Two schema and tables relations without using SDFile

Dear Support,

I'm discovering Instant JChem in order to answer one question: Can I do with Instant JChem, what I'm doing in Java using JChem API.

Basically, I'm working with two databases, one is a source for tools and the second source and output.

From the first database I read a small table (structure are stored as MDL Molfile in Clob field) and store all structure as Molecule object in an java Array.

Then in the second database I process all the structure (stored as MDL Molfile in CLOB field). The process convert String molecule to Molecule object and detect fragment using the first table. I remove the identified fragment from the molecule object and extract data which I store in a new fields (as for example a new CLOB field to store format of new structure without identified fragment).

I didn't see any possibility in Instant JChem to have a relation between two schema (two databases).

Is it possible to load SDFile has array of structure and use it to detect fragment from a structure table?

When I need to write the result of transformation (e.g. strandardizer) can I write it as output in a field of a table or do I always need to write output SDFile?

Can I do the same things using Groovy script as I'm doing in java using JChem API?

Is it possible to use java classes or java script in Instant JChem as plugins?

 

Thank you very much for your help?

 

Kind Regards,

Jacques

 

Thank you ver

Dear Jacques,  

let me answer what you can do in IJC GUI first.

I didn't see any possibility in Instant JChem to have a relation between two schema (two databases).

It's is indeed possible to have relations between tables in different DB schemas, but they must be in the same database. And it's not supported on Derby (local) DB. Dedicated help page can be found at http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/editing_database/multi_schema.html .

Is it possible to load SDFile has array of structure and use it to detect fragment from a structure table?

Not directly. However, it's possible to load a SDFile to the table and perform Overlap Analysis on it. This can be done on tables from different databases (IJC schemas) or even from different projects. For more info please refer to http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/chemistry_functions/performing_overlap_analysis.html . Note that this only identifies fragments (eg. duplicates, substructures, superstructures) and write the results to two additional columns. No other trasformation as removing fragment... can be done(this must be scripted).

When I need to write the result of transformation (e.g. strandardizer) can I write it as output in a field of a table or do I always need to write output SDFile?

I'm not sure what other transformation do you mean. IJC Standardizer can be really used only on files if you want to keep the input form. Other option is to set a standardizer on the table (entity). It is described in this tutorial: http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/tutorials/Standardizer/htmlFiles/Standardizer.html . There is also an examle how to use the stadardizer in Groovy scripts: http://www.chemaxon.com/instantjchem/ijc_latest/docs/developer/scripts/table_standardizer.html .

Can I do the same things using Groovy script as I'm doing in java using JChem API?

I would say that mostly yes, because all the JChem API functions can be accessed in Groovy within IJC. You just need to import the proper classes like in Java.

Is it possible to use java classes or java script in Instant JChem as plugins? 

Any java classes can be used to create your own IJC plugin. Java script is currently unsupported. More information about plugin development is in developer's documentation: http://www.chemaxon.com/instantjchem/ijc_latest/docs/developer/#plugins .

Please let us know if you want more info for your particular needs about any of these topics.

Best Regards,
Filip 

Dear Filip,

Thank you very much for your help and all the documentation. That's exactly what I was looking for. It answers all my questions.

A huge thank for your help.

Jacques

I'm glad it helps.

Cheers,
Filip