Hmm..trying to ecnode a simple rxn.

[I must preface my comment with my sheer amazement on how good the chemaxon suite of tools are, wow, you guys have done ana amzing job, I vow to force this package upon every chemist I meet].





I'm going to try to do a large scale "virtual library" synthesis and am having trouble with some basics, just general dumbness on my part.





Trying to encode the basic actylene azide rxn (attached, gif and rdf). If I just make an rdf with an acetylene and an azide, I get four products using two simple reactants, fair enough.





I tried specified the functional groups as terminal by trying:





1) R Groups


2) SMARTS queries ([C], [C,c], etc.)





And I get no products.


I'm not forgetting to map my atoms.





Could anyone clue me in as to how I specify my functional groups as terminal?

What do you mean by "terminal"?

Sorry for unclear terminology.





I just don't seem to understand how to define my R groups properly so that reactor gives me only the one regiospecific product (as shown in the attached gif above).

You do not need to define "terminal atoms" with R-groups or whatever. Rather consider each reactant of the reaction scheme as a substructure query. The components of the scheme are really used as queries to find the reaction sites in the input molecules.





Additionally, reaction mapping assigns the corresponding atoms on the two sides of the reactions scheme. In our sense, every atom having changing bonds have to be mapped. (Although we also support Daylight style mapping and have an automapper as well.)





I attached the modified reaction scheme (image as well) and two starting compounds for testing.

Code:

$ react -r mapped_acetyleneazid.rxn azide.mol acetylene.mol CC(C)CC1=CN(N=N1)C2=CC=CC=C2

or displaying the result as a reaction piped into MarvinView:

Code:

$ react -r mapped_acetyleneazid.rxn azide.mol acetylene.mol -t reaction | mview -