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