10:13:02

Dear Bob,

The default.abbrevgroup is not published to the marvin folder anymore.

For the charge you can add a FormattedLabel property in your custom.abbrevgroup file, you can read about it in the documentation (Formatting user-defined abbreviated groups section). In the FormattedLabel you can 'escape' the charge symbol with a '\' character, so that the autoformatting will skip the superscripting of the '-' character. In the documentation the example shows this with the i-Bu abbreviation.


Regards,
István 

User 870ab5b546

15-09-2014 16:10:11

I guess I would encourage you to republish the deafult.abbrevgroup file. I like what you have done with the formatting, except for the superscripted t and i. It would be nice to be able to modify it. I would rather not have to edit all the entries in my own version of the file.

User 870ab5b546

17-09-2014 16:18:11

OK, playing around with the new shortcut group formats. I notice that when a bond points to the left to an i-Bu shortcut group, the bond doesn't point to the right of the group label, but more to the middle. See the screen shot to compare to the COOi-Bu group.

ChemAxon 2c555f5717

18-09-2014 13:28:58

Dear Bob,


   We always try to connect the bond to the attachment atom of the abbreviation. The current algorithm can not solve the case when the attach atom is not represented in the abbreviation of the group. I am sorry for this inconvenience.


Regards:
Balázs