number of reactants(JChem version 3.1.6)

User 91ff5e7a58

12-04-2006 18:16:27

I tried to follow the example given at the beginning of the reactor page but when I issue the command 'react -r reaction.rxn reactants.sdf' I receive the error:





chemaxon.reaction.ReactionException: The number of reactant files (1) does not match the requirement of the reaction (2).


chemaxon.reaction.ReactionException: The number of reactant files (1) does not match the requirement of the reaction (2).


at chemaxon.reaction.Reactor.importReactants(Reactor.java:1695)


at chemaxon.reaction.Reactor.run(Reactor.java:1949)


at chemaxon.reaction.Reactor.main(Reactor.java:2264)





I attach the relevant files





Thanks

ChemAxon fb166edcbd

13-04-2006 12:17:19

The problem is that the reactant file should contain two separate molecules instead of one molecule which has two fragments. I attach the appropriate reactant file:





react -r reaction.rxn reactants.sdf


CC(C)CNC(=O)C1=CC=CC=C1


Cl








Remark: you can just as well use two files or strings for the two reactants:





react -r reaction.rxn "ClC(=O)C1=CC=CC=C1" "CC(C)CN"


CC(C)CNC(=O)C1=CC=CC=C1


Cl





You will get the result in SDF firmat if you specify the -f sdf parameter:





react -r reaction.rxn reactants.sdf -f sdf

User 91ff5e7a58

17-04-2006 03:52:55

How does one create the .sdf with multiple molecules and not fragments within Marvin Sketcher? Or does one simply concatenate several single structure files?





Thanks,





Kelsey

ChemAxon 7c2d26e5cf

18-04-2006 13:41:55

In the following topic, you can find the answer for your question: http://www.chemaxon.com/forum/ftopic1367.html