general usage questions

I'm a chemically knowledgeable but Unix-ignorant user. I want to start using Reactor as a component of the ACE Organic homework software. I have looked over the Reactor documentation, but most of it seems to be oriented toward server-side and the cheminformaticist. I have several questions for you.





I understand that MarvinSketch is used to draw the basic reaction and map the reactive atoms. If I want to add a reaction to a collection of reactions, do I save the .mrv file in a particular folder that is then referenced by Reactor, or is there a single file that contains a list of such reactions?





To add the restrictions to a reaction, such as "brominate only the most nucleophilic atoms on a substituted benzene", do I need to understand a special language for designing these restrictions? Is this language well-documented? That is, could a nonprogrammer such as myself easily add such restrictions to a new reaction?





I see from http://www.jchem.com/examples/reactor/jsp/index.jsp (very helpful page, BTW; I had many more questions before I found it) that you provide a preprogrammed set of reactions. How large is the list? Are the reactions in the set documented?





How do I name each reaction for easy reference and retrieval?





In your examples, you often say that an atom can be any one of a set of possibilities. E.g., in the reaction acidhalide+nucleophile, one atom is called L and is set as [F,Cl,Br,I]. Another is also set as aliphatic. How do I set these properties in MarvinSketch?





Thanks for your help.

I am glad to see you in the virtual synthesis session, Bob!





Our JChem tools are usually avavilable via API and command line interfaces. However, I think, that Reactor could be a valuable tool in the hands of organic chemists who are more familiar with GUI applications only. Thus, we put together a JSP sample application for designing and testing reactions, learning the concept (http://www.jchem.com/examples/reactor/jsp/index.jsp). You can select an existing reaction on the first page or design your own one. The second page lets you test your reaction by specifying the input reactants, and executing the reaction.





Although the current implementation is not a finished GUI and could be much more user friendly, it contains links to the related documentations and probably useful for tool for reaction designers. Reaction rules can be defined in Chemical Terms, the format we use throughout the JChem toolkit from search filters to drug design goal functions as a language for chemists. It is intended to be human readable and still computer processable. I think, that it is not too hard to learn the syntax even if you do not have programming experience.





We started to build a library of reusable virtual reactions for organic chemistry. The first reactions can be accessed on the web page mentioned above. The final version of the library will contain several hundred generic reactions (classical preparative and named reactions). We are in the middle of the work, we extend the library in each major JChem release. The reactions in the library contain many additional data fields including name (there is an text box to edit the name).





Since preparative organic chemistry is an experimental science full of surprising results, all rules can be customized. We count on the community of organic chemists to help improving the reaction library.





You can edit a whole library of reactions using an other JSP application at http://www.jchem.com/examples/reactor/jsp/libedit.jsp. Please note, that we might extend/modify the current format as we add new reaction types with new selectivities (we are pioneering this area).





I usually use the JSP applications for designing and testing the reaction definitions, but I prefer the command line interface to process reactions in combichem mode achieving the highest speed of reaction processing.





Regarding the query properties on the reaction scheme, if you press the "More" toolbar button in Marvin sketcher, you will find atom list and other standard query features (aliphatic/aromatic, connection count) in the dialog popping up.

I guess we crossed one another's paths. See my modified post below. Thanks for replying so quickly.

Ah, I'm starting to get the hang of it. I figured out how to make an atom list with the More button.





So, how do I designate that a bond can be double or triple? The bond button's pop-up menu doesn't have many choices.

Although, this could be the most straightforward approach, there is no double-or-triple query bond at the moment (not a Molfile feature). You should apply an other approach, for example:





1. Use SMARTS. Paste this into the MarvinSketch source editor (Edit/Source) and import it into the Sketcher:


C=,#C


(Direct pasting into the Marvin window will work soon when we corrected a bug)


2. Make two reactions, one with double bond and an other with triple bond.


3. Use R-groups (only if the double or triple bond does not take part in the reaction)


4. Simply draw an ANY bond and refine the reaction scheme in the Reactivity rule with match functions.


http://www.jchem.com/doc/user/EvaluatorTables.html#matchex





You can find a good document about the available query features here:


http://www.jchem.com/doc/user/Query.html