Azide + Double Acetylene -> One Field Output

I am using Reactor (5.2.2) to create a library of compounds generated by Huisgen Cycloaddition between an Azide and an Acetylene. I have one azide and a 4000 acetylenes; while the reaction is occuring correctly in Reactor it gives me both isomers of the reaction even though I specify the product with the R groups on seperate sides (see attached) totaling 8000 compounds.

 

How do I specify that I only want the "trans" product?

 

Edit: A second question follows (down).

The R2 group in your reaction definition will match both atoms connected to the alkyne carbons. For example if your second reactant is propyne (CC#C), then the R2 group will match the methyl group, and also the hydrogen.

To overcome this problem hydrogen connected to the alkyne group should be explicitly indicated. I attached the corrected reaction.

The corrected reaction generates the expected products:

$ react -r HuisgenCycloaddition.mrv azide.smiles acetylenes.smiles
CN1C=CN=N1
CN1C=C(C)N=N1
CCC1=CN(C)N=N1
CCCC1=CN(C)N=N1

Zsolt

Thank you! Your help is very much appreciated.

The reactor output has been much improved; however, the library I am attaching azides to contains approximately 50 non-symmetrical double acetylene compounds (image attached) which, as expected, outputs two possible reaction.

Is it possible to have reactor output both of these possible reactions into one field (one ID with two structures) so that each substrate only produces one product field?

cLogP wrote:

Is it possible to have reactor output both of these possible reactions into one field (one ID with two structures) so that each substrate only produces one product field?

No it is not yet possible.  Product IDs can be used to identify the products belonging to the same reaction. See http://www.chemaxon.com/jchem/doc/user/Reactor.html#cmdcid for more.

Zsolt

That helps once again, but is there a way to simplify the resulting product ID? This is what I'm passing to reactor in the command-line:

react -r %ReactionFile% -m comb %AzideFile% %AcetyleneFile% -f sdf -o %OutputName% -i R1 -R Click_ID -P PID

The output under the PID column is as follows:

R1(1,CLK001_A02):1

However, only one reaction type is being used and only one compound is in the first library, so the first "R1(1," section is unnecessary.

How do I omit these fields so I get an output similar to CLK001_A02:1 or (CLK001_A02):1?

Synthesis code must describe multistep synthesis of various multimolecular reactions. So its format is quite generic. If you would like to have a different product identifier, you need to convert the synthesis code. You can probably parse and convert it with the help of a script or a simple program.