promoting JCMan table into cartridge index on standard table

User bf3dbc99cf

29-07-2013 01:41:21


I am using IJC and JChem cartridge 6.0.3 on Linux.

I'd like to use large molecular table (1.2M structures of ChEMBL_16, or 35M structures of ZINC) in IJC.


As loading 1.2M structures takes too long in IJC, I tried to use JCMan to load the structures.

After the table was created, structures were loaded in JCMan, I tried to promote this table in IJC.

But promotion made this table only to <JChemBase table>, which used the resource of client-PC for structure searching. 

I want this table to be  the <Cartridge index on a standard (non-JChemBase) table>.


In the post,

you said that create empty entity in IJC and load data in JCMan, but JCMan cannot recognize the table create in IJC.


How can I use this table (which was made in JCMan) in IJC (Cartridge index on a standard (non-JChemBase) table mode) ?


Thanks in advance.

Chong Hak Chae,

ChemAxon 2bdd02d1e5

29-07-2013 08:25:02

Hi Chong Hak,

If the table is already created and has JChemBase table type, you can not simpy use it as Standard table with cartridge index. It has completely different table structures.

From my brief observation, JCMan works only with JChemBase tables. Not with Standard tables with Cartridge index. So it looks like JCMan is out of possibility.

I have to proposals for you:
1. Import the data from Instant JChem.
or rather
2. Import it directly to the database e.g. use SQL Plus and create Cartridge index on the DB.

The first option is simple, but rather slow for milions of structures.

I recommend the second option if you are familiar with direct DB operations. For ChEMBL they provide some instructions how to proceed. Cartridge indexes have to be created manually then, please refer to This second option will probably need some experimentation with cartridge memory and index settings.

Please let us know how is it going.