Exclusion ?

Hi. Could you let me know how to make some exception for this reaction.

I want this reaction rule to be not triggered if either R group is halogen.

and where can I find the explanation about all commands Reactor uses like the one shown below ?

[Cl:4][C:3]=O.[#7:2][H:1]>>[#7:2][C:3]=O.[Cl:4][H:1]..r:charge(ratom(4)) > 1.2..s:tpsa(product(0));-charge(ratom(2))..t:0.5;0.001

I want to know what this means. e.g. what is ratom() and charge(). 

Thank you for your kind help in advance.

Hi, 

The following documentation pages will help you to understand Reactor's reaction definitions:

Regarding exclude rules, you can find an example here:
https://www.chemaxon.com/jchem/doc/user/ReactorFAQ.html#notamide

Find the description of ratom() above the inserted example on this page:
http://www.chemaxon.com/jchem/doc/user/reactor_glossary.html#rules

You can use chemical terms functions to add more chemistry to your reaction definition.

The following pages contain description and examples of using chemical terms in reaction context:
http://www.chemaxon.com/marvin/help/chemicalterms/ChemicalTerms.html#context

http://www.chemaxon.com/marvin/help/chemicalterms/ChemicalTerms.html#reactioncontextexamples

http://www.chemaxon.com/marvin/help/chemicalterms/EvaluatorFunctions.html />Full list of available chemical terms functions; Note that, the last column contains "Reaction Context" examples, too.  

If you still have questions, do not hasitate to contact us.

Best regards,

Viktoria

Please, fInd attached your reaction containing exclude halogen atoms definition.

Best regards,

Viktoria 

Thank you for your kind answer.

I wil have a close look at the links you gave. Let me ask you one more question.

When I open your MRV file that you kindly made for me, I can't see any codes for the exclusion.

and I can see those conditions represented in a molecule itself as ~L. How do you do that ?

and what does L stand for ? Am I supposed to use L instead of R?

Since Reactor searches the reaction equation specified substructure in the reactant molecules, to help the substructure search, reaction definitions can be set by using advanced query properties.

For example, if you save the reaction definition in an mrv, rdf, or rxn file, you can define certain exclusions by using atom lists, NOT lists, query atoms, or atom query properties:  
http://www.chemaxon.com/marvin/help/sketch/sketch-chem.html#atomlist />http://www.chemaxon.com/marvin/help/sketch/sketch-chem.html#notlist />http://www.chemaxon.com/jchem/doc/user/query_features.html#atlist

However, reaction rules can be set differently depending on the preferred Reactor application.

Which Reactor interface do you use?

Reactor is available as a standalone application and has also been integrated into Instant JChem and JChem4Excel. It is also available in the workflow management tools KNIME and Pipeline Pilot.
In its standalone version it can be used through the GUI (https://www.chemaxon.com/jchem/doc/user/reactor_gui.html), as a command line application (https://www.chemaxon.com/jchem/doc/user/reactor_cline.html) and also through a full featured Java API (http://www.chemaxon.com/jchem/doc/dev/reactor/index.html).

Best regards,

Viktoria

Thank you so much! This is what I wanted to find.

Everything looks clear to me now.

Have a good day.