one of our Chemists has exported a database from ISIS/Base containing reactions. Each record contains an additional structure field showing the product. We have exported the database into RDF and imported into IJC without problems. IJC detects the reaction as "Structure" field, and we have imported the second structure as CLOB.
Now she would like to calculate the MW of the product. Is it possible to do this?
Also, if she decided she wants to have the product structure as her main structure field instead of the reaction (so that she can do calculations), is it possible to do this when importing the data?
After looking at the options, I don't see any easy way how to achieve your goals. MW can be only calculated from primary Structure fields and primary structure field is detected automatically.
Possible way might be using script for extracting molecules from the "text field" and save them as a structures which can be imported(on the first place, then merge other data). But I'm not sure how much complex task this would be.
Well, there is one easy way. Just unmap the Structure field and map it to the text field "Products". Reaction can be imported to secondary structure field. It also calculates the MW of a product. Is it that what you wanted to achieve?
thanks for your answers. I tried your suggestion (unmapping the structure field and remapping to the Product) . This by the way also required changing the Table Contents from Reactions to Any Structures (I didn't think of that at first and I kept getting errors). It worked, now I have the product as the main structure field and the reaction is stored in a CLOB field and displayed using the structure renderer.
Now the product mw was calculated, but this has the obvious disadvantage that one cannot search in the reaction field. Also, when the Chemists wants to add another row of data, she needs to copy-paste the reaction from somewhere because she cannot just double-click the reaction field to edit, as for IJC this is a simple text field. So I was thinking, would it be possible in principle to use a Groovy script to grab the product from the reaction and calculate the molecular weight?
Groovy is a powerful tool so in priciple it is possible. The question is how much general and how much complicated the solution will be. I will discuss this issue with my colleagues.
I'm thinking about the product child table. It means only Products and id's imported to new child table(and one to one relationship between parent with reactions and child with products). Then both structures could be edited and both could easily use chemical term fields for property calculations. But I believe you considered this as an option and found another disadvantage in this approach?
I actually hadn't thought of this! I have tried it now and it works well. I think this is a good workaround.
Thanks a lot!