searching and R decomposition

User 99339bfc89

17-10-2011 12:42:35


I really like having the ability to perform R group decompositions from within IJC, as available under the 5.6 release. There are times, however, when I want to decompose some parts of the molecule as formal R groups, while other parts of the molecule I want to allow to be unspecified. Now I understand that when I use the R group decomposition tool I lose the ability to do simple substructure searching, but isn't there a way to use some of the powerful search specification tricks to mark a particular part of the molecule as 'could be anything'?  As an example, let's say that I want to use 2 R groups to analyze the molecules in a combinatorial library, but in a third location on the molecule there might or might not have a methyl group ( it might be just an H ), and I still want to bring out all the possibilities.  I've tried marking that third location as "AH" (and everything else I can think of), but I still can't pull back all of the molecules, both with and without the methyl group. In fact, even if I give up on maintaining only two R groups, and I identify the carbon in question ( the one that might have a CH3 and might have an H) as connecting to a third R group, I still can't pull back all the possibilities ( understandably I suppose, "H" is not considered a valid R group, so in this search I only get the molecules WITH the methyl group ).  Is there anyway that I can pull back all the matching molecules, with and without the methyl, with a single search, or am I stuck performing two distinct searches and merging the results together?

Thanks for the help, Ben

ChemAxon fa971619eb

17-10-2011 13:27:01

Hi Ben,

Did you try using the R-group search options?
See here:

The 'Group or H' option lets you specify that an R-group can be substituted or can be H.


ChemAxon a3d59b832c

17-10-2011 16:04:42

That's right, please check out the different R-group matching options.

The behaviour of these search options are described here:


The options with "Group" in the name disallows any substitutions where R-atom is not present in the query.

In this case, you should draw R-atoms at each position and use the mentioned "Group or H" option.

An alternative could be to use option "Any". That will allow additional substitutions, but in case of linking R-atoms, only one atom will be matched in the database structure. (By linking R-atom, I mean an R-atom with more than one bond.)


Best regards,