Marvin Abbrev Group File & SMILES

The marvin applet comes with a file titled "default.abbrevgroup" in the /marvin/chemaxon/marvin/templates directory which contains a number of abbreviated shortcut groups and their corresponding SMILES definitions.





I haven't been able to find any documentation on this file and have a couple of questions about it. First of all, what is the exact format of this file? From looking at it, I've deduced the following:





Field 1: shortcut group name


Field 2: SMILES definition


Field 3: number





I'm not sure what field 3 is used for. Also, fields 1 and 2 appear to be separated by a [tab] character. However, some have a [tab] and a [space] character between them. Is the space an additional field or just a spurious whitespace character?





Do you have a documented API call which will allow me to specify a shortcut group by name and then return a string with the SMILES definition of that shortcut group? For now, I wrote a method as part of a utility class to retrieve this information, but I thought you might have a published method to do this. If so, I'd rather use your method since the file format appears to be unpublished and subject to change in the future...








Thanks,





Nolan Whitaker


University of Kentucky

This file contains built in abbreviated groups in a compact form. We did not document it because it was created primarily for internal use.





The current format is very simple:


Field 1: abbreviation


Field 2: structure in SMILES


Field 3: index of the atom containing the first connection point


Field 4: index of the atom containing the second connection point





The trailing space characters were just some unintentional white spaces. There is no public or unpublished API to extract the SMILES by abbreviation.





We will change the current format of this file soon to improve the abbreviated group handling, however, we will keep the first two fields in place (the rest might change).

Dear Nolan,


If you want to add your own abbreviated groups to Templates menu, please see the following topic: http://www.chemaxon.hu/forum/ftopic105.html

Thanks for the unexpectedly quick reply and information.





Nolan