Storing and searching reaction data in Instant JChem?

Hello,

Could you tell me if it is possible to store
reaction data (starting material, product, associated numerical data etc) in a local IJC
database, and perform reaction substructure searches on such a
database?

Thanks and regards,

 

Tim Ritchie.

Hello Tim,

using local Apache Derby DB (IJC local database) for reaction data should not be a problem at all. 

Wishing all the best

 

David

Hello,

Is it possible to import the reactions as SMIRKS? I already have a set in spreadsheet format.

Regards,

Tim.

As SMIRKS consists of SMILES and SMARTS, which we do support, it should be also fine. I have tested the support myself and it was working fine.

 

Wishing all the best

David

Hello again,

I tried to import the following test data into a new local IJC database. The importer seems to recognise that the first column is a reaction, but when I import I get errors (see below).

Is there something that I am doing wrong?

Regards, Tim.

 

REACTION Value

c1ccccc1>>Cc1ccccc1 1

c1ccnnc1>>Cc1ccnnc1 2

 

Created new field Value

REACTION is mapped to current field Structure

Starting to import data...

Warning: Failed to import row 1: chemaxon.jchem.base.search.structurerecord.StructureRecordMakerException: Inserting reactions is not allowed for table: (APP.IJCTEST1). The table is not a reaction table.

Warning: Failed to import row 2: chemaxon.jchem.base.search.structurerecord.StructureRecordMakerException: Inserting reactions is not allowed for table: (APP.IJCTEST1). The table is not a reaction table.

Import completed in 0s.

0 entries successfully imported.

2 Errors.

Dear Tim,

the error you see is caused by incompatible "Table Content" type. As it seems, the import wizard does not recognise that the structure column is a reaction soon enough to create the table with proper Content type.

I would suggest the following as a workaround:

1. Open Schema Editor


2. Create a "New Data Tree and Structure Entity" under the Data trees section of the Schema Editor


3. When the wizard for creating an Entity appears, set the "Table Content" type to "Reactions" (other possibility that would work is "Any structures") - see attached screenshot


4. When done, import the file to the entity
   
   
   
   • In Schema Editor by right clicking the entity under "Entities" tab and selecting "Import file to..."
   
   
   • In the Projects Window by right clicking the Data Tree and selecting "Import file to..."
   
   
   
   

Let me know if it works fine. 

 

All the best 

David

Hi David,

Yes, the import worked after specifying the table contents to be 'Reactions'.

Thanks a lot,

Tim.

Hello again,

Recently I have had problems importing text files using the method above.

Now when I import the text file

reaction	value
c1ccccc1>>Cc1ccccc1	1
c1ccnnc1>>Cc1ccnnc1	2

The reaction field is not recognised as chemistry but only as text ("reaction [Text,List(Text)]), so the importer cannot match any field to the reaction structure field (Error: Structure field must be mapped or a merge field specified).

Any thoughts on why this happens?

Thanks and regards,

Tim.

PS. Why is there a 'Back' button on the importer but this is never active?

Hello Tim,

what kind of text file did you use? CSV? If that is the case, then this might be a bug that we will have to fix. Sorry for the inconvenience. Is there a way for you to work around this? You mentioned before that the import was working for you. What format did you use that time?

Regarding the inactive back button, this is deactivated whenever an error during the import occurs. You need to cancel the wizard and start the import again.

 

Wishing all the best

David

I tried importing tab- and comma-delimited text files but I get the same issue.

In the end, I exported the file from JChem for Excel into .mrv format, which can then be imported into IJC successfully but this adds additional steps.

Regards, Tim.